RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application Serial No. 62/410,329, filed on October 19, 2016, entitled "METHODS AND COMPOSITIONS FOR CHANGING THE COMPOSITION OF THE SKIN MICROBIOME USING COMPLEX MIXTURES OF BACTERIAL STRAINS," and U.S. Provisional

Application Serial No. 62/536,761, filed on July 25, 2017, entitled "METHODS AND

COMPOSITIONS FOR CHANGING THE COMPOSITION OF THE SKIN MICROBIOME USING COMPLEX MIXTURES OF BACTERIAL STRAINS," the entire disclosure of each of which is incorporated by reference herein in its entirety.

FIELD OF INVENTION

The invention relates to methods and compositions for modifying the skin microbiome.

BACKGROUND OF INVENTION

The human body is host to a highly complex and rich microbial community. These microorganisms are generally harmless and contribute to a healthy state by producing vitamins, cooperating with digesting food, or stimulating the immune system. The human microbiota mainly resides on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts.

It has been demonstrated, primarily in the gut, that human microbiota have fundamental roles in human health and disease. The skin is colonized by a large number of microorganisms, most of them are beneficial or harmless. However, the skin microbiome has specific

compositions in diseases states of skin that are different compared to healthy skin. Diseases such as acne vulgaris are associated with strong alterations of the microbiome.

SUMMARY OF INVENTION

Aspects of the invention relate to a composition for topical administration to the skin comprising two or more different live Propionibacterium acnes (P. acnes) bacterial strains, wherein the composition comprises a P. acnes single-locus sequence typing (SLST) type C3 strain and/or a P. acnes SLST type K8 strain, and wherein the composition further comprises peptone.

In some embodiments, the composition further comprises a P. acnes SLST type A5 strain. In some embodiments, the composition further comprises a P. acnes SLST type F4 strain.

In some embodiments, the concentration of peptone is from about 0.05%- 1%. In some embodiments, the concentration of peptone is about 0.25%. In some embodiments, the peptone is trypsin-digested peptone from casein.

In some embodiments, the composition further comprises a thickener. In some

embodiments, the thickener comprises hydroxyethyl cellulose. In some embodiments, the hydroxyethyl cellulose comprises NATROSOL® hydroxyethylcellulose (HEC). In some embodiments, the concentration of the thickener is from about l%-5%. In some embodiments, the concentration of gelling agent is about 2.5%.

In some embodiments, the concentration of each live P. acnes bacterial strain is at least 5% of the composition. In some embodiments, a P. acnes SLST type C3 strain and a P. acnes SLST type K8 strain are at approximately equal concentrations within the composition. In some embodiments, a P. acnes SLST type C3 strain is present at a higher concentration than the other live P. acnes bacterial strains.

In some embodiments, the composition comprises a P. acnes SLST type C3 strain, a P. acnes SLST type A5 strain, a P. acnes SLST type F4 strain, and a P. acnes SLST type K8 strain, optionally wherein the relative concentration of each strain is approximately 55%, 30%, 10%, and 5%, respectively.

In some embodiments, the composition includes at least 10 ⁴ colony-forming units per milliliter (CFU/ml) of each live P. acnes bacterial strain. In some embodiments, the composition includes about 10 ⁴ -10 ⁹ colony-forming units per milliliter (CFU/ml) of each live P. acnes bacterial strain.

In some embodiments, the composition is in the form of a gel, cream, ointment or lotion. In some embodiments, the composition further comprises an additional P. acnes bacterial strain selected from the group consisting of: Dl, HI, H2, H3, Kl, K2, K4, K6, K9, and LI SLST type strains. The invention, in some embodiments, is a method comprising administering the composition to a subject. In some embodiments, the subject is a human subject. In some embodiments, the method comprises improving the appearance of the skin and/or maintaining healthy skin. In some embodiments, the method comprises treating or preventing a condition selected from the group consisting of: acne, oily skin, progressive macular hypomelanosis, dandruff, atopic eczema, atopic dermatitis and rosacea.

In some embodiments, the composition is for use in improving the appearance of the skin and/or maintaining healthy skin in a subject. In some embodiments, the composition is for use in treating or preventing a condition in a subject selected from the group consisting of: acne, oily skin, progressive macular hypomelanosis, dandruff, atopic eczema, atopic dermatitis and rosacea. In some embodiments, the subject is a human subject.

Aspects of the invention relate to use of a composition for improving the appearance of the skin and/or maintaining healthy skin in a subject, wherein the composition comprises two or more different live Propionibacterium acnes (P. acnes) bacterial strains, wherein the

composition comprises a P. acnes SLST type C3 strain and/or a P. acnes SLST type K8 strain, and wherein the composition further comprises peptone.

Further aspects of the invention relate to use of a composition for treating or preventing a condition in a subject selected from the group consisting of: acne, oily skin, progressive macular hypomelanosis, dandruff, atopic eczema, atopic dermatitis and rosacea, wherein the composition comprises two or more different live Propionibacterium acnes (P. acnes) bacterial strains, wherein the composition comprises a P. acnes SLST type C3 strain and/or a P. acnes SLST type K8 strain, and wherein the composition further comprises peptone.

In some embodiments, the composition further comprises a P. acnes SLST type A5 strain. In some embodiments, the composition further comprises a P. acnes SLST type F4 strain. In some embodiments, the concentration of peptone is from about 0.05%- 1%. In some embodiments, the concentration of peptone is about 0.25%. In some embodiments, the peptone is trypsin-digested peptone from casein. In some embodiments, the composition further comprises a thickener. In some embodiments, the thickener comprises hydroxyethyl cellulose. In some embodiments, the hydroxyethyl cellulose comprises NATROSOL® hydroxyethylcellulose (HEC). In some embodiments, the concentration of thickener is from about l%-5%. In some embodiments, the concentration of gelling agent is about 2.5%. In some embodiments, the concentration of each live P. acnes bacterial strain is at least 5% of the composition. In some embodiments, a P. acnes SLST type C3 strain and a P. acnes SLST type K8 strain are at approximately equal concentrations within the composition. In some embodiments, a P. acnes SLST type C3 strain is present at a higher concentration than the other live P. acnes bacterial strains. In some embodiments, the composition comprises a P. acnes SLST type C3 strain, a P. acnes SLST type A5 strain, a P. acnes SLST type F4 strain, and a P. acnes SLST type K8 strain, and wherein the relative concentration of each strain is

approximately 55%, 30%, 10%, and 5%, respectively. In some embodiments, the composition includes at least 10 ⁴ colony-forming units per milliliter (CFU/ml) of each live P. acnes bacterial strain. In some embodiments, the composition includes about 10 ⁴ -10 ⁹ colony-forming units per milliliter (CFU/ml) of each live P. acnes bacterial strain. In some embodiments, the composition is in the form of a gel, cream, ointment or lotion.

In some embodiments, the composition further comprises an additional P. acnes bacterial strain selected from the group consisting of: Dl, HI, H2, H3, Kl, K2, K4, K6, K9, and LI SLST type strains.

In some embodiments, a composition described herein does not include a ribotype 6 (RT6) strain of P. acnes. In some embodiments, a composition described herein does not include a Phylotype III strain of P. acnes. In some embodiments of methods described herein, the composition does not include a ribotype 6 (RT6) strain of P. acnes. In some embodiments of methods described herein, the composition does not include a Phylotype III strain of P. acnes. In some embodiments of uses described herein, the composition does not include a ribotype 6 (RT6) strain of P. acnes. In some embodiments of uses described herein, the composition does not include a Phylotype III strain of P. acnes.

Each of the limitations of the invention can encompass various embodiments of the invention. It is, therefore, anticipated that each of the limitations of the invention involving any one element or combinations of elements can be included in each aspect of the invention. This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. BRIEF DESCRIPTION OF DRAWINGS

The accompanying drawings are not intended to be drawn to scale. In the drawings, each identical or nearly identical component that is illustrated in various figures is represented by a like numeral. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:

FIG. 1 depicts the consumption of cis-9, cis-12 linoleic acid of different P. acnes strains in RCM media.

FIG. 2 depicts the concentration of the trans- 10, cis-12 linoleic acid isomer after 86 h shaking incubation of different strains in glucose free medium. The concentrations are normalized for growth by OD (600nm).

FIG. 3 depicts a time course of isomer concentration in a variety of strains.

FIG. 4 depicts the relative amount of C3 strain in a mixture at day 5 or day 6 after inoculation. When present at a high percentage in the starting mixture, C3 stays the dominant strain. Surprisingly, when present at lower starting concentration, the overall percentage of C3 is reduced in the late stationary phase.

FIG. 5 depicts a growth curve of the strains C3, F4, CI and K8 in RCM media at 37°C.

FIG. 6 depicts a growth curve of the strains C3, F4, CI, K8, a 2-strain mixture (C3 and K8) and a 4-strain mixture (A5, C3, F4, and K8) in glucose free PY media at 37°C.

FIG. 7 depicts the change of relative concentrations of different P. acnes strains within a mixture of strains determined by sequencing reads before and after 5 days of growth on RCM agar. Surprisingly the strain K8, which was very slow-growing when used as isolate, became the dominant strain within the culture after 5 days of growth in a mixture of strains.

FIG. 8 A depicts the administration schedule used in a pilot clinical study. 14 subjects were split into two arms where each arm received a different bacterial formulation. FIG. 8B depicts an administration schedule for a larger clinical study.

FIG. 9 depicts averaged relative ratios of the nine most abundant bacteria in the skin microbiome of all subjects in the 14 subject pilot study.

FIG. 10 depicts the relative ratios of subjects classified as acceptors or non-acceptors.

FIGs. 11 A and 1 IB depict the relative amount of P. acnes within the complete bacterial skin microbiome. FIG. 11A shows the dynamic development of the P. acnes population in acceptors and non-acceptors throughout the pilot study. In the acceptors group, P. acnes initially represented only 34% of the bacterial skin microbiome. After the BPO treatment, this value was further reduced before it increased to nearly the double after the bacterial gel was applied. The P. acnes population stabilized at 60% on Day 42. The dynamics in the non-acceptor group were similar. The non-acceptors ground state started at a higher level of 40% and in contrast to the acceptor group, the increase in the population was not significant on Day 42. FIG. 1 IB shows the relative ratios of P. acnes as box plots illustrating the spread of the data points. The difference between Day 1 and Day 42 in the acceptor group is highly statistically relevant (p=0.001) while the acceptor group is similar on Day 42 to Day 1.

FIG. 12 depicts counts of non-inflamed lesions represented as box plots. Three pairs of boxplots are shown: overall; A2 formulation; and B4 formulation. The p-value for statistical significance is given below the plots.

FIG. 13 depicts the number of non-inflamed lesions for acceptors and non-acceptors. For both groups, the reduction is statistically significant.

FIG. 14 depicts the count of inflamed lesions represented as box plots. Three pairs of boxplots are shown: overall; A2 formulation; and B4 formulation.

FIG. 15 depicts the number of inflamed lesions for acceptors and non-acceptors.

FIG. 16 depicts development of the skin pH throughout the pilot study for acceptors and non-acceptors.

FIG. 17 depicts distribution of subject counts based on the average value of their answers.

FIG. 18 depicts a heatmap showing the relative abundance of the 15 most commonly found P. acnes strains. The heatmap represents the average of 6 subjects classified as acceptors who showed very good establishment of the new bacteria. A clear change in the composition of the microbiome is visible between Day 1 and Day 42.

FIG. 19 depicts a graph showing results of a picture based comparison. Results from Day 1 to Day 28 were compared with results from Day 1 to Day 42. Each Picture was rated with +1 if the subject improved, 0 if the subject appeared not to change and -1 if the subject worsened. The averages are Day 1 to 28: -0,17 and Day 1 to 42: 0,29. The difference is statistically significant, p<0,05.

FIG. 20 shows results of a patient assessment summary, demonstrating improvement of inflamed and non-inflamed lesions during the 42 day clinical study. FIG. 21 depicts OD ₆₀₀ of pH-controlled cultures and cultures without pH control

("acidifying") of P. acnes K8 and C3 strains, as described in Experiment 1.2. The graphs show data from duplicate cultures.

FIG. 22 depicts viable count of pH-controlled cultures and cultures without pH control ("acidifying") of P. acnes K8 and C3 strains, as described in Experiment 1.2. The graphs show data from duplicate cultures.

FIG. 23 depicts OD ₆₀₀ of pH-controlled cultures ("acidifying") of P. acnes K8

and C3 strains, as described in Experiment 1.3.

FIG. 24 depicts phase contrast microscopy (500x) of cultures of P. acnes K8 (left) and C3 (right) strains, as described in Experiment 2.2.

FIG. 25 depicts the change of relative concentrations of different P. acnes strains following administration of formulations A2 and B4.

DETAILED DESCRIPTION

Provided herein are compositions and methods for modulation of the skin microbiome. Compositions comprising two or more live P. acnes bacterial strains are described herein for use in maintaining healthy skin, such as skin that is free of acne, or for treating or preventing acne. Compositions comprising two or more live P. acnes bacterial strains can help skin to revert microbiome disease states to healthy microbiome states.

Without wishing to be bound by any theory, P. acnes may convert a signal precursor molecule (linoleic acid), which is naturally present in the sebum, to an active signaling molecule (trans-10, cis-12 linoleic acid), which stimulates in return sebum secretion, which is important for P. acnes colonization of the skin. Significantly, the production of this signaling molecule provides a connection between different aspects of the current understanding of the onset of acne.

As shown in Example 1, it was surprisingly found that different P. acnes strains have different levels of linoleic acid isomerase activity or final thresholds of concentration of trans-10, cis-12 linoleic acid. For example, a P. acnes SLST type Al strain was found to produce the most trans-10, cis-12 linoleic acid isomer, while P. acnes SLST type strains C3, CI, F4, A5, Kl, K2, K8 and LI showed very little production of trans-10, cis-12 linoleic acid isomer. It was also surprisingly found that some strains exhibited different growth patterns when grown in a mixture of strains than when grown individually. For example, a P. acnes SLST type K8 strain was found to grow slowly individually, but when grown within a mixture of strains, it became the dominant strain within the composition after 5 days of incubation (FIG. 7).

Accordingly, aspects of the invention relate to mixtures of strains that exhibit advantageous growth properties even when containing individual strains that may grow slowly in nature and would likely be outcompeted in nature.

It was also surprisingly found herein that mixtures of strains were able to tolerate higher levels of preservatives than individual strains. Accordingly, aspects of the invention relate to mixtures of P. acnes strains that can be established on the skin and that will have improved survival against exposure to certain compounds, such as products containing preservatives, compared to single P. acnes strains. This feature provides an unexpected advantage for bacterial mixtures compared to individual strains for the establishment and long term persistence on the skin of a human subject.

It is also surprisingly demonstrated herein, using two different formulations of two or more live P. acnes strains, that administration of live P. acnes strains can lead to a substantial reduction in non-inflamed lesions in subjects having acnes. In a pilot clinical study described in Example 5, 85% of subjects reported improvement in symptoms associated with acne following administration of formulations described herein.

This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of "including," "comprising," or "having," "containing," "involving," and variations thereof herein, is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

Aspects of the invention relate to the microbiome. As used herein, "microbiome" refers to all of the microorganisms inhabiting the body. The human microbiome has a fundamental role in human health and disease (Consortium, 2012; NIH HMP Working Group et al., 2009). The development of Next Generation Sequencing (NGS) technologies has allowed the study of these microbial communities with an unprecedented depth and resolution (see Human Microbiota issue, Nature 2012). More than 10,000 different bacterial strains colonize the human body, and there are ten times more bacteria than human cells in an average human body. Recent research has indicated that the composition of bacterial communities in the body is tightly connected to the health of the human body (Belkaid and Segre, 2014; Consortium, 2012; Zhao, 2010). As a result, distortions of the microbiome are linked to a variety of diseases.

