RELATED APPLICATIONS

This application claims the benefit of priority to U.S. Provisional Patent Application serial number 62/291,665, filed February 5, 2016, which is hereby incorporated by reference herein in its entirety.

GOVERNMENT SUPPORT

This invention was made with Government support under Grant No. R01GM099530 awarded by the National Institutes of Health. The Government has certain rights in the invention.

BACKGROUND

Propionibacterium acnes is a major commensal bacterium residing on the human skin. It plays important roles in maintaining skin health, but has also been implicated in the pathogenesis of several diseases and infections, including sarcoidosis, SAPHO syndrome, endodontic lesions, eye infections, prosthetic joint infections, prostate cancer, and acne vulgaris (commonly called acne). Acne is the most common skin disease affecting more than 80% of adolescents and young adults worldwide. Despite the clinical importance of the disease, the etiology of acne is not yet clear. P. acnes dominates the skin of both acne patients and healthy individuals, and thus its role in acne pathogenesis has not been well understood.

SUMMARY

In some aspects, the invention relates to a method of preventing or treating a skin condition in a subject, comprising administering to the skin of the subject a composition comprising an RTl, RT2, RT3, RT6, RT8, RT16, or Type III strain of Propionihacteriiim acnes. In some embodiments, compositions are formulated for oral delivery for treating a skm condition or maintaining skin health, comprising an RTl, RT2, RT3, RT6, RT8, RT16, or Type III strain of Propionibacterium acnes. In some embodiments, the compositions comprise more than one strain. A strain of P. acnes may be selected from HL042PA3, HL050PA2, HL025PA 1, HL001PA1, HL103PA1, HL106PA1, HL110PA3, HL025PA2, HLQ46PA1, HLl 10PA2, HL053PA2, HL059PA 1, HL201PA1, 17A, and 20C. The condition may be acne, skin aging, rosacea, or porphyria cutanea tarda.

In some aspects, the invention relates to a topical composition for treating a skin condition or maintaining skin health, comprising an RT2 strain of Propionihacterium acnes. The strain may be, for example, HLOOIPAI . HLOOI PAI is a clonal complex 72 (CC72) strain based on the Belfast MLSTs classification scheme: and HLOOIPAI is a clonal complex

60 (CC60) strain based on the Aarhus MLST9 classification scheme.

In some aspects, the invention relates to a method for determining the risk that a subject will develop vitamin Bn-induced acne, comprising measuring the porphyrin production of P. acnes obtained from the subject.

In some aspects, the invention relates to a method for determining a risk that a subject will develop vitamin Bn-induced acne, comprising identifying one or more strains of P. acnes obtained from the subject, and diagnosing the subject with an elevated risk of developing vitamin Bn-induced acne if one or more of the strains of P. acnes is sensitive to vitamin B12. In some aspects, the invention relates to a method for determining a risk that a subject will develop vitamin Bn-induced acne, comprising identifying one or more strains of

P. acnes obtained from the subject, and diagnosing the subject with an elevated risk of developing vitamin Bn-induced acne if one or more of the strains of P. acnes produces elevated levels of porphyrins.

In some aspects, the invention relates to a topical composition, comprising a nucleic acid encoding deoR. In other aspects, the invention relates to a composition formulated for oral delivery comprising a nucleic acid encoding deoR.

In some aspects, the invention relates to a method for treating a skin condition in a subject, comprising: measuring the porphyrin production of P. acnes obtained from the subject; and treating the subject with photodynamic therapy if the porphyrin production is above a threshold value. In some embodiments, the invention relates to a method for treating a skin condition in a subject, comprising determining the identity of a strain of P. acnes obtained from the subject: and treating the subject with photodynamic therapy if the strain of

P. acnes produces elevated porphyrin levels.

In some aspects, the invention relates to compositions and methods for treating a skin condition in a subject, comprising administering to the subject a composition comprising P. acnes, wherein the P. acnes comprises a nucleic acid encoding deoR. The composition may be formulated for topical delivery. The compositions may be formulated for oral delivery. In some aspects, provided herein are methods of reducing the amount of porphyrins on the skin of a subject by administering a composition comprising one or more strains of Propioniba tetium acnes to the subject. The subject may have acne, skin aging, rosacea, or porphyria cutanea tarda.

In some aspects, provided herein are compositions formulated for oral delivery for treating a skin condition or maintaining skin health, comprising an RT1, RT2, RT3, RT6, RT8, RT16, or Type III strain of Propionibacterium acnes. In other aspects, provided herein are compositions (e.g., oral or topical compositions) for treating a skin condition or maintaining skin health, comprising a strain οΐ Propionibacterium acnes, wherein the strain of Propionibacterium acnes comprises a nucleic acid encoding deoR. A strain of P. acnes may be selected from HL042PA3, HL050PA2, HL025PA1 , HL001PA1 , HL103PA 1, HL106PA1, HL110PA3, HL025PA2, HL046PA1, HL110PA2, HL053PA2, HL059PA1, HL20IPA1, I7A, or 20C. BRIEF DESCRIPTION OF THE FIGURES

Figure 1. Acne-associated type IA-2 P. acnes strains produced significantly more porphyrins than health-associated type II