The gut microbiome, and methods for targeted manipulation of the gut microbiome, has been investigated in depth (Dore and Blottiere, 2015). An example of such a therapy is the treatment of the antibiotic-resistant bacteria Clostridium difficile with the help of "fecal transplantation" (van Nood et al., 2013; Olle, 2013).

Researchers recently began to investigate the skin microbiome (Belkaid and Segre, 2014; Oh et al., 2014). The skin is colonized by a large number of microorganisms, most of which are beneficial or harmless (Grice and Segre, 2011). However, diseases such as acne vulgaris are associated with strong alterations of the microbiome (Bek-Thomsen et al., 2008; Holmes, 2013; Kong et al., 2012). Acne, in particular, is considered to be linked to a distortion of the human skin microbiome (Fitz-Gibbon et al., 2013). This distortion is likely caused by a specific subset of the skin bacterium P. acnes (Lomholt and Kilian, 2010).

Herein, compositions and methods apply knowledge of the skin microbiome to develop treatments against skin disorders that originate or are influenced by distortions of the skin microbiome.

Acne

As used herein, "acne vulgaris" and "acne" are used interchangeably and refer to a skin condition that affects millions of people worldwide and is especially prevalent in teenagers. Acne is frequently associated with the formation of inflammatory and non-inflammatory lesions on the skin. Without wishing to be bound by any theory, acne may be associated, at least in part, with hair follicles that become clogged and/or inflamed. Acne is considered to be linked to the distortion of the human skin microbiome. This distortion may be caused by specific strains of the skin bacterium P. acnes (Fitz-Gibbon et al., 2013; Holmes, 2013; Lomholt and Kilian, 2010).

The development of acne is linked to the onset of sebum secretion from the sebaceous glands (Makrantonaki et al., 2011; Zouboulis, 2004). Also, the population density of P. acnes is directly linked to the amount of sebum produced (Kearney et al., 1984; King et al., 1982; Mourelatos et al., 2007). However, a clear molecular link between the presence of P. acnes and the disease acne, could until now, not be established. This is due, at least in part, to the fact that the skin of most adult humans is colonized by P. acnes, while symptoms of acne do not occur in many of those adults. In order for acne to occur, an inflammatory reaction must be triggered, which is accompanied by a change in the volume and composition of the sebum (Pappas et al., 2009).

Currently, standard treatment for acne is either long-term antibiotic treatment, such as treatment with Macrolide and/or Tetracycline antibiotics, or the systemic use of Isotretinoin (Berson et al., 2003). These treatments exhibit strong side effects and high relapse rates. For example, Isotretinoin causes skin irritation and also has teratogenic effects (causing birth defects) (McLane, 2001). In addition, the relapse rate with Isotretinoin is also unfavourable, at above 40% (Azoulay et al., 2007). Isotretinoin has been shown to reduce the volume of sebum production, thereby indirectly reducing the bacterial density on the skin (King et al., 1982). While antibiotics are a common treatment, in the last several decades, the number of bacterial strains that are resistant to one or more antibiotics has increased dramatically. (Leyden, 2001; Ross et al., 2001).

Another group of acne treatments include over-the-counter (OTC) products and cosmetics. Commonly used OTC products are broadband disinfection agents including benzoyl peroxide {e.g. Benzaknen, Galderma S.A., Lausanne, Switzerland and Aknefug, Dr. August Wolff GmbH & Co. KG Arzneimittel, Bielefeld, Germany) and salicylic acid. Additionally, there are a number of natural product lines which have limited or no proven efficacy.

Current therapies for skin disorders such as acne, that are linked to a distortion of the microbiome, are either ineffective or they are accompanied by severe side effects (McLane, 2001; Tripathi et al., 2013). Usually, the skin of a subject with acne improves during classical treatments, such as with antibiotics or hormones. However, the subject in most cases relapses after the end of the treatment. Isotretinoin has about a 41% relapse rate (Azoulay et al., 2007). Therefore, subjects are required to undergo long term treatments to keep the beneficial effects. This extreme relapse rate can be explained by the recolonization of the skin with the microbiome after stopping the therapy.

Compositions and methods described herein address an unmet need for an effective treatment of acne without notable side effects, and with prevention of relapse. The novel approach described herein can involve transplantation of a healthy microbiome. Surprisingly, strains of P. acnes, the same bacterial species that is thought to be involved in causing acne, can be used to treat or prevent acne, or to maintain skin in a condition where it is free of acne.

Described herein are compositions comprising two or more live bacterial strains that can provide an improved skin condition without causing notable side effects. The live bacterial strains within the compositions described herein are P. acnes bacterial strains.

In some embodiments, the composition is a cosmetic. As used herein, a "cosmetic" refers to a product that is intended to enhance appearance. Cosmetic composition comprising one or more live bacterial strains as described herein can also be referred to as a

"cosmeceuticals" (Draelos, 2009).

Aspects of the invention relate to administering compositions comprising two or more live P. acnes bacterial strains to the skin of a subject either alone, in combination with other therapies, or following another therapy. In some aspects, a composition comprising two or more live P. acnes bacterial strains can help the skin revert from a microbiome disease state to a healthy microbiome state. In some embodiments, the skin of the subject has already been treated with a standard acne therapy, such as with antibiotics, disinfectants, or hormones. Compositions comprising two or more live P. acnes bacterial strains described herein can be used as complementary recovery methods to standard treatments for acne, whereby the composition comprising two or more live P. acnes bacterial strains can reduce the relapse rate of acne after antibiotic treatment. For example, a composition comprising two or more live P. acnes bacterial strains can be applied after an antibiotic or disinfectant treatment when the skin of a subject is cleared of the majority of its natural bacteria. The live bacteria in the composition can displace pathogenic bacterial strains and help to recover a diverse, healthy and balanced skin microbiome. Accordingly, in some embodiments, methods described herein involve eradicating pathogenic bacterial strains from the skin and then adding live P. acnes bacteria to the skin to create a healthy skin microbiome.

Compositions comprising two or more live P. acnes bacterial strains as described herein can be used to decrease or increase the volume of the sebum production of an individual.

Compositions comprising two or more live P. acnes bacterial strains as described herein can also be used to produce trans- 10, cis-12 linoleic acid in the follicles or sebaceous glands and thereby deliver this active compound to the environment of the sebaceous glands. These methods circumvent problems associated with the standard topical application of trans- 10, cis-12 linoleic acid.

Compositions comprising two or more live P. acnes bacterial strains as described herein can also be used to increase or decrease the bacterial density on the skin by providing a bacterial strain to the skin which will increase or decrease the sebum production on the skin, thereby indirectly changing the bacterial density.

Compositions comprising two or more live P. acnes bacterial strains as described herein can also be used to modify the ratio of select bacterial species compared to other bacterial species or compared to other components of the microbiota such as fungi or mites by administering a live bacterial strain to the skin that alters the sebum production, thereby indirectly altering the bacterial density of P. acnes on the skin.

Compositions comprising two or more live P. acnes bacterial strains as described herein can be used to maintain healthy skin, such as skin that is free of acne. In some embodiments, administration of such compositions can assist in preventing formation of acne. In some embodiments, such compositions can be used to treat acne or can be used to prevent

reoccurrence of acne in a subject who has received a standard acne treatment.

The compositions comprising two or more live P. acnes bacterial strains include one or more strains of live bacteria that naturally colonise the skin. In some embodiments, the one or more strains are naturally occurring. However, the composition comprising the two or more bacterial strains is not naturally occurring. The composition comprising the two or more bacterial strains has different properties than the individual strains in nature.

Propionibacterium acnes (P. acnes)

P. acnes is a species of anaerobic Gram-positive rod bacteria that is associated with acne as well as other conditions such as chronic blepharitis and endophthalmitis. P. acnes strains are present on the skin of most people. It has been reported that some strains of P. acnes are pathogenic, while other strains of P. acnes are not. (Fitz-Gibbon et al., 2013; Lomholt et al., 2010.) As used herein, "pathogenic" P. acnes strains refers to P. acnes strains that are associated with acne. Disclosed herein are assays by which pathogenic and non-pathogenic strains of P. acnes can be identified and selected. Strains of P. acnes have been shown to differ significantly in their metabolism and phenotypic behavior (Lomholt and Kilian, 2010). These differences include but are not limited to expressing neuraminidase, a-glucosidase or hyaluronidase and the ability to perform hemolysis of horse blood, ribose fermentation, erythritol fermentation or sorbitol fermentation. Further it has been shown that P. acnes express an active linoleic acid isomerase, which specifically converts cis 9, c-12 linoleic acid into trans-10, cis-12 linoleic acid (Rosson et al., 2004). Linoleic acid is a key molecule in the regulation of sebum production and a reduction of linoleic acid has been linked in multiple studies to the onset of acne (Downing et al., 1986; Letawe et al., 1998).

Further it has been shown that P. acnes dead cells or supernatants are able to increase lipid production in hamster sebocytes (Iinuma et al., 2009a).

Species of P. acnes have been classified into Clades I - III, further including subtypes: IA and IB. (Lomholt et al.) IA has been further subdivide into IAi and IA ₂ (McDowell et al., 2012). Genetic analysis of P. acnes strains has been conducted to determine which strains may be pathogenic and associated with acne, and which strains may be non-pathogenic and not associated with acne. (Fitz-Gibbon et al., 2013, Lomholt et al., 2010, and Kasimatis et al., 2013). In some embodiments, a non-pathogenic P. acnes strain is a strain from one of the following classes of P. acnes: 1-2, II and IB. In some non-limiting embodiments, a non-pathogenic strain of P. acnes is selected from the group of non-pathogenic strains consisting of: Dl, A5, C3, HI, H2, H3, Kl, K2, K4, K6, K8, K9, LI, and F4 SLST type strains, as described in Scholz et al. (2014) PLOS CWE 9(8) el04199.

As described in Scholtz et al., and as would be understood by one ordinary skill in the art, strains of P. acnes can be identified using single-locus sequence typing (SLST), involving PCR amplification and DNA sequencing of a target locus. An SLST scheme for P. acnes was developed and described in Scholz et al. using the target locus PPA2385 (referred to in Scholz et al. as the "SLST target sequence"). A P. acnes database associated with the SLST scheme described in Scholtz et al. is available online at medbac.dk/slst/pacnes. Exemplary SLST type strains include A1-A24, B l, C1-C4, D1-D3, E1-E9, F1-F10, Gl, H1-H5, K1-K14, and L1-L6. Users can enter a P. acnes sequence into the online database to identify SLST type strains. Other P. acnes strain identification and naming systems include MLST9 and MLST8 schemes, ribotyping, and type assignments based on recA and tly sequence analysis. Figure 1 of Scholtz et al. demonstrates these different naming conventions. One of ordinary skill in the art would understand how a P. acnes strain could be identified and classified according to the different naming systems known in the art.

As used herein, "typing" a bacterial strain refers to identifying the bacterial strain, such as by using SLST. Table 1 lists allelic sequences used in SLST to identify strains described herein, such as P. acnes SLST type Dl, A5, C3, HI, H2, H3, Kl, K2, K4, K6, K8, K9, LI, and F4 strains. One of ordinary skill in the art would understand the strain designations used herein, corresponding to those disclosed in Scholtz et al., and would understand how to identify whether a P. acnes strain corresponds to any of these specific strains by using, e.g., SLST.

Accordingly, the P. acnes strains are described herein based on SLST-type designation using the target locus PPA2385 described in Scholtz et al. For example, "P. acnes strain C3" refers to P. acnes SLST type C3, using the target locus PPA2385 described in Scholtz et al. "P. acnes strain K8" refers to P. acnes SLST type K8, using the target locus PPA2385 described in Scholtz et al. "P. acnes strain A5" refers to P. acnes SLST-type A5, using the target locus PPA2385 described in Scholtz et al. and "P. acnes strain F4" refers to P. acnes SLST-type F4, using the target locus PPA2385 described in Scholtz et al.

Bacterial compositions described herein comprise two or more strains of P. acnes. For example, a bacterial composition can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more than 20 strains of P. acnes. In some embodiments, the composition comprises 2, 3, 4, or 5 different strains of P. acnes. One or more of the strains of P. acnes can be nonpathogenic strains. In some embodiments, all of the strains of P. acnes in a bacterial

composition are non-pathogenic strains. In some embodiments strains of P. acnes are genotyped in order to identify the strain and to make a selection as to whether to include the strain in a composition. Strains of P. acnes included in bacterial compositions described herein can be selected to increase or decrease lipid production.

In some embodiments, a composition comprising two or more different P. acnes bacterial strains comprises P. acnes strain C3, P. acnes strain K8, or both P. acnes strain C3 and P. acnes strain K8. In some embodiments P. acnes strain C3 and P. acnes strain K8 are at approximately equal concentrations within the composition. In other embodiments, P. acnes strain C3 is at a higher concentration than P. acnes strain K8 within the composition. In other embodiments, P. acnes strain C3 is at a lower concentration than P. acnes strain K8 within the composition. In some embodiments, a composition comprising two or more different P. acnes bacterial strains comprises P. acnes strain A5 and/or P. acnes strain F4. For example, a composition can include P. acnes strain C3 and/or P. acnes strain K8, and/or P. acnes strain A5 and/or P. acnes strain F4. In some embodiments, a composition includes P. acnes strain C3 and P. acnes strain K8 and P. acnes strain A5 and P. acnes strain F4.

In some embodiments, mixtures of P. acnes strains include one or more Clade I strains and one or more Clade II strains. Without wishing to be bound by any theory, Clade II strains may be less pathogenic; however, these strains can also be slower-growing than Clade I strains, and less likely to be able to colonize the skin on their own. Accordingly, aspects of the invention relate to mixtures of strains that include both Clade I and Clade II strains and which allow for colonization of the skin by Clade II strains.

In some aspects, compositions comprising one or more live P. acnes bacterial strains described herein include the P. acnes strain HI (6609). (Hunyadkiirti et al.) The genome of this P. acnes strain has been sequenced and is available at GenBank accession number CP002815. (Hunyadkiirti et al.) In some embodiments, compositions comprising one or more live P. acnes bacterial strains described herein include strains of P. acnes that have certain CRISPR/CAS9 sequences. (Briiggemann, 2012, Fitz-Gibbon 2013). In some embodiments, compositions comprising one or more live P. acnes bacterial strains described herein include comprise one or more of P. acnes strains Kl, K4 and HI (6609). In some embodiments, compositions comprising one or more live P. acnes bacterial strains described herein comprise each of P. acnes strains Kl, K4, Dl, A5, C3 and HI (6609).

Aspects of the invention relate to mixtures of P. acnes strains. Selection of P. acnes strains can involve, at least in part, a determination of whether the strain is pathogenic. This determination can be based on public information, prior reports, and/or experimental testing to determine whether a P. acnes strain is pathogenic or not. In some embodiments, only nonpathogenic P. acnes strains are selected.

Selection of P. acnes strains can also involve, at least in part, a determination of which strains, or combinations of strains, are stable in conditions that would be appropriate for use in a cosmetic or pharmaceutical composition. In some embodiments, P. acnes strains that exhibit increased stability are selected. Stability can be assessed using methods known in the art, such as by measuring a change in colony-forming units (CFU). Strains of P. acnes included in bacterial compositions described herein can be naturally occurring or can be genetically modified. Strains that are genetically modified can be modified by natural mutagenesis and/or by genetic engineering. In some embodiments, the genetic modification of the P. acnes strain influences the production of trans- 10, cis-12 linoleic acid and/or increases or decreases its linoleic acid isomerase activity. In some embodiments, P. acnes strains show different level of linoleic acid isomerase, which can be used to classify bacterial strains and/or to select specific bacterial strains.

In some embodiments, one or more of the P. acnes bacterial strains is selected based on its ability to produce trans- 10, cis-12 linoleic acid. In some embodiments, one or more of the P. acnes bacterial strains is selected based on the amount of trans- 10, cis-12 linoleic acid it produces in its natural environment. In some embodiments, one or more of the P. acnes bacterial strains is selected based on the maximum concentration of trans- 10, cis-12 linoleic acid it produces. In some embodiments, one or more of the P. acnes bacterial strains is selected based on the activity of the enzyme linoleic acid isomerase it produces. In some embodiments, a P. acnes strain with no linoleic acid activity is selected. In other embodiments, a P. acnes strain with low levels of linoleic acid activity is selected. In other embodiments, a P. acnes strain with high levels of linoleic acid activity is selected.

In some embodiments, production of trans- 10, cis-12 linoleic acid by P. acnes strains is detected using methods described in and incorporated by reference from US Patent No.

6,743,609, entitled "Linoleate isomerase," which granted on June 1, 2004. In some

embodiments, the amount of trans- 10, cis-12 linoleic acid produced is detected using FAME (Fatty acid methyl esters) and/or GC (Gas Chromatography).

In some embodiments, a P. acnes strain can convert from 500 pm linoleic acid up to 250 ppm trans- 10, cis-12 linoleic acid and then can keep this concentration constant. In some embodiments, a P. acnes strain is selected that has higher capacity for conversion of linoleic acid to trans- 10, cis-12 linoleic acid. In other embodiments, a P. acnes strain is selected that has lower capacity for conversion of linoleic acid to trans- 10, cis-12 linoleic acid.

Without wishing to be bound by any theory, in some embodiments, a bacterial composition in which the P. acnes strains have zero to low levels of linoleic acid isomerase may be beneficial for preventing or treating acne because such compositions may reduce sebum secretion. In some embodiments, such a composition may be helpful in avoiding relapse of acne after finishing standard acne treatment (such as disinfection or antibiotics).

In some embodiments, bacterial compositions can be used to increase levels of trans- 10, cis-12 linoleic acid in the skin follicles. In other embodiments, bacterial compositions can be used to decrease levels of trans- 10, cis-12 linoleic acid in the skin follicles. In some

embodiments, a combination of P. acnes strains is used to deliver trans- 10, cis-12 linoleic acid directly to the sebaceous glands either for cosmetic or medical purposes.

In some embodiments, a bacterial composition described herein is used to reduce sebum production on skin that has high levels of sebum production, such as oily skin. In other embodiments, a bacterial composition described herein is used to increase sebum production on skin that has low levels of sebum production, such as dry skin. In some embodiments, a combination of strains with high linoleic acid isomerase activity is applied to the skin of individuals who lack sufficient sebum production. In some embodiments, such individuals are elderly people who may experience a decrease in sebum production.

In some embodiments, the amount of trans- 10, cis-12 linoleic acid produced by a P. acnes strain is evaluated by comparing production of trans- 10, cis-12 linoleic acid in the strain being tested to a P. acnes strain that is known not to produce trans- 10, cis-12 linoleic acid or that produces negligible or lower than average amounts of trans- 10, cis-12 linoleic acid. In other embodiments, the amount of trans- 10, cis-12 linoleic acid produced by a P. acnes strain is evaluated by comparing production of trans- 10, cis-12 linoleic acid in the strain being tested to a P. acnes strain that is known to produce average or higher than average amounts of trans- 10, cis- 12 linoleic acid. In some embodiments, the relative amount of trans- 10, cis-12 linoleic acid produced is measured or evaluated. In other embodiments, the absolute amount of trans- 10, cis- 12 linoleic acid produced is measured or evaluated.

In some embodiments, the amount of cis-9, cis-12 linoleic acid degraded by a P. acnes strain is evaluated by comparing the degradation rate of cis-9, cis-12 linoleic acid in the strain being tested to a P. acnes strain that is known not to degrade cis-9, cis-12 linoleic acid or that degrades negligible or lower than average amounts of cis-9, cis-12 linoleic acid. In other embodiments, the amount of cis-9, cis-12 linoleic acid degraded by a P. acnes strain is evaluated by comparing degradation rate of cis-9, cis-12 linoleic acid in the strain being tested to a P. acnes strain that is known to have an average or higher degradation rate than average of cis-9, cis-12 linoleic acid. In some embodiments, the relative amount of cis-9, cis-12 linoleic acid degraded is measured or evaluated. In other embodiments, the absolute amount of cis-9, cis-12 linoleic acid degraded is measured or evaluated.

In some embodiments, one or more of the P. acnes bacterial strains within the

composition exhibits slow or negligible degradation or conversion of cis-9, cis-12 linoleic acid. In some embodiments, all of the P. acnes bacterial strains within the composition exhibit slow or negligible degradation or conversion of cis-9, cis-12 linoleic acid.

In some embodiments, one or more of the P. acnes bacterial strains within the

composition is selected based on its slow or negligible degradation or conversion of cis-9, cis-12 linoleic acid. In some embodiments, one or more of the P. acnes bacterial strains within the composition is selected based on the amount of cis-9, cis-12 linoleic acid it degrades in its natural environment. In some embodiments, one or more of the P. acnes bacterial strains within the composition is selected based on the maximum concentration of cis-9, cis-12 linoleic acid it degrades.

In some embodiments, one or more of the P. acnes bacterial strains within the

composition is genetically modified to degrade less cis-9, cis-12 linoleic acid or to degrade cis-9, cis-12 linoleic acid more slowly.

Individual and combinations of strains can be tested using routine methods to determine which combinations lead to stable compositions. In some embodiments, such compositions are stable at room temperature for at least 1 week, 2, weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks or more than 30 weeks. In some embodiments, such compositions are stable at room temperature for at least 1 month, 2 months, 3 months, 4 months, 5 months, 6 months or more than 6 months.

In some embodiments, compositions are stable when refrigerated, at approximately 4 °C for at least 1 week, 2, weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks or more than 30 weeks. In some embodiments, compositions are stable when refrigerated, at approximately 4 °C for at least 1 month, 2 months, 3 months, 4 months, 5 months, 6 months or more than 6 months.

In some embodiments, a bacterial composition is formulated by taking a sample from the skin microbiome of a donor subject. For example, the sample can be taken from a subject who does not have acne. In other embodiments, a sample is taken from a subject who has mild, moderate or severe acne. In some embodiments, the sample is taken from a subject who has acne or is susceptible to acne, but bacterial strains associated with causing acne are removed from the sample. A sample can be cultured and can optionally be combined with other components to form a bacterial composition. In other embodiments, a bacterial composition can be formed from one or more isolated bacterial strains.

A sample taken from a donor subject can be tested to see if it contains non-pathogenic P. acnes strains. In some embodiments, one or more non-pathogenic P. acnes strains from the skin of a donor subject are selected and are administered to a recipient subject. The recipient subject can be the same subject as the donor subject or can be a different subject from the donor subject.

In some embodiments, a bacterial composition can include one or more strains of other bacteria, such as other non-pathogenic bacteria, in addition to one or more strains of P. acnes. In some embodiments, the one or more strains of other non-pathogenic bacteria have antibiotic properties. In some embodiments, a bacterial composition can include one or more S.

epidermidis strains.

In some embodiments, a P. acnes strain described herein comprises a sequence selected from SEQ ID NOs: 1-76. In some embodiments, a P. acnes strain described herein comprises a sequence that is at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a sequence selected from SEQ ID NOs: 1-76.

In some embodiments, a composition comprises a P. acnes strain that is at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO:27 and/or a P. acnes strain that is at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO:64. In some embodiments, a composition comprises a P. acnes strain that comprises SEQ ID NO:27 and/or a P. acnes strain that comprises SEQ ID NO:64.

In some embodiments, a composition described herein does not include a ribotype 6 (RT6) strain of P. acnes. In some embodiments, a composition described herein does not include a Phylotype III strain of P. acnes.

Table 1: Sequences used to identify P. acnes strains by SLST

Table 2: Primer sequences used to type bacterial colonies

Linoleic acid and its isomer trans-10, cis-12 linoleic acid

Linoleic acid is a C18 fatty acid with two unsaturated double bonds. Usually, the main isomer is cis-9, cis-12. This isomer is also secreted as free fatty acid in the sebum. In vitro, linoleic acid stimulates the lipid production in sebocytes and may be involved in a feedback loop regulating sebum production. It also has antibacterial properties, with different P. acnes strains exhibiting different susceptibility to linoleic acid (Hong Lioe Ko et al., 1978; Madli Puhvel and Reisner, 1970). However linoleic acid also serves as a stimulant for sebum production, which represents the food source of P. acnes. Without wishing to be bound by any theory, an equilibrium may exist, represented by the linoleic acid concentration in the sebum determined by the bacterial population and the host's sebum production. This equilibrium depends on the degradation /conversion rate of cis, cis-12 linoleic acid by the P. acnes population colonizing the follicle.

Conjugated isomers of linoleic acid, namely cis-9, cis- 11 linoleic acid and trans-10, cis- 12 linoleic acid, have attracted attention as food supplements (Churruca et al., 2009). Linoleic acid trans- 10, cis 12 acts on the PPAR receptor family (peroxisome proliferator-activated receptor) (Moya-Camarena et al., 1999). Activation of PPAR-a activates lipid synthesis in epidermal skin models, including cholesterol (Rivier et al., 2000). It has also been reported that trans- 10, cis-12 linoleic acid increases ROS (reactive oxygen species) and has anticancer activity (Pierre et al., 2013).

Staphylococcus epidermidis (S. epidermidis)

S. epidermidis is a Gram-positive bacteria that is a normal component of human skin. S. epidermidis can produce 5 lantibiotics, including: epidermin, Pep5, epicidin 280, epilancin K7, and epidermicin NI01. A lantibiotic refers to an antibiotic-like peptide that contains the nonprotein amino acids lanthionin and 3-methyllanthionine (Schnell et al., 1988). Epidermin is highly active against P. acnes (Allgaier et al., 1985). Gotz et al. describe epidermin in further detail. Wang et al. report that S. epidermidis can mediate fermentation of glycerol to inhibit the growth of P. acnes.

Strains of S. epidermidis included in bacterial compositions described herein can be naturally occurring or can be genetically modified. Strains that are genetically modified can be modified by natural mutagenesis and/or by genetic engineering. In some embodiments, the genetic modification of the S. epidermidis strain increases its antibiotic properties. In some aspects a bacterial composition can contain one or more strains of P. acnes and one or more strains of S. epidermidis. The one of more strains of P. acnes can be resistant to the antibiotic properties of the one or more strains of S. epidermidis. In some embodiments, the one or more strains of P. acnes are genetically modified to increase their resistance to antibiotic properties of one or more other bacterial strains, such as one or more strains of S. epidermidis. In some embodiments, the one or more P. acnes strains are modified by natural mutagenesis and/or by genetic engineering to increase their resistance to the antibiotic properties of one or more other bacterial strains.

In some embodiments, compositions comprising one or more live P. acnes bacterial strains described herein can contain one or more of an antibiotic, a disinfectant {e.g., BPO), or salicylic acid. One of ordinary skill in the art would appreciate that any antibiotic or disinfectant may be compatible with certain embodiments of the invention. Skin microbiome transplantation

Aspects of the invention relate to modulation of a skin microbiome, such as by transplantation. Transplantation can occur between one or more subjects. In some

embodiments, transplantation occurs in one subject and the same subject is the donor and the recipient. In other embodiments, transplantation occurs between two or more subjects. In some embodiment, there is one donor subject and one recipient subject. In other embodiments, there are multiple donor subjects and/or multiple recipient subjects. Multiple methods of

transplantation can be used, resulting in different formulations of a bacterial composition. In some embodiments, a non-modified microbiome is transplanted, meaning that a donor microbiome is isolated, and prepared for delivery to a recipient. In other embodiments, a formulated microbiome is transplanted, meaning that a donor microbiome is isolated, optionally genotyped, and specific strains are selected for a formulation {e.g., strains with specific genotypes). In some embodiments a formulated and gene edited microbiome is transplanted, meaning that a donor microbiome is isolated, genotyped, specific strains are selected, genetic mutants are isolated from the strains, and a formulation is generated.

In some embodiments, methods comprise: obtaining one or more live bacterial strains from the skin of a donor subject, wherein the live bacterial strains are P acnes strains;

determining whether the one or more live bacterial strains are pathogenic; and administering the one or more live bacterial strains to the skin of a recipient subject in need thereof following administration of a disinfectant or antibiotic to the skin of the subject if the one or more live bacterial strains are not pathogenic. In some embodiments, an assay is conducted to determine whether the one or more live P acnes strains are pathogenic. For example, an assay can be conducted to assess how the live bacterial strains convert or degrade cis-9, cis-12 linoleic acid. In some embodiments, one or more of the P. acnes bacterial strains within the composition is selected based on its slow or negligible degradation or conversion of cis-9, cis-12 linoleic acid.

Other Skin Conditions

In addition to acne, compositions described herein may be used to treat or prevent other skin conditions such as dandruff, progressive macular hypomelanosis, atopic dermatitis or rosacea. Dandruff is associated with a disequilibrium in the proportion of the skin microbiome. Dandruff can be experienced chronically or as a result of certain triggers, which can be accompanied by redness and irritation. The main contributors are Propionibacterium acnes and Staphylococcus epidermidis, and can also include Malassezia restricta. With dandruff, there is a lower incidence rate for P. acnes in comparison to Staphylococcus epidermidis and Malassezia restricta (Clavaud et al., 2013; Wang et al., 2015). This indicates that supplementation therapy with P. acnes bacteria may be beneficial for a dandruff treatment.

P. acnes is known to be involved in progressive macular hypomelanosis, which is a common hypopigmentation mainly on the central parts of the trunk, predominantly in young adults, and especially in women (Westerhof et al., 2004). As it is manifested through white spots on the skin, it is mostly diagnosed in patients with darker skin color. Recently, a report showed that progressive macular hypomelanosis is associated with Clade III of P. acnes (Barnard et al., 2016). Compositions described herein contain Clade I and II strains and not Clade III strains. Therefore, compositions described herein may be used to treat or prevent progressive macular hypomelanosis.

Atopic dermatitis (also known as atopic eczema) is associated with flares exhibiting a strong dysbiosis of the skin microbiome. The inflammation results in red, swollen, itchy, and cracked skin. The backs of knees, front of the elbows, hands, and feet are the most affected areas. Emollient treatments have been shown to be effective in the treatment of atopic dermatitis.

Patients receiving bacterial compositions herein display a generally improved skin condition. Therefore, compositions described herein may be used to treat or prevent atopic dermatitis.

Rosacea is a skin condition that is characterized by facial redness, small and superficial dilated blood vessels on facial skin, pustules, papules, and swelling. There are four types of rosacea, three of which affect the skin. The disorder can be confused or co-exist with acne vulgaris or seborrheic dermatitis. The presence of rash on the scalp or ears suggests a different or co-existing diagnosis because rosacea is primarily a facial diagnosis, although it may

occasionally appear in these other areas. Treating rosacea varies depending on severity and subtypes. Supplementation therapy with P. acnes using compositions described herein may be used for treating or preventing rosacea. Treatment

As used herein, the term treat, treated, or treating when used with respect to a disorder such as acne refers to improving at least one symptom of acne, such as a reduction or

improvement of lesions associated with acne. As used herein, preventing acne refers to preventing formation of symptoms of acne such as lesions, and/or preventing at least one symptom of acne from getting worse, such as preventing further lesions or preventing existing lesions from becoming worse.

Aspects of the invention relate to improving the appearance of skin and/or maintaining healthy skin. Further aspects of the invention relate to treating or preventing a condition selected from the group consisting of: acne, oily skin, progressive macular hypomelanosis (Barnard et al., 2016), dandruff, atopic eczema, atopic dermatitis, and rosacea.

Subjects

Compositions described herein can be administered to human or non-human subjects. In some embodiments, a subject is a human or non-human who has acne or is at risk of developing acne. In some embodiments, the subject is a human. In some embodiments, the subject is a domestic animal such as a house pet, such as a cat or a dog. In some embodiments, the subject is a farm animal such as a cow, goat, horse, pig or sheep. It should be appreciated that any animal that has skin could be compatible with aspects of the invention.

In some embodiments, a subject who has acne has inflamed lesions and/or non-inflamed lesions. In some embodiments, subjects with high counts of non-inflamed lesions are selected. In some embodiments, subjects are randomized based on the number of non-inflamed lesions.

Effective amounts

Compositions described herein can be administered in effective amounts. The term "effective amount" of a composition of the invention refers to the amount necessary or sufficient to realize a desired biologic effect. For example, an effective amount of a composition for treating acne is that amount sufficient to improve at least one symptom of acne, such as a reduction or improvement in lesions. The effective amount for any particular application can vary depending on such factors as the condition being treated, the particular composition being administered, the size of the subject, or the severity of the condition. One of ordinary skill in the art can empirically determine the effective amount of a particular composition of the invention without necessitating undue experimentation.

Compositions

Compositions, including cosmetic or pharmaceutical compositions, for topical administration, include transdermal patches, ointments, lotions, creams, gels, drops, sprays, including aerosol sprays, suppositories, liquids, serums or powders. In some embodiments, the preparation is a two-component dispensing system. In addition, conventional pharmaceutical carriers, aqueous, powder or oily bases, or thickeners may be used in pharmaceutical

preparations for topical administration. Examples of such ingredients include various

hydroxylated compounds, such as monomeric glycols, e.g., propylene glycol, ethyl alcohol, glycerin and butylene glycol, polymeric moisturizers such as polyglycerylmethacrylate, derivatives of palmitates and stearates, triglycerides of fatty acids, lanolin, vegetable or mineral oils, and waxes.

It was surprisingly found herein that an efficient way to establish nonpathogenic P. acnes strains on the skin is within a mixture of multiple strains. Within a mixture of strains, slow- growing strains can be established on the skin. In some embodiments, strains are selected so that the resulting population established on the skin will have low linoleic acid isomerase activity. While in the natural context, new strains are occasionally added to the skin microbiome (Oh et al., 2016), it is unlikely that a population with a high isomerase activity would be replaced by one with a low isomerase activity. The approach described herein (involving the combination of disinfection and inoculation) provides an unnatural replacement of a population with high isomerase activity with a low isomerase activity population.

As disclosed herein, some slow-growing strains, such as the non-pathogenic P. acnes K8 strain, were unexpectedly found to grow more efficiently within a mixture of strains and in some embodiments to become the dominant strain within a mixture of strains. Accordingly, in some embodiments, a mixture of different P. acnes strains can be used to more efficiently colonize the skin with slow growing strains by mixing them with other faster growing strains.

In some embodiments, compositions include media for stabilizing bacterial count. Media can include pure water, PBS, peptone, and/or a diluted or undiluted version of a suitable growth medium or any combination thereof. In some embodiments, the bacterial composition {e.g., a gel) contains a low percentage of peptone which assists in stabilizing the bacteria. In some embodiments, the percentage of peptone in the bacterial composition is about 0.05% or about 0.1%. The percentage of peptone can range in some embodiments from 0.005% - 1%, or from 0.05% - 1%. For example, the percentage of peptone can be about 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 or 1.0%. In some embodiments, the percentage of peptone is less than 0.005%. In some embodiments, the percentage of peptone is greater than 1%. In some embodiments, the percentage of peptone is about 0.25%.

In other embodiments, a suitable growth medium is used in place of peptone.

In some embodiments, the source of peptone is from casein, such as trypsin-digested peptone from casein. However, it should be appreciated that any form or source of peptone can be compatible with aspects of the invention. For example, in some embodiments, the peptone is acid-digested, rather than trypsin-digested. In some embodiments the peptone is from meat.

In some embodiments, the composition contains a buffer component to help stabilize the pH. In some embodiments, the pH is between 4.5-8. For example, the pH can be approximately 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9 or 8.0, including any value in between. In some embodiments, the pH is approximately 7.0.

Non-limiting examples of buffers can include ACES, acetate, ADA, ammonium hydroxide, AMP (2-amino-2-methyl-l-propanol), AMPD (2-amino-2-methyl-l,3-propanediol), AMPSO, BES, BICINE, bis-tris, BIS-TRIS propane, borate, CABS, cacodylate, CAPS, CAPSO, carbonate (pKl), carbonate (pK2), CHES, citrate (pKl), citrate (pK2), citrate (pK3), DIPSO, EPPS, HEPPS, ethanolamine, formate, glycine (pKl), glycine (pK2), glycylglycine (pKl), glycylglycine (pK2), HEPBS, HEPES, HEPPSO, histidine, hydrazine, imidazole, malate (pKl), malate (pK2), maleate (pKl), maleate (pK2), MES, methylamine, MOBS, MOPS, MOPSO, phosphate (pKl), phosphate (pK2), phosphate (pK3), piperazine (pKl), piperazine (pK2), piperidine, PIPES, POPSO, propionate, pyridine, pyrophosphate, succinate (pKl), succinate (pK2), TABS, TAPS, TAPSO, taurine (AES), TES, tricine, triethanolamine (TEA), and Trizma (tris).

In some embodiments the fomulation includes a thickener. Non-limiting examples of thickeners can include hydroxyethylcelluloses (e.g. NATROSOL®), starch, gums such as gum arabic, kaolin or other clays, hydrated aluminum silicate, fumed silica, carboxyvinyl polymer, sodium carboxymethyl cellulose or other cellulose derivatives, ethylene glycol monostearate and sodium alginates.

In some embodiments, the thickener is hydroxyethyl cellulose. In some embodiments, the hydroxyethyl cellulose comprises NATROSOL® hydroxyethylcellulose (HEC) (Ashland Inc.). In some embodiments, the NATROSOL® is NATROSOL® HX (Caesar & Loretz GmbH, order no 4482, CAS: 9004-62-0) or NATROSOL® G (Caesar & Loretz GmbH, order no 4484, CAS: 9004-62-0). It should be appreciated that any form of hydroxyethyl cellulose can be compatible with aspects of the invention. In some embodiments, the viscosity type is HHR-P, HH, H4, H, MH, M, K, G, E or L.

In some embodiments, the concentration of the thickener, such as hydroxyethyl cellulose, is between approximately l%-5%. For example, the concentration can be about 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, or 5.0%. In other embodiments, the concentration of thickener, such as hydroxyethyl cellulose, is less than 1% or more than 5%. In some embodiments, the concentration of thickener, such as hydroxyethyl cellulose, is approximately 1.5%. In some embodiments, the concentration of thickener, such as

hydroxyethyl cellulose, is approximately 2.5%.

In some embodiments, a composition comprises one or more live P. acnes strains at colony-forming units (CFU) of at least 10 ⁴ -10 ⁹ /ml. For example, the CFU can be at least 10 ⁴ , at least 10 ⁵ , at least 10 ⁶ , at least 10 ⁷ , at least 10 ^s , at least 10 ⁹ or more than 10 ⁹ /ml. In some embodiments, all of the P. acnes strains are present in a composition at colony-forming units (CFU) of at least 10 ⁴ -10 ⁹ /ml. In some embodiments, the bacterial composition exhibits a stable CFU over at least three months at room temperature. In some embodiments, the CFU count shortly fluctuates in the initial storage phase {e.g., 2 weeks) and then stabilizes.

In some embodiments, a composition comprises about 2.5% of a thickener, such as NATROSOL® hydroxyethylcellulose (HEC); about 0.25% peptone, such as trypsin-digested peptone from casein; and a CFU of about 10 ⁴ -10 ⁹ /ml of two or more live P. acnes strains {e.g., about 10 /ml of each live P. acnes strain).

Aspects of the invention relate to compositions comprising mixtures of different live P. acnes strains. Mixtures can include two or more strains. In some embodiments, the composition includes at least two different live P. acnes strains. The two different strains can be present at equal concentrations or at unequal concentrations. In some embodiments, the composition comprises a 2-strain mixture of P. acnes strain C3 and P. acnes strain K8. In certain

embodiments, both strains are present at equal concentrations. In certain embodiments, both strains are present at a CPU of approximately 5 x 10 ⁶ /ml.

In some embodiments, the composition comprises at least 4 different live P. acnes strains. In certain embodiments, the composition comprises a 4-strain mixture of P. acnes strain C3, P. acnes strain A5, P. acnes strain F4 and P. acnes strain K8. The four different strains can be present at equal concentrations or at unequal concentrations. In certain embodiments, the relative concentrations of strains C3, A5, F4, and K8 are approximately 55%, 30%, 10%, and 5%, respectively. In some embodiments the CPU values for strains C3, A5, F4, and K8 are approximately 5.5 x 10 ⁶ /ml, 5.5 x 10 ⁶ /ml, 1 x 10 ⁶ /ml, and 5 x 10 ⁵ /ml, respectively.

In some embodiments, each live P. acnes bacterial strain constitutes at least

approximately 5% of the composition.

In some embodiments, the compositions further include salicylic acid. In some embodiments, the compositions include 0.05 -10% salicylic acid. For example, the compositions can include approximately 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, or 10% salicylic acid. In other embodiments, compositions include less than 0.05% salicylic acid or more than 10% salicylic acid. In some embodiments, in a composition that is kept on the face for an extended time, the percentage of salicylic acid is less than or equal to 2%. In some embodiments, in a composition that is washed off the face and not kept on the face for an extended time, the percentage of salicylic acid is less than or equal to 3%. P. acnes strains are surprisingly not inhibited by salicylic acid, allowing the inclusion of salicylic acid within compositions described herein for treatment of skin conditions {e.g., acne or dandruff).

In some embodiments, the bacterial composition is combined with one or more antiinflammatory compounds. Without wishing to be bound by any theory, the anti-inflammatory compound may reduce the inflamed lesions in the short term, while the bacterial composition may address the underlying problem and produce a long-term effect. In some embodiments, compositions comprise emollients such as those disclosed in an incorporated by reference from US Patent No. 5,525,336. Non-limiting examples of emollients include stearyl alcohol, glyceryl monoricinoleate, glyceryl monostearate, propane- 1,2-diol, butane- 1,3-diol, mink oil, cetyl alcohol, isopropyl isostearate, stearic acid, isobutyl palmitate, isocetyl stearate, oleyl alcohol, isopropyl laurate, hexyl laurate, decyl oleate, octadecan-2-ol, isocetyl alcohol, cetyl palmitate, dimethylpolysiloxane, di-n-butyl sebacate, isopropyl myristate, isopropyl palmitate, isopropyl stearate, butyl stearate, polthylene glycol, triethylene glycol, lanolin, sesame oil, coconut oil, arrachis oil, castor oil, acetylated lanolin alcohols, petroleum, mineral oil, butyl myristate, isostearic acid, palmitic acid, isopropyl linoleate, lauryl lactate, myristyl lactate, decyl oleate, myristyl myristate.

In some embodiments, a protein stabilizing agent such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non- limiting examples include glycerol, ethylenediaminetetraacetic acid, cysteine, and proteinase inhibitors such as leupeptin, pepstatin, antipain, and cystatin.

In some embodiments, a humectant such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non-limiting examples of humectants include glycerin, sorbitol, sodium 2-pyrrolidone-5-carboxylate, soluble collagen, dibutylphthalate, gelatin.

In some embodiments, an astringent agent such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non-limiting examples of astringent agents include arnica flowers or extracts thereof, lower alkyl alcohols, witch hazel, boric acid, lactic acid, methol, camphor, zinc phenol sulphonate, aluminum acetate, aluminum sulfate, and zinc chloride or sulfate.

In some embodiments, a pigment such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non-limiting examples of pigments include titanium dioxide, micas, iron oxides, barium lake, calcium lake, aluminum lake, bismuth oxychloride, zirconium lake and calcium oxides.

In some embodiments, a coloring agent such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non-limiting examples of coloring agent include shikonin, β-carotene, paprika, monascus, safflower red, safflower yellow, red cabbage color, purple sweet potato color, lycopene, cacao color, grape color, cochineal, lac color, beet red, hematein, Red. No. 215, Red. No. 218, Red. No. 223, Red. No. 225, Orange No. 201, Orange No. 206, Yellow No. 201, Green No. 202, and Purple No. 201, Red. No. 2, Red. No. 3, Red. No. 102, Red. No. 104 (1), Red. No. 105 (1), Red. No. 106, Yellow No. 4, Yellow No. 5, Green No. 3, Blue No. 1, Blue No. 2, Red. No. 201, Red. No. 213, Red. No. 214, Red. No. 227, Red. No. 230 (1), Red. No. 230 (2), Red. No. 231, Red. No. 232, Orange No. 205, Orange No. 207, Yellow No. 202 (1), Yellow No. 202 (2), Yellow No. 203, Green No. 201, Green No. 204, Green No. 205, Blue No. 202, Blue No. 203, Blue No. 205, and Brown No. 201.

In some embodiments, UV-A and UV-B radiation filters, sunscreens, free-radical blockers, vitamin extracts, or antioxidants such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 are included in compositions.

In some embodiments, a surfactant or a solvent such as those disclosed in an

incorporated by reference from US Patent No. 5,525,336 is included in the composition. Non- limiting examples of solvents include water, ethyl alcohol, toluene, methylene chloride, isopropanol, n-butyl alcohol, castor oil, ethylene glycol monoethyl ether, diethylene glycol monobutyl ether, diethylene glycol monoethyl ether, dimethyl sulphoxide, dimethyl formamide and tetrahydrofuran. i) Anionic surfactants, such as metallic or alkanolamine salts of fatty acids for example sodium laurate and triethanolamine oleate; alkyl benzene sulphones, for example triethanolamine dodecyl benzene sulphonate; alkyl sulphates, for example sodium lauryl sulphate; alkyl ether sulphates, for example sodium lauryl ether sulphate (2 to 8 EO);

sulphosuccinates, for example sodium dioctyl sulphonsuccinate; monoglyceride sulphates, for example sodium glyceryl monostearate monosulphate; isothionates, for example sodium isothionate; methyl taurides, for example Igepon T; acylsarcosinates, for example sodium myristyl sarcosinate; acyl peptides, for example Maypons and lamepons; acyl lactylates, polyalkoxylated ether glycollates, for example trideceth-7 carboxylic acid; phosphates, for example sodium dilauryl phosphate; Cationic surfactants, such as amine salts, for example sapamin hydrochloride; quartenary ammonium salts, for example Quaternium 5, Quaternium 31 and Quaternium 18; Amphoteric surfactants, such as imidazol compounds, for example Miranol; N-alkyl amino acids, such as sodium cocaminopropionate and asparagine derivatives; betaines, for example cocamidopropylebetaine; Nonionic surfactants, such as fatty acid alkanolamides, for example oleic ethanolamide; esters or polyalcohols, for example Span; polyglycerol esters, for example that esterified with fatty acids and one or several OH groups; Polyalkoxylated derivatives, for example polyoxy:polyoxyethylene stearate; ethers, for example polyoxyethe lauryl ether; ester ethers, for example Tween; amine oxides, for example coconut and dodecyl dimethyl amine oxides. In some embodiments, more than one surfactant or solvent is included.

In some embodiments, preservatives, antiseptics, pigments or colorants, fragrances, masking agents, and carriers, such as water and lower alkyl, alcohols, such as those disclosed in an incorporated by reference from US Patent No. 5,525,336 are included in compositions.

In some embodiments wherein a composition is in a powder, the powders may include chalk, talc, fullers earth, colloidal silicon dioxide, sodium polyacrylate, tetra alkyl and/or trialkyl aryl ammonium smectites and chemically modified magnesium aluminum silicate as disclosed in an incorporated by reference from US Patent No. 5,525,336. In some embodiments, a composition can include a perfume.

When administered, the compositions of the invention are applied in a therapeutically effective, pharmaceutically acceptable amount as a pharmaceutically acceptable formulation. Any of the compositions of the present invention may be administered to the subject in a therapeutically effective dose. When administered to a subject, effective amounts will depend on the particular condition being treated and the desired outcome. A therapeutically effective dose may be determined by those of ordinary skill in the art, for instance, employing factors such as those described herein and using no more than routine experimentation.

In some embodiments, one or more of the following agents is included in compositions described herein: topical antibiotics (e.g., clindamycin, erythromycin, tetracycline,

metronidazole), oral antibiotics (e.g., tetracycline, erythromycin, minocycline, doxycycline, clindamycin), topical retinoids (e.g., adapalene, tazarotene, tretinoin), oral retinoids (e.g., isotretinoin), benzoyl peroxide, salicylic acid, sulfur, azelaic acid, and antimicrobial peptides and derivatives thereof (e.g., lipohexapeptide HB 1345, oligopeptide- 10, magainins (e.g., pexiganan), protegrins (e.g., iseganan), indolicidins (e.g., omiganan, MBI 594AN), histatins (e.g., PI 13 P113D), human bactericidal/permeability-increasing proteins (e.g., XMP.629, neuprex), cathelicidins (e.g., cathelicidin-BF).

In some embodiments, compositions are administered in a topical form, such as in a cream or ointment. In some embodiments, administration of compositions described herein comprises part of a combination treatment or follows from an earlier treatment of the skin of a subject.

The appropriate amount of a composition to be applied can depend on many different factors and can be determined by one of ordinary skill in the art through routine experimentation. Several non-limiting factors that might be considered include biological activity and

bioavailability of the agent, nature of the agent, mode of administration, half-life, and

characteristics of the subject to be treated.

In some embodiments, the bacterial composition is not applied to subjects with sensitive skin. In some embodiments, when using a bacterial composition for the treatment or prevention of acne, the subject being treated avoids unnecessary sun exposure and uses a sunscreen. In some embodiments, if the treated skin is irritated, characterized by redness, swelling, burning, itching, or peeling, the product is used less frequently or in a lower concentration.

In some embodiments, a composition described herein is administered to the skin of a subject to maintain healthy skin. A composition can be administered once or multiple times. In some embodiments, a composition is administered at regular intervals while in other

embodiments it is administered in irregular intervals. For example, a composition can be administered about every 15 minutes, 30 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 24 hours, 48 hours, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks or more or less frequently including all values in between.

In some embodiments, a composition is administered to a subject who also receives or has previously received a standard acne treatment, such as a disinfectant or an antibiotic, as would be recognized by one of ordinary skill in the art. In some embodiments, the composition is administered in parallel with the standard acne treatment. In other embodiments, the composition is administered after the standard acne treatment. The composition can be administered either immediately after the previous treatment or there can be a delay between the previous treatment and administration of the composition. The composition can be administered once or multiple times after the previous treatment. In some embodiments, a composition is administered at regular intervals after the previous treatment while in other embodiments it is administered in irregular intervals after the previous treatment. For example, a composition can be administered about every 15 minutes, 30 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 24 hours, 48 hours, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks or more or less frequently including all values in between after a previous treatment.

Aspects of the invention encompass mutating bacterial strains, such as in S. epidermis strains. Mutations can be made in some embodiments by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid or polypeptide. Variant polypeptides can be expressed and tested for one or more activities to determine whether a mutation provides a variant polypeptide with desired properties. Further mutations can be made to variants (or to non-variant polypeptides) which are silent as to the amino acid sequence of the polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., E. coli, are well known to those of ordinary skill in the art. Still other mutations can be made to the noncoding sequences of a gene or cDNA clone to enhance expression of the polypeptide. The activity of variant polypeptides can be tested by cloning the gene encoding the variant polypeptide into a bacterial or eukaryotic expression vector, introducing the vector into an appropriate host cell, expressing the variant polypeptide, and testing for a functional capability of the polypeptides as disclosed herein.

Bacterial cells according to the invention can be cultured in a variety of media, including rich or minimal media. As would be understood by one of ordinary skill in the art, routine optimization would allow for use of a variety of types of media. Media can be supplemented with various additional components, including sugar sources. Some non-limiting examples of supplemental components include glucose, amino acids, antibiotics and ATCC Trace Mineral Supplement. Similarly, other aspects of the medium, and growth conditions of the cells of the invention can be optimized through routine experimentation. For example, pH, temperature, and concentration of components within the compositions are non-limiting examples of factors which can be optimized.

Liquid and/or solid cultures used to grow cells associated with the invention can be housed in any of the culture vessels known and used in the art.

In some embodiments, the bacterial strains are grown in batches. In some embodiments, the bacterial strains are grown in fermenters. In some embodiments, compositions comprising the bacterial strains are packaged. In certain embodiments, compositions comprising the bacterial strains are packaged in enteral syringes or sachets. Kits

The present invention also provides any of the above-mentioned compositions in kits. In some embodiments, a kit comprises a container housing live bacteria or a container housing freeze-dried live bacteria. Kits can include a second container including media such as peptone. In some embodiments, kits can include antibiotic(s), disinfectant(s) (e.g., BPO) and/or salicylic acid. In some embodiments, the antibiotic(s), disinfectant(s) and/or salicylic acid are used to pre- treat the skin before application of the composition comprising live bacteria. Kits can also include instructions for administering the composition. In certain embodiments, instructions are provided for mixing the bacterial strains with other components of the composition. In some embodiments, a kit further includes an applicator to apply the bacterial composition to a subject.

The present invention is further illustrated by the following Examples, which in no way should be construed as further limiting. The entire contents of all of the references (including literature references, issued patents, published patent applications, and co pending patent applications) cited throughout this application are hereby expressly incorporated by reference.

EXAMPLES

Example 1: Different P. acnes strains have different levels of linoleic acid isomerase activity or final thresholds of concentration of trans- 10, cis- 12 linoleic acid

Experiments were performed to characterize the linoleic acid isomerase activity of multiple different P. acnes strains. The P. acnes strains were grown in a growth medium lacking linoleic acid (Rosson et al., 2004). Cis-9, cis- 12 linoleic acid was added to the growth medium and then the amount of cis-9, cis- 12 and trans- 10, cis- 12 linoleic acid isomer was determined at different time points, using an assay involving conversion to fatty acid methyl esters and subsequent gas chromatography. Established methods for distinguishing cis and trans isomers of unsaturated fatty acids are described in Kramer et al., 2004, which is herein incorporated by reference in its entirety.

Surprisingly, the choice of media and incubation conditions were found to be important variables for conducting these experiments. To measure the degradation of linoleic acid in the media, reinforced clostridial media (RCM) was used because it was observed that in some other types media, the linoleic acid precipitated. Results showing degradation of cis-9, cis-12 linoleic acid are shown in FIG. 1. A very rapid decrease of cis-9, cis-12 linoleic acid was observed, with most of the degradation occurring in the first 48 h of the experiment. It was also observed that while strain Al depletes the linoleic acid completely from the medium, the strain C3 surprisingly slows down in degradation of linoleic acid reaching an equilibrium concentration. Without wishing to be bound by any theory, acne patients usually have a lower linoleic acid concentration in the sebum compared to healthy subjects. Accordingly, a population of slow degrading strains will result in a higher

concentration of linoleic acid in sebum, which may be advantageous.

Only small amounts of trans- 10, cis-12 linoleic acid isomer were detected in rich media, such as RCM, likely because rich medias such as RCM do not represent the environment encountered in sebaceous glands. In particular, glucose is normally limited in the sebaceous glands and could influence the metabolic program of the bacteria (Im and Hoopes, 1974). All previous commonly used media for P. acnes {e.g., RCM, BHI, GAM) contain at least 3g/L of glucose, whereas in the sebaceous glands, glucose only occurs at comparably low concentrations {e.g., ~ 0.6-1.4 g/kg dry weight (Im and Hoopes, 1974)).

Therefore, a glucose-free media in which all P. acnes strains grow was designed herein and used to test and characterize I I P. acnes strains. A minimal media was established out of peptone and yeast extract (PY-media) which allows the growth of bacteria and the measurement of the production of trans- 10, cis-12 linoleic acid isomer since it resembles the natural environment encountered by the bacteria.

Conditions were developed for assessing production of trans- 10, cis-12 linoleic acid isomer involving shaking samples in a minimal media. A time course analysis conducted with multiple strains is shown in FIG. 3. As the growth of the individual strains varied, the reading was normalized corrected by the Optical Density (OD) measured at 600 nm, which was confirmed by CFU counts on agar plates. To normalize the OD, the OD of each culture was used as a measure for the biomass of each strain. All OD measurements were then divided by the highest measured value, providing a factor representing relative growth. The measured trans- 10, cis-12 linoleic acid concentration was then multiplied with this factor for each strain. The underlying assumption is that a strain that will have grown to high optical density might have still produced less isomerase per cell than a slow growing strain. The corrected concentrations of trans 10, cis 12 linoleic acid isomer is shown in FIG. 2. Strain Al, which is generally associated with acne (McDowell et al., 2012, PLoS ONE 7, e41480), produced the most trans- 10, cis-12 linoleic acid isomer. Strains with very little production of trans- 10, cis-12 linoleic acid isomer were C3, CI, F4, A5, Kl, K2, K8 and LI. The K strains and LI strain showed very little growth. These strains also grow very slowly in rich media and are rarely occurring in nature.

Unexpectedly, as discussed below, in certain combinations with other strains, the K8 strain shows improved growth.

Materials and Methods

Each strain was grown as a pre-culture and the pre-cultures were normalized by OD. A fresh media containing 1.7 mM cis 9, cis 12 linoleic acid was prepared before each experiment. The cultures were then incubated at 37°C either still or shaking at 220 rpm. The samples were taken at various time points and immediately frozen at -80°C until the lipid extraction and gas chromatography (GC) analysis.

For the GC analysis, the lipids in the media were extracted and converted to their methyl esters. For this, 100 μΐ of a media sample was diluted with 900 μΐ H ₂ 0. 20 μg of Heptadecanoic acid was added as an internal standard and the complete lipid fraction was extracted with ethylacetate. The organic phase was then separated and dried under nitrogen. The lipids were then converted with a 14% Borontrifluoride-Methanol solution (Sigma-Aldrich, St. Louis, MO, catalog number B 1252), extracted with hexane, dried under nitrogen and resuspended in 100 μΐ of hexane. The samples were then analyzed on a Varian CP 3800 Gas chromatograph with FID detector. The column used was a CP-WAX 58 (FFAP) Capillary column 25m x 0.32 mm I.D from Agilent Technologies, Santa Clara, CA. and the temperature program was 120°C (lmin) - 120°C to 250°C (20°C/min) - 250°C (12min).

Example 2: Optimization of Mixtures of Bacterial Strains

Example 1 demonstrates that isolated P. acnes strains differed significantly in their growth behavior. Generally, strains from Clade I were found to be fast growers, while strains from Clade II were found to be slow growers (see, e.g., Figure 5). In general, strains which are considered not to be associated with acne are more likely to originate from Clade II (Lomholt and Kilian, 2010; Yu et al.). This slow growth indicates that these strains are less likely to colonize the skin after a disinfection. Strains from Clade II are also less commonly found in human subjects. In nature, skin tends to be colonized by fast growing strains from Clade I. By contrast, described herein are mixtures of strains that allow for colonization of the skin by Clade II strains.

Further growth curve experiments showed that mixtures of 2 or 4 strains grow similarly as fast as the fastest pure isolates in the mixtures. Surprisingly, when compositions of mixtures consisting of 6 strains grown for 5 days on agar were analyzed, the majority of the bacteria was found to originate from the strain K8 (FIG. 7), which was a strain that was observed to grow slowly when grown individually. Accordingly, mixtures of strains can be created which have advantageous growth properties even though they contain individual strains that grow slowly in nature and would likely be outcompeted in nature.

Strains within Clade IA1 have been reported to be associated with acne vulgaris

(Lomholt and Kilian, 2010, PLoS One 5; McDowell et al., 2012, PLoS ONE 7, e41480). To select strains from Clade IA1 to mix with strains from Clade II to co-colonize the skin, the criteria of conversion of cis 9, cis 12 linoleic acid to the trans 10, cis 12 isomer was used for strain selection. Colonization of the skin with such a mixture of strains is unlikely to occur naturally in part because the increased use of cosmetics with preservatives and hygienic products leads to natural selection of fast growing strains, which become the dominant occupants on the skin. Accordingly, in a naturally occurring transfer of P. acnes strains {e.g., by close body contact), the vast majority of transferred bacteria would be from only one strain.

Based on both growth behavior and production of trans 10, cis 12 linoleic acid, strain C3 was selected as a strain for colonization to use in the compositions comprising mixtures of bacterial strains. The effect of varying starting concentrations of the composition on the skin was then tested. 6 different strains were mixed in equal amounts and one of the 6 strains was added in excess. After 5 and 6 days of growth, the composition of the mixture was then assessed. Based on this data in conjunction with growth curves, the final concentration of strains in the compositions comprising mixtures of bacterial strains was selected.

A high concentration {e.g., less than or equal to 60%) of a strain from Clade I was added, which exhibited a low conversion rate of cis 9, cis 12 linoleic acid, grew to medium high ODs and showed a decrease in relative amount of the mixture from day 5 to day 6. A mixture was prepared in which a given strain maximally represents 50% of the population. In nature, most of the time one P. acnes strains likely represents more than 90% of the observed P. acnes population on one host.

It was observed that the growth behavior of P. acnes is for some strains heavily dependent on the starting CFU count. Therefore, it was investigated how the relative proportion of one strain in a mixture develops once the culture has reached a stationary phase. Surprisingly, it was found that the underlying dynamics by which a strain becomes a dominant strain is determined at least in part by the starting amount of bacteria and varies from strain to strain.

Pre-cultures were grown in RCM media and, after centrifugation, were resuspended in PBS. The cultures were normalized to OD 0.5. Then 1 ml of medium was inoculated with 50 μΐ of the normalized suspension. The plates were airtight sealed and the cultures were then incubated at 37°C in a Tecan Spark. The cultures were shaken every 30 min and the OD at 600 nm was measured. RCM media was obtained from BD (BD/Difco catalog no. 218081). PY media is a custom media, which only consists of 2% yeast extract (Sigma catalog number Y1625-250G) and 3% peptone (Sigma 70172-500G). This media contains no glucose and thereby more accurately reflects the low glucose environment encountered by P. acnes in the sebaceous glands than rich media with a high glucose content like RCM or BHI.

FIG. 4 shows the relative amount of C3 strain in a mixture at day 5 or day 6 after inoculation. When there is a high percentage of C3 in the starting mixture, C3 stays the dominant strain. Surprisingly, a lower starting concentration of C3 reduces the overall percentage in the late stationary phase.

FIG. 5 shows a growth curve of the strains C3, F4, CI and K8 in RCM media at 37°C. FIG. 6 shows a growth curve of the strains C3, F4, CI, K8, a 2-strain mixture (strains C3 and K8) and a 4-strain mixture (A5, C3, F4, and K8) in glucose-free PY media at 37°C.

Example 3: Competition Experiments With Combinations of Strains

An in vitro experiment was performed to determine the synergistic effect of various bacterial mixtures. Fresh bacterial cultures were revived from -80°C stocks and were grown on RCM agar plates. From the agar plates, a BHI liquid medium was inoculated and grown for 5 days until stationary phase. Then the cultures were harvested by centrifugation (4000 g for 10 min at 4°C) and resuspended in 1.4 ml of 0.1 % Peptone (trypsin-digested peptone from casein). The bacterial suspensions in peptone were then normalized to an OD of 0.8. The strains were stored overnight at room temperature (RT) in the peptone solution to simulate storage before application. The next morning, all strains were then mixed in equimolar concentrations and this mixture was diluted further 1.6 fold with the peptone solution. Accordingly, each strain was at a 1: 10 dilution in the mixture compared to the stock solution. Then a 96-well master plate was generated which contained different combinations (Table 3).

Table 3. Strains

This resulted in the following concentrations (Table 4):

Table 4: Concentrations

The 10 μΐ of each mixture was added in the middle of a 96-well agar plate and incubated for 4 days. The media used was RCM-agar supplemented with 0.5 mg/ml linoleic acid.

The plate was harvested according to the following protocol. To each well, 10 μΐ sterile PBS was added. After a short incubation time, the bacteria in each well was individually resuspended and transferred to a fresh plate. The cells were then pelleted by centrifugation and washed twice with MilliQ water. The pellets were then resuspended in 90 μΐ freshly prepared 0.05 M NaoH (100 μΐ of 30% NaOH in 20 ml of MilliQ Water). The plates were then incubated in a PCR machine at 60°C for 45 min. Then the reaction was neutralized by adding 9.2 μΐ Tris pH 7 and 5μ1 of the supernatant was used as template in a 20μ1 PCR reaction. PCR was conducted to amplify the SLST allele in order to characterize the population. The Primer sequences used were:

SLST FW: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCAGCGGCGCTGC TAAGAACTT (SEQ ID NO: 81) and

SLST-RV: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCGGCTGGCAA

ATGAGGCAT (SEQ ID NO: 82) (Scholz et al., 2014).

Samples were amplified using a Kappa polymerase (5 min 95°C; 35 cycles of: (98°C 20s, 62°C 25s, 72°C 30s); 1 min 72°C). The sequencing library was constructed using two rounds of PCR. The first round used SLST primers which included sequences compatible with Illumina sequencing. The second round (10 cycles) was used to barcode the different samples for sequencing in a single Illumina flowcell. The PCR reactions and the 3-S-Biokit DNA extractions were purified using Magnetic beads which were prepared according to (Rohland and Reich, 2012). The indexed reactions were pooled and purified from an agarose gel using the promega WIZARD® SV Gel and PCR Clean-Up System. The final libraries were then quality controlled on an Agilent TapeStation and quantified by qPCR using the KAPA library quantification kit KK4854 on a Roche LightCycler 480. Illumina MiSeq sequencing was conducted using a MiSeq Reagent Kit v3 with 2*300Bp reads (MS-102-3003).

Samples were analyzed using an internally developed computational pipeline (S- genotyping). Quality filtering; samples were mapped into an internal database using bwa software; data processing and visualization was conducted with R statistical language. The latest library of the P. acnes SLST types was downloaded from medbac.dk/slst/pacnes.

This experiment showed that the growth behavior of individual strains differs from their growth behavior as mixtures. It was expected that strains which grow fast in isolation like A5 would take over the culture. Surprisingly a slow growing strain (K8) which would have been expected to contribute only a minor amount to the final mixture was the main contributor to the final biomass if grown in the presence of other strains. FIG. 7 shows the change of relative composition of a mixture of different P. acnes strains determined by sequencing reads before and after 5 days of growth on RCM agar. Surprisingly, the strain K8 which was very slow-growing when used as insolate took over most of the culture in the 5 days of the experiment. Before the experiment, all strains were normalized according to their OD to represent 16% of the biomass in the starting culture. After the experiment, K8 was the most dominant strain with 69%. Only E3 was also able to increase its share in the biomass. The portion of C3 reduced to 8% while A5, CI and F4 reduced to below 1%.

Example 4: Determination of Minimum Bactericidal Concentration (MBC) and Minimum Inhibitory Concentration (MIC) For Isolated Strains and Mixtures of Strains with DMDM Hydantoin and Benzoic Acid, Common Preservatives Found in Cosmetic Products

Experiments were conducted to simulate the application of a cosmetic product containing preservatives on the skin of a human subject and to assess the effect of those preservatives on the skin microbiome of the subject. It was investigated whether there is any difference between the effect of the preservative on a single strain or on a mixture of multiple strains.

Four individual strains of P. acnes were grown in separate cultures as inoculum.

Subsequently, each culture was normalized according to its OD and challenged with DMDM Hydantoin or benzoic acid, which are two preservatives commonly used in cosmetics. Each strain was tested alone and in combination with other strains. Individual strains and

combinations of strains were exposed for 24 h to the preservative and then subsequently plated on agar to determine minimum bactericidal concentration (MBC) and minimum inhibitory concentration (MIC) of the preservative.

The strains A5, C3, F4 and K8 were grown from -80°C stocks in Reinforced Clostridial Medium (RCM) (Becton-Dickinson, catalog number 218081, Franklin Lakes, NJ). For each strain, 50 ml of RCM was inoculated with 0.5 ml of an OD 1.0 stock. The OD was measured in regular intervals while the bacteria were incubated at 37°C. For the MIC testing, the bacteria were harvested in exponential phase and normalized as described below. For the MBC testing, the bacteria were grown until reaching stationary phase and incubated at 37°C for another 24h before they were processed for the experiment. The samples were then normalized to an OD of 0.5, using RCM media as a diluent.

Working solutions of DMDM Hydantoin (Sigma- Aldrich, St. Louis, MO, catalog number PHR1358-1ML) and Benzoic acid (Sigma- Aldrich, St. Louis, MO, catalog number 242381-25G) were prepared in RCM media, with test concentrations of 1%, 0.25%, 0.125%, and 0.1% for DMDM Hydantoin, and 2.5%, 0.63%, 0.31 and 0.25%, as blank control consisting of only RCM. These concentrations represent dilutions corresponding to commonly used amounts in cosmetics. DMDM Hydantoin is limited by the EU to concentrations up to 1% in cosmetics and Benzoic acid is limited by the FDA in "rinse-off-products" to 2.5% and in "leave-on-products" to 0.5%. The exposure was performed in 96-well plates, and each condition was tested in triplicate. For each sample, 200 μΐ of media containing the preservative was inoculated with 20 μΐ of normalized bacteria solution.

Strains were added either individually to the challenge media or as a mixture. For each strain, the same overall bacterial count (determined by OD measurement) was used when the strain was added individually or when the strain was added as a component of a mixture. The mixtures consisted of either 2 strains or 4 strains. The two-strain mixture included strains C3 and K8, with each strain representing approximately 50% of the bacterial mass. The four-strain mixture included strains A5 (-35%), C3 (-55%), F4 (-10%) and K8 (-5%). Both the MBC and MIC test were set up in a 96-well plate. To avoid a plate effect, the outermost wells were filled with water. For the MIC test, the bacteria were grown in the presence of the preservative for 5 days in liquid culture under anaerobic conditions before they were analyzed (Table 5).

For the MBC test, the bacteria were exposed to the preservative in the RCM medium for 24 h in an anaerobic environment at 37°C. After 24 h, 10 μΐ of each test well was transferred to a agar plate (96-well plate) which had each well filled with 200 μΐ of RCM agar (Sigma- Aldrich, St. Louis, MO, catalog number 91365-500 g) and was incubated for four days at 37°C in the absence of oxygen. After 4 days, each plate was analyzed for visible growth of colonies to determine the MBC (Table 6).

Table 5. MIC concentrations of different preservatives in liquid RCM medium

Table 6. MBC after 24h exposure to DMDM Hydantoin and benzoic acid

Resw/ts

The m vzYro test simulated two scenarios. The MIC test represented a scenario in which P. acnes contaminates a classical cosmetic product. The MBC test simulated a scenario in which bacteria living on the skin are exposed to a preservative from topically applied cosmetics.

As expected, in the MIC test, both preservatives efficiently inhibited growth when present in the liquid growth media. Even at significantly lower concentrations than commonly used in cosmetics, no growth of the individual P. acnes strains or mixtures was detected.

In the MBC test, the results were surprisingly different from the MIC test. Benzoic acid, a common preservative, affected the growth of all strains at concentrations greater than 0.31% vol/vol. However, differences were observed between the different strains. Strains A5 and C3 survived 24 h exposure to 0.31% benzoic acid, while strains F4 and K8 were not able to grow after this exposure. The mixtures of strains grew only to the maximum concentration of benzoic acid 0.31% that was tolerated by the individual strains. "Leave-on" products contain a maximum concentration of 0.5% of benzoic acid. Based on the data, such a concentration might affect only some of the P. acnes strains while others will survive such a concentration.

Surprising results were obtained when performing the same test with DMDM Hydantoin. Unexpected growth of the mixture of strains was observed at concentrations higher (0.13%) than those tolerated by any individual strains alone (0.1%). This indicates that a bacterial community of P. acnes strains established on the skin will have improved survival against the exposure to products containing preservative such as DMDM Hydantoin compared to single bacterial strains established on the skin. This provides an unexpected advantage for bacterial mixtures compared to individual strains for the establishment and long term persistence on the skin of a human subject. The combinations of two strains provided a better resistance against a formaldehyde releasing agent like DMDM Hydantoin than any individual strains tested. Example 5: Clinical Study In Acne Patients (ACBAC)

A clinical pilot study in acne patients was performed. The pilot study evaluated bacterial engraftment of the microbiome as well as safety and efficacy trends. Based on the pilot study, including criteria such as safety, stability and responder rate, one of the mixtures tested in the pilot study was chosen for a larger clinical study.

Pilot Study Schedule

The pilot study was performed for 6 weeks with 14 subjects between 18-23 years. The primary endpoints were safety and efficacy trends. Two different bacterial formulations: A2 (a 2- strain mixture comprising strains C3 and K8 of P. acnes) and B4 (a 4-strain mixture comprising strains C3, K8, A5, and F4 of P. acnes) were tested. Consistent with the data described in Example 2, the subjects receiving the A2 formulation showed a higher or equal relative abundance of K8 on the skin relative to C3, suggesting that strain C3 helps the slower growing K8 strain to colonize the skin (FIG. 25).

Both formulations showed an excellent safety profile with no adverse effects. A significant reduction in non-inflamed lesions and a slight trend in reduction of inflamed lesions were observed. Further, a decrease in the skin pH, which is generally considered as a positive development in healthy skin, was observed. Due to noisy sebumeter measurement, potential changes in the sebum production are still being investigated. The analysis of the more sophisticated sebutape measurement is still ongoing. In some of the subjects, the increase of the applied strains was clear and significant {e.g., an increase by at least 15% on both Day 21 and Day 42 compared to Day 1). The relative abundance of strains was measured with amplicon sequencing of the SLST (NGS). These subjects were defined as acceptors. As discussed below, the acceptor subjects exhibited effects, for example, on non-inflamed lesions and pH. Therefore, the results from the pilot study were positive and led to a larger clinical study.

Pilot study design

Subjects were randomly distributed into two arms with different bacterial formulations administered to the subjects in each arm. Bacterial formulations were double-blinded: Arm 1: n=8 subjects received formulation A2. Arm 2: n=6 subjects received formulation B4. Subjects were evaluated on Day 1, Day 7, Day 21, and Day 42. In the first week, between Day 1 and Day 7, all subjects received Benzoyl peroxide (BPO) treatment (applied once a day). In the following 5 weeks, between Day 7 and Day 42, all subjects received bacterial formulation (gel applied 2 x per day). FIG. 8A depicts the design of the pilot study.

Subjects were examined during 4 visits - on Day 1, Day 7, Day 21, and Day 42. Table 7 shows measurements taken and documented during each visit.

Safety

The safety of the administered formulations was evaluated, for example, by visual evaluation of the redness, irritation or any other skin problems during each visit. No safety issues were observed during the study. Seven subjects reported dry or red skin during the use of BPO (Day 1 - Day 7). However, the skin of the subjects did not get red, irritated or otherwise disturbed during the administration of live bacteria. No adverse effects were observed associated with the administration of live bacteria.

Table 7. Pilot Study

Microbiome samples

Bacterial species resolution (16S)

The composition of bacterial species (16S) in the microbiome samples were analyzed on each visit. FIG. 9 depicts the relative ratios of the nine most abundant bacteria in the skin microbiome of all of the subjects in the study. A decrease in the total P. acnes population was observed after BPO application (Day 7) (FIG. 11A). A significant increase in the total P. acnes population was then observed after two weeks of bacterial application (Day 21) (FIG. 11 A). A slight decrease in the total P. acnes proportion was observed after five weeks of bacterial application (Day 42). Without wishing to be bound by any theory, this decrease may represent a balanced state of the microbiome and/or an increase in the diversity of the bacterial population. FIG. 1 IB shows the relative ratios of P. acnes as box plots. These observations show a positive trend in the microbiome composition development following administration of formulations described herein.

Strain level resolution of P. acnes (SLST)

Using Single Locus Sequence Typing (SLST), the P. acnes strain level composition of microbiome samples taken on each visit (Day 1, 7, 21 and 42) was determined.

Commonly found strains were dominant in most samples on Day 1 (ground state).

Following administration of the bacterial formulations, in most subjects, a shift in the

composition of the skin microbiome towards the applied strains was observed. In some subjects, the increase of the applied strains was clear and significant (increased amount of defined strain by at least 15% on both Day 21 and Day 42 compared to Day 1). These subjects were classified as acceptors. In some subjects, the increase of the applied strains was less noticeable. These subjects were classified as non-acceptors. FIG. 10 depicts the relative ratios of subjects classified as acceptors and non- acceptors.

Overall, 43% of subjects were classified as acceptors and 57% were classified as non- acceptors. Split by formulation, 50% acceptors and 50% non-acceptors were observed in the A2 formulation group, while 33% acceptors and 67% non-acceptors were observed in the B4 formulation group. Due to the small size of both groups, the difference between the two groups is not statistically significant.

No other confounding factors, such as age, gender, use of anti-bacterial products, or showering pattern, that would be likely to significantly influence the probability of being an acceptor were observed.

Bacterial species (16S) and strain level (SLST) analysis

When relating the bacterial species (16S) data with the strain level data (SLST) of P. acnes, it was observed that on Day 1 (ground state) the relative abundance of P. acnes was lower in acceptors (34%) compared to non-acceptors (41%). During the study, the average relative abundance of P. acnes in acceptors increased almost twice (60%) towards the Day 42 (final visit). Relative abundances were determined using classical 16S amplicon sequencing. In this method, which is well-known in the art, a specific part of the 16S ribosomal subunit is amplified out of all bacterial DNA in the sample by PCR. Different bacterial species present in the sample are identified by sequencing the amplicon. Next generation sequencing allows for assessment of the complete relative distribution of all sequences/species in the sample.

The non-acceptor group exhibited only a minor and not statistically significant increase of P. acnes during the study as analyzed by a t-test (FIG. 11).

Summary of microbiome results

In a subset of patients, the applied bacteria was effectively established following administration. This subset of subjects was characterized by a lower proportion of P. acnes at the beginning of the study and a significantly increased P. acnes proportion at the end of the study.

Acne lesion count

During the visit on Day 1 (ground state) and Day 42 (final visit), a dermatologist counted the number of lesions on the face of the subjects. Lesion counts were split into inflamed and non-inflamed lesions.

Non-inflamed lesions

Non-inflamed lesions are also known as comedones. Comedones may be open

(blackheads) or closed (whiteheads).

A substantial reduction of non-inflamed lesion (by 37%, P = 0.006) in both formulations was observed. The reduction in the A2 formulation corresponded to 55%, P = 0.05, and in the B4 formulation corresponded to 35%, P =0 .06. (FIG. 12).

Comparing the reduction of non-inflamed lesions between acceptors and non-acceptors (subjects who changed / not changed their skin microbiome composition), most of the lesion reduction was observed within the acceptor group (FIG. 13).

After stratifying the groups into acceptors and non- acceptors, the effect was statistically significant in both groups, with p-values below 0.03. The non-acceptors had overall less non- inflamed lesions in the ground state (Day 1); however, because of the smaller spread and less pronounced lesion reduction, the result was still highly statistically significant (FIG. 13)

Inflamed lesions

An inflamed lesion usually follows rupture of the wall of a closed comedone (non- inflamed lesion). It may also arise from normal-appearing skin. Inflammatory lesions in acne can include in some embodiments small red bumps (papules), pustules, large red bumps (nodules) and pseudocysts (fluctuant nodules).

A reduction in the number of inflamed lesions was observed following administration of bacterial formulations. The average of all subjects (across both formulations) was 19 inflamed lesion before the treatment and 16 afterwards, corresponding to a reduction of approximately 15% after the treatment. The A2 formulation produced an approximate 20% reduction (20/16), while the B4 formulation produced an approximate 9% reduction (17/15.5) (FIG. 14). While this difference was not statistically significant, and a significant difference was not noted between acceptors vs. non-acceptors (FIG. 15), the lack of statistical significance was likely due at least in part to the short duration of the study, the small sample size, and the low number of total lesions, leading to a high standard deviation. Without wishing to be bound by any theory, treatment with live bacteria may exhibit a slower effect on inflamed lesions relative to non-inflamed lesions because non-inflamed lesions are precursors to inflamed lesions. Based on the observed data, a statistically significant effect on reduction of inflamed lesions is expected in a study of longer duration.

Sebum measurement

Two types of assays were used to assess the sebum production of the subjects. Sebumeter measurement was conducted during each visit (Day 1, 7, 21 and 42), while sebutape

measurement was only conducted on Day 1 (ground state) and Day 42 (final visit) as the sampling is time-consuming. Initial readings with a sebumeter did not reveal a general trend. However, the sebumeter simply provides a quick measurement but is less reliable than some other assays because it is strongly influenced by external factors like washing, sweating etc. Skin pH measurement

The pH of the subjects' skin was measured during each visit (Day 1, 7, 21, and 42) using a pH meter. A decrease in skin pH of the subjects was observed by 0.4 points between Day 1 and Day 42. Decrease in pH is considered a positive development towards healthy skin.

Similar to the non-inflamed lesions, the effect was more pronounced in subjects classified as acceptors and less pronounced in subjects classified as non-acceptors (FIG. 16). A correlation based on the specific formulation administered was not observed. The observed effect is in the same magnitude as reported by Nodake et al. (2015).

Self-evaluation

Subjects answered a questionnaire during each visit. The questionnaire related to self- evaluation of their skin and about the use of the product. The following skin aspects were reviewed: appearance of pimples, number of pimples, appearance of redness associated with the pimples, size of pimples, severity of pimples, oiliness of skin, shininess of skin, dryness of skin, flakiness of skin, skin smoothness, and overall appearance of skin.

Using the average of the above-mentioned questions, 85% of subjects reported improvement and 15% of subjects reported no change between Day 1 and Day 42. The average improvement overall (average of all questions among all subjects on Day 1 versus Day 4) was by 1.62 points (on scale 1-10). Higher satisfaction was observed among the A2 formulation users (2.05 points) and among the acceptors (1.75 points).

Among all subjects, the most improvement was observed in "Dryness of skin" (by 2.21 points) followed by "Overall appearance of skin" (2.07 points) and "Skin smoothness" (2.00 points).

Based on top-box analysis, the scale was split into three boxes: Bottom = points 1-3, Middle = points 4 - 7 and Top = points 8-10. FIG. 17 shows a distribution of subjects based on their average value of all answers for each visit (Day 1, 7, 21 and 42). A clear shift towards higher scores is visible throughout the study. A high acceptance rate of the product and a general positive feedback from the subjects in the self-evaluation was observed.

FIG. 18 shows a heatmap of the relative abundance of the 15 most commonly found P. acnes strains. FIG. 19 shows data from a picture-based comparison. FIG. 20 shows data from a patient assessment summary. Some subjects exhibited an initial decline on visit 3 but showed a general improvement by visit 4. Without wishing to be bound by any theory, adapting to newly established strains could contribute to a temporary flare up. At the beginning and the end of the study a lesion count was performed. The majority of subjects showed a decrease in acne lesions.

Summary of pilot study

A statistically significant decrease in the number of non-inflamed lesions was observed. This was surprising because in standard-of-care treatments, a reduction of non-inflamed lesions is generally only observed over the long term. In a comprehensive meta-analysis comparing BPO and other state-of-the-art treatments (Seidler and Kimball, 2010) the placebo arm showed a decrease by 6.7% in non-inflamed lesions. In the study described herein, the acceptor group had a reduction of nearly 50%, indicating that an effect beyond the placebo could be observed. The magnitude of the effect could potentially outperform current state-of-the-art treatments in the ability to target non-inflamed lesions.

Based on analysis of the 16S microbiome data and correlation with the strain-level resolution of the P. acnes population, it was apparent that the subjects who accepted the applied bacterial strains (classified as acceptors) exhibited an increase in the relative proportion of P. acnes compared to all other bacteria. The non-acceptors maintained their relative ratio of P. acnes throughout the study, but were characterized by a higher relative percentage of P. acnes at the baseline visit (Day 1). Without wishing to be bound by any theory, the non-acceptors may have already been fully colonized by P. acnes, such that the disinfection treatment which was administered before the bacterial strains were administered may not have been sufficient to eliminate the resident P. acnes population, which may have remained hidden in the follicles. By contrast, the acceptors may not have yet been fully colonized allowing the disinfection treatment to reduce or eliminate the resident P. acnes population before administration of the bacterial strains. Modified disinfection procedures may allow for an increase in the acceptor rate.

The effect observed for the skin pH was on the same magnitude as that reported by other randomized double blinded clinical trials using skin bacteria (Nodake et al., 2015). It is also encouraging that not only did the pH drop, but it also decreased its variance throughout the study, suggesting a normalization of the subjects' skin pH.

Many subjects in the pilot study reported a smoother skin, which is in correlation with the decrease of non-inflamed lesions as documented by the dermatologists participating in the pilot study. In addition, many subjects noted a less greasy skin, which could be an indicator of reduced sebum production.

The data show that modulation of the skin microbiome at the strain level was well tolerated. The majority of the subjects experienced an overall improvement of their skin condition. Specifically a decrease in itchiness, less noticeable acne lesions, and better overall skin appearance was reported. None of the subjects experienced a significant deterioration or a prolonged flare-up. There were no dropouts in this clinical study.

Materials and Methods

Materials used for P. acnes production included: 1L schott bottles; Cell Culture flasks Magnet; Serological pipets; Pipet tips with filter, ΙΟΟΟμΙ; Falcons; Cups for spinning large batches; Petri dishes; Syringes 2.5ml; Straw for syringes; Caps for syringes; and Eppendorfs. Chemicals used include: NATROSOL® 250 Hx Pharm., Hydroxyethylcellulosum; Kat-Hefe Media; Dextrose (a-D-Glucose), anhydrous 96%, Aldrich, ref: 158968; Sodium Chloride (NaCl); Reinforced Clostridial Agar; and Peptone from Casein, tryptic digest.

Bacterial media preparation: RCM Agar was prepared by following the supplier instructions, including for each liter: autoclaving the mixture in a Liquids program; adding 200μ1 of Furazilidone lOOmg/ml to each 1L final volume before distributing the agar; and distributing the prepared RCM Agar to Petri dishes and flat-bottom 96 well plates (200μ1 each well).

The following solutions were prepared:

1) Media based solution mix in a 1L Schott bottle which includes: 20g of Kat-Hefe protein; 5g of NaCl; and 900ml of water

2) 10 x Dextrose solution mix in a 100ml Schott Bottle, which includes: 30g of Dextrose (a-D-Glucose) and 100ml of water.

Both solutions were autoclaved. After cooling aseptically, 100ml of 10 x Dextrose solution was added to the media based solution (1L bottle) forming the final media. The final media contained the following concentrations: 20g/L of Kat-Hefe protein; 5g/L NaCl; and 30g/L of Dextrose.

A peptone solution mix was prepared in a 1L Schott Bottle, which includes: 2.5g of peptone from casein, tryptic digestion and 1L water. This solution was autoclaved in a liquids program. The final solution contained 0.25% peptone. Bacteria Culture

Bacterial pre-culture preparation was started from a confirmed pure strain. Each falcon was filled with 50ml of RCM media. A syringe containing the desired strain at room

temperature is thawed and 0.5 ml gel is transferred into the corresponding falcon, according to strain. The bacterial cultures are grown at 37°C.

Steps to create the bacteria culture are outlined below:

• 50ml pre-culture was added to 450ml Kat-Hefe media in 750ml sterile cell culture flask (main culture). The samples were placed in the incubator at 37°C and growth was monitored by regular OD measurements

• Samples were spun down for lOmin and the supernatant was removed

• Samples were washed once in 50ml of 0.25% Peptone from casein, tryptic digestion

• Samples were spun down for lOmin and supernatant was removed

• Each pellet was re-suspended in 50ml of 0.25% Peptone from casein, tryptic digestion

• Bacteria suspensions were normalized

• Bacterial mixtures were prepared according to the desired formulation

• Sterile Hec powder was added to prepare the gel and it was allowed to rest

• Syringes were filled

A P. acnes C3 strain and a P. acnes, K8 strain were each deposited on October 19, 2017 at DSMZ (Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH), InhoffenstraBe 7 B, 38124 Braunschweig, Germany.

Example 6: Production of P. acnes for large scale clinical study

Samples of bacterial strains to be used in a large scale clinical trial were produced, as well as placebo samples without bacteria, using Food Grade procedures. The samples produced included 9000 1-ml aliquots of a gel medium containing a 1: 1 blend of two P. acnes strains in a concentration of at least 1x10 cfu per aliquot, packed aseptically in sealed laminated aluminum foil sachets and stored at -80°C, and 5500 1-ml aliquots of the gel medium without bacteria, packed in the same sachets and stored at -80°C (placebo samples). Methods used for the production of the P. acnes bacterial strains and associated results are described herein. The work was divided in two phases. In Part 1, protocols for growth, harvesting, and storage of the bacteria were developed and evaluated. Part 2 consisted of production and packaging of the blend of bacteria and the placebo samples.

Materials and Methods

Strains, media and cultivation conditions

P. acnes strains K8 and C3 were obtained as cultures diluted in 2.5%

hydroxyethylcellulosum (HEC) in sterile 1-ml syringes. The syringes were stored at -80°C.

Stock cultures: strains K8 and C3 were prepared by inoculating about 0.05 ml from the syringe cultures on Brain Heart Infusion Agar (BHIA; Tritium Microbiologie, Eindhoven, Netherlands) plates and overnight incubation at 37°C in an anaerobic jar. Bacterial material from the plates after incubation was diluted and spread on fresh BHIA plates to obtain single colonies. After overnight anaerobic incubation at 37°C, a single colony from each strain was inoculated in BHI broth (Tritium Microbiologie) and incubated anaerobically overnight at 37°C. The resulting cultures were mixed with a sterile 60% glycerol solution to a final glycerol concentration of 15%, divided into multiple subsamples and stored at -80°C. These stock cultures were used to inoculate precultures in BHI medium used in fermentation Experiments 1.1, 1.2, 1.3 and 2.1. Fresh stock cultures were produced starting from the syringe cultures prior to execution of Experiment 2.2.

The media used in the studies were: Brain Heart Infusion broth (BHI) and Brain Heart Infusion Agar (BHIA); Medium A: 3% dextrose, 0.5% sodium chloride, 2% yeast extract (Ohly Kat, Germany), pH 6.7; Medium B: Medium A plus 1% soy peptone (AM41, Organotechnie, La Courneuve, France), pH 6.7; Medium C: 3% dextrose, 0.5% sodium chloride, 2% yeast extract (Springer 0251/0-MG-L, Biospringer, Maisons-Alfort, France), pH 6.7; Medium D: Medium C plus 1% soy peptone, pH 6.7; and Medium E: Medium D, adjusted to pH 6.3.

A total of five fermentation experiments were conducted, three in Part 1 and two in Part 2, as described below.

Experiment 1.1: P. acnes K8 and C3 were cultivated in 100-ml flasks containing 100 ml Medium A, B, C or D. The media were inoculated with 10 ml from overnight cultures in BHI. The flasks were stored in anaerobic jars incubated without shaking for 24 h at 37°C.

Experiment 1.2:

P. acnes K8 and C3 were cultivated in 400 ml medium D in 0.5-L volume fermentor vessels, equipped with units to control temperature, stirring, and pH (Multifors 2 system, Infors, Bottmingen Switzerland). The medium was inoculated with 40 ml of overnight cultures in medium D (10% inoculation), which were prepared by inoculation of 1 ml of overnight cultures in BHI. The cultivation conditions were: temperature of 37°C; stirring speed of 150 rpm; pH controlled at pH 6.0 with 2.5 N sodium hydroxide or without pH control; head space flushed with 95% N2/5% C02 (flow 125 ml/min).

Experiment 1.3:

Same set-up and cultivation conditions as described for Experiment 1.2, except that the medium was inoculated with 8 ml of overnight cultures in medium D (2% inoculation).

Experiment 2.1:

P. acnes K8 and C3 were cultivated in 2.0 L medium D, in 3-L volume fermenter vessels, equipped with units to control temperature, stirring and pH (Applikon Biotechnology, Delft Netherlands). The inoculation procedure and cultivation conditions were the same as described for Experiment 1.3.

Experiment 2.2:

Set-up, inoculation procedure and cultivation conditions were the same as described for Experiment 2.1, except that the medium was adjusted to pH 6.0 (medium E; see paragraph 2.1.2) and the stirring speed was increased to 250 rpm.

Harvesting

Experiment 2.2 was used for the production of sachets with P. acnes strains. For both strains, a volume of 2.0 L of culture was harvested by means of centrifugation for 10 min at 16,000 x g in 1-L centrifugation bottles at ambient temperature. Pellets were resuspended in 200 ml of 0.25% soy peptone (AM41, Organotechnie, La Courneuve, France) solution and centrifuged once more. The bacteria were resuspended in 200 ml of 0.25% soy peptone solution of ambient temperature and processed within 30 min. The optical density at 600 nm (Οϋ _ό οο) of these concentrated suspensions was 54.3 for P. acnes C3 and 48.4 for P. acnes K8.

Gel medium with P. Acnes and placebo gel medium

Volumes of 19 ml and 21 ml of concentrated suspension of P. acnes C3 and K8, respectively were diluted in 0.25% soy peptone solution to a final volume of 2.0 L. The OD ₆₀₀ of this suspension was 1.1 and the ratio between the strains 1 : 1 on OD ₆₀₀ basis. Sterilized HEC was dissolved in this suspension to a final concentration of 1.5% (w/v) under vigorous mixing. This was repeated nine times in total. The batches were mixed to give a total volume of 18 L of gel medium with P. acnes K8 and C3. The gel medium was kept at ambient temperature for 1 h before starting packaging in foil sachets. The placebo gel medium consisted of 1.5% HEC in 0.25% peptone solution with iso-valeric acid to a final concentration of 10 μΙ/L. A total volume of 10 L was produced. The procedure to dissolve HEC was the same as described for the gel medium with P. acnes.

Sacheting, packaging and storage

Sachets containing gel medium with P. acnes or placebo gel medium were produced in independent runs using a sachet packaging machine. The machine consisted of a pump, a sacheting section and a thermo transfer printing unit. The gel medium was pumped from a container to the sacheting section. The sacheting section consisted of sterilized stainless steel tubing (one for gel medium and one for nitrogen gas), around which the sachets were folded, and vertical and horizontal sealing elements operating at a temperature of 130°C. The printing unit, located before the sacheting section, was used to label the sachets. Sachets were produced from 65 x 65 mm sheets of laminated aluminum foil, which were folded and heat- sealed along three sides (seal width approximately 12 mm). The final sachets were 65 x 30 mm in size and had a volume of approximately 2 ml. The machine was operated at a production speed of 28 sachets per min and a quantity of gel medium of 1.2 (+ 0.15) gram per sachet; the rest of the sachet volume is N2 headspace. During filling, the head space of the sachets was flushed with sterile nitrogen gas. At the start of the filling operation and after interruptions 10 to 20 sachets were discarded. At the end of the filling operation, samples of gel medium were taken for

microbiological analyses (P. acnes viable count and pathogen analysis). Sachets containing gel medium with P. acnes were packed in plastic bags (18 sachets per bag). In the course of the filling operations, sachets were transferred to a -80°C freezer in series of 1000 to 1500 sachets. The sachets were stored at -80°C until shipment. Sachets with P. acnes and sachets with placebo sachets were produced in independent runs.

Analyses

Growth measurement and microbiological analyses

Bacterial mass in cultures was determined by measurement of OD ₆₀₀ - Viable count of P. acnes in cultures and gel medium was determined by plating of serial dilutions on

BHI agar, incubated anaerobically for 24 to 30 h at 37°C. To confirm the absence of pathogens in gel medium with P. acnes and placebo, gel medium samples were analyzed by an external laboratory (Merieux NutriSciences , Ede, Netherlands) for the following

Pathogens listed in Table 9:

F ACS flow cytometry

Total counts and viability of cultures was determined using FACS flow cytometry. Viability was determined after staining of cells with a mixture of two nucleic acid stains (green- fluorescent SYTO™ 9 dye and red-fluorescent propidium iodide), using the LIVE/DEAD™ BACLIGHT™ Bacterial Viability and Counting Kit (ThermoFisher scientific cat# L34856). Results

Part 1

The main objective of Part 1 was to evaluate and improve the protocol for growth of P. acnes strains. The protocol consisted of anoxic cultivation in flasks for 2 to 3 days, giving final biomass yields of OD ₆₀₀ 0.6 to 1.2. The experiments aimed to increase the yield, to reduce the cultivation time, and to use an up-scalable cultivation system.

Experiment 1.1:

Experiment 1.1 was conducted to optimize the medium composition with respect to yield. Two sources of yeast extract were compared and the effect of addition of soy peptone to the medium was determined. The bacteria were cultivated in flasks. Table 10 shows the viable count and OD ₆₀₀ of the cultures. The data showed that higher OD ₆₀₀ values and viable counts were achieved with Springer yeast extract than with Kat yeast extract. Furthermore, a beneficial effect of soy peptone on OD ₆₀₀ and, to a lesser extent, viable count was detected. Higher OD ₆₀₀ and viable counts were obtained with strain K8 than with strain C3. Based on these results, the subsequent experiments were conducted with medium containing peptone and Springer yeast extract.

Table 10. Effect of yeast extract source and presence of soy peptone in the medium on viable counts and OD ₆₀₀ of cultures of P. acnes C3 and K8 after 24 h and 48 h incubation at 37°C.

Experiment 1.2:

Experiment 1.2 was conducted to test the growth characteristics of the strains during cultivation in fermenters and to determine the effect of cultivation at a constant pH of 6.0.

Results of OD ₆₀₀ and viable count measurements are shown in FIGs. 22 and 23, respectively. The pH-controlled cultures had substantially higher OD ₆₀₀ and viable count than the cultures without pH control. Viable counts of cultures without pH control were approximately 25 times lower after 21 h incubation than after 4 h incubation. This finding indicates that in this embodiment, bacteria died, probably due the low pH of the cultures without pH control (pH 5.25). The results depicted in Figure 22 also showed that the maximum OD ₆₀₀ value was reached within 21 h cultivation. The recording of base titration during cultivation of the pH-controlled fermenters (not shown) indicated that the stationary phase was reached already about 14 h after inoculation. In contrast to the results of Experiment 1.1, higher OD ₆₀₀ and viable counts were obtained for strain C3 than for strain K8. Based on these results, the subsequent fermentations were conducted with pH-control set at pH 6.0.

The stability of P. acnes C3 and K8 in gel medium during storage of bacteria at -80°C was tested by measuring the viable count before storage and after 3 weeks of storage. The bacteria were harvested and suspended in gel medium (2.5% HEC). The pH-controlled culture of K8 and the cultures of C3 and K8 without pH control showed no or a small reduction of the viable count during the storage period. In contrast, the viable count of the pH-controlled culture of C3 declined by about 60% (Table 11).

Table 11. Effect of 3 weeks storage at -80°C on the viable count (cfu/ml) of P. acnes strain C3 and K8 cultivated with or without pH control and suspended in 2.5% HEC gel medium.

Experiment 1.3:

Experiment 1.3 was conducted to confirm the observations of Experiment 1.2 and to test whether the inoculation level could be reduced from 10% to 2%. OD ₆₀₀ during cultivation is shown in Figure 24. In agreement with the results of Experiment 1.2, a higher OD ₆₀₀ was observed for strain C3 than for strain K8. The results also suggest that strain C3 grows slightly faster than strain K8. In addition, the results confirmed that it was possible to reduce the inoculation level to 2%. The OD ₆₀₀ measurements indicated that the stationary phase was reached about 14 h and 18 h after inoculation for strain C3 and K8, respectively.

Part 2

Production of placebo sachets

Approximately 6000 sachets containing placebo gel medium were produced. The average quantity per sachet was 1.25 g (range 1.10 to 1.40 g). Microbiological analysis demonstrated that the material was free of Salmonella, Listeria monocytogenes, Enterobacteriaceae, sulphite- reducing Clostridia and coagulase-positive staphylococci (Table 12).

Table 12. Results of analysis of pathogens in samples of gel medium with P. acnes and placebo gel medium.

Production of sachets with P. acnes

Strains C3 and K8 were cultivated. The fermentation period was 14 h. In agreement with Experiment 1.2 and 1.3, slightly higher OD ₆₀₀ and viable count were observed for strain C3 than for strain K8. Based on OD ₆₀₀ values, the concentrated cultures of strain C3 and K8 were mixed in a ratio of 47:53, to give a final ratio of 1: 1 in the blend to which 1.5% HEC was added and which was packaged in sachets. Table 13 summarizes the results. Microscopic pictures of the bacteria (FIG. 24) showed the typical morphology of P. acnes. In addition to measurement of viable count, the concentration of bacteria was also determined by FACS flow cytometry (Table 4). This method can discriminate between live, damaged and dead cells by means of two different DNA dyes. The results for viable count and FACS-live cells were similar for both strains. The percentage of FACS-dead cells (percentage of the total) in the cultures of strain C3 and K8 was 18% and 40%. Unexpectedly, the percentage of FACS-dead cells in the concentrated cell suspensions were lower than in the cultures: 8% and 16% for C3 and K8, respectively.

Table 13. OD ₆₀₀ , viable count and FACS flow cytometry count of P. acnes strain C3 and strain K8 cultures before harvesting, after concentration of the bacteria in 0.25% peptone solution, after dilution and blending of the strains, and in gel medium from sachets (Experiment 2.2).

A total of approximately 10,000 sachets were produced, of which 9000 sachets were packed in plastic bags (18 sachets per bag). The quantity of gel medium per sachet was adjusted to 1.2 g per sachet. This quantity enabled the removal of at least 1 mL from sachets upon regular opening and squeezing. The quantity of gel medium per sachets was measured every 500 to 1000 sachets (six replicates each time point). The quantity per sachet varied from 1.17 g to 1.38 g, with an average of 1.28 g. The total run time of the production of sachets was 7 h. The viable count of gel medium in sachets was determined four times in the course of the production run and varied between 3.8 x 107 and 4.3 x 107 cfu/ml, with an average of 4.0 x 107 cfu/ml (Table 13). Based on these results, the average viable count per sachet prior to storage at -80°C was 5.1 x 10 7 cfu. The viable count of gel medium in sachets after 7 days storage at -80°C was 2.9 x 107 cfu/ml (Table 4), corresponding to 3.7 x 10 cfu per sachet. Microbiological analysis demonstrated that the gel medium with the blend of P. acnes bacteria was free of Salmonella, Listeria monocytogenes, Enterobacteriaceae, sulphite-reducing Clostridia and coagulase-positive staphylococci (Table 12). Table 14 shows the specifications of the laminated aluminum foil used for sachet production.

Table 14. Specifications of the laminated aluminum foil used for sachet production

Summary

The medium composition for cultivation of P. acnes C3 and K8 was modified by using an alternative source of yeast extract and inclusion of peptone. The P. acnes strains were grown in pH-controlled fermenters in 14 h to final biomass yields of OD ₆₀₀ of 4.0 to 5.0, corresponding to approximately 5 x 10 8 cfu/ml. A total of more than 9000 sachets containing 5.1 x 107 cfu/sachet of a 1: 1 blend of P. acnes strains C3 and K8 were produced and stored at -80°C.

The modifications of the cultivation procedure (alternative yeast extract source, inclusion of peptone in the medium, and cultivation in pH-controlled fermenters) resulted in 5 to 10 times higher yield of P. acnes C3 and K8.

The ratio between viable count and OD ₆₀₀ was quite consistent throughout the

7 8

experiments: 5 x 10 to 1 x 10 cfu/ml for cultures or suspensions with OD ₆₀₀ 1-0. This cell concentration is low in comparison with cultures of many other bacteria, for instance

Lactobacillus species, Lactococcus species and Escherichia coli. This suggests that the P. acnes cells are larger than cells of these species.

The concentration of P. acnes in sachets stored for 1 week at -80°C was only slightly lower than the concentration prior to freezing (4.0 x 10 7 and 2.9 x 107 cfu/ml respectively) (Table 4), indicating that the bacteria survived the freezing event well.

Example 7: Large Scale Clinical Study

Based on the analysis of the pilot study, the following aspects were incorporated into a large scale clinical study: formulation A2 was selected for testing; 23 subjects were allocated to the active arm and 23 to the placebo arm; strain-level analysis of some species in the microbiome is included; and an optimized disinfection protocol is included to increase the rate of acceptors. Acne patients were selected at least in part based on those that had higher counts of lesions, and higher acne grade, and if they were subjects with pure teenage acne (excluding hormonal acne, adult acne etc.).

Subjects are individuals with facial acne vulgaris grade 1.5 - 4 (Leeds scale). Subjects include both males and females, aged 16 - 23 years old.

On day 1, all subjects receive a benzoyl peroxide product (Akneroxid gel 50 mg/g, Almirall) to apply once a day on the face for 7 days (day 1 - 7). On Day 8, subjects receive the test product (either bacterial product or placebo). Subjects apply the test product to the face twice a day (morning and evening) after washing the face. Subjects keep applying the product for 11 weeks (day 8 - day 84). After this phase, there is a 2- week follow up phase without any application. Measurements and samples are taken on day 1, day 7, day 28, day 56, day 84, day 91 and day 98 (Table 8, FIG. 8B). In Table 8, "X" indicates which method of analysis is conducted on each indicated day of the study.

Table 8. Large Clinical Study

Measurement methods

Lesion count is conducted visually by a trained investigator. Safety evaluation is assessed by the investigator or a study nurse by visual evaluation of the redness, irritation or any other skin problems. An image is taken at each visit. During the pilot phase study discussed in Example 5, a normal camera was used, while in the larger clinical study, imaging is conducted by visible, cross -polarized or blue fluorescent light taken by a trained investigator or a study nurse to document the state of the skin.

Lipid analysis using a sebumeter is conducted by a study nurse. Lipid analysis using sebutape provides more details on the content and quantity of sebum in the skin. For the measurement, skin of the subject is prepared by degreasing the test area with 70% isopropanol impregnated swab or similar product. The sebutape is then placed for 30 minutes on the skin (forehead) of the subject to take the measurement.

The pH analysis is performed by using a skin pH-meter. It is a non-invasive instant method without any preparation of the skin. Microbiome analysis using sterile swab is a non-invasive instant method in which a swab is moved over the skin, rotating for 30 seconds to collect the bacterial community living on the surface of the skin.

Microbiome analysis using a strip 3-S-Biokit (Skin surface Technology) allows for reaching bacterial communities in the follicles. It is a non-invasive method in which a plastic strip with a drop of skin-friendly cyanoacrylate is gently pressed on the skin and left to dry for 1 minute. Then it is gently removed. In reactive skin, redness can be observed for a few minutes after removing the strip. However, longer or more pronounced irritation is not expected.

Statistical Methods

For continuous variables, number, mean, median, standard error, minimum and maximum are assessed given. The significance threshold is 5%.

A descriptive analysis is performed on the inclusion data. The inclusion and non- inclusion criteria are described (number and percentage) and the deviation is listed. Withdrawal patients are also described (number and percentage) and reasons for stopping are listed.

The primary analysis is carried out in the intention-to-treat population which contains all patients that are randomized and have at least one post-baseline visit. Sensitivity analyses are carried out in the per-protocol population comprising all patients with complete data and without major protocol violations. Safety analyses are carried out in the safety population covering all patients that received at least one treatment with microbes (experimental or control).

Sample size calculation: The sample size calculation is based on the efficacy endpoint in total lesions, as data about the expected change in the bacterial population are not available. In a previous acne study at the University Clinic of Dermatology in Magdeburg (Thielitz et al., 2015) three different gels were compared. Over a treatment period of 12 weeks, averaged over the three treatments, a reduction of the count of total lesions of 40% + 32% (mean + standard deviation) was observed. A similar effect in the active treatment group of the larger clinical study described herein is expected. In the control group, a residual effect (by trial attended measures and placebo effect) of up to about 15% reduction could be observed. Accordingly, a sample size of at least 27 patients per study arm is included to detect a difference in a two-sided t test with error level 0.05 and 80% power. Including an additional 10% of subjects to compensate for diluting effects of drop outs, 30 patients per treatment arm are included. If not all 60 patients can be recruited in one cohort, an adaptive design with an interim analysis is executed. A first cohort will be run, and after completion of this cohort, an analysis of the change of the microbiome composition is conducted. If already a clear and statistically significant signal for a change of the microbiome composition is observed, then the clinical parameters will be evaluated. If the clinical parameters also show a statistically significant result, then the study will be closed and a full analysis run. If the results are not statistically significant, or if the statistical significance of the results is unclear, then a second cohort of patients is tested.

Efficacy analysis: Efficacy is considered at two different levels - the change in the composition of bacteria and in clinical parameters (primary: total lesion count, secondary: sebum production).

Descriptive analyses: For both treated and not treated subjects, a descriptive analysis is performed at each time of evaluation (Pilot: Day 1, Day 7, Day 21 and Day 42; Larger clinical study: Day 1, Day 7, Day 28, Day 56, Day 84, and Day 112) and on the differences (Day of evaluation - DO). The number, mean, median, standard error, minimum and maximum are given.

Analysis for primary clinical endpoint: The total lesion counts are considered as percentages of the baseline measurement for each patient (or logarithm of it if the distribution is skewed). The difference from baseline to week 12 is compared between both study arms in a linear mixed model for repeated measures including all visits after baseline until week 12, enabling the inclusion of patients with missing values at some visits without explicit imputation techniques. Fixed factors are the treatment arm and gender and the absolute baseline count of total lesions and age as co-variables. If the test for the treatment effect is significant (p < 0.05) then the analog test is carried for the difference in the counts from baseline to week 16 also at level 0.05. This hierarchical procedure ensures error level control over both steps. As secondary analysis, the whole procedure is carried out in the per-protocol population.

Analysis of secondary clinical endpoints: The secondary clinical endpoints are treated analogously to the primary clinical endpoint.

Analysis of bacterial composition: The primary analysis of the bacterial composition comprises the relative abundances of the four bacterial strains that are compounds of the active treatment. The analysis is done analogously to the primary endpoint, but at a Bonferroni- adjusted significance level of 0.05/4 = 0.0125 for the parallel assessment of four bacterial strains. For secondary multivariate analyses, microbiome differences are computed comparing the vectors that describe the microbiome. Each position of the vector contains a number, indicating the number of times that a certain strain has been detected. Correlation distance is used to measure differences between different microbiomes. Further, the distance of the P. acnes microbiome towards the composition of the applied mixture is calculated using the same method as above. A simple spearman correlation can be used, but other statistical methods can also be applied. Further analyses include comparison of the distribution of the different bacteria {e.g., expressed as Shannon index) and its stability over time between both study arms.

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EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

All references, including patent documents, disclosed herein are incorporated by reference in their entirety. The entire disclosure of WO2016/172196, filed on April 20, 2016, entitled "Methods and Compositions for Changing the Composition of the Skin Microbiome Using Complex Mixtures of Bacterial Strains" is incorporated by reference herein in its entirety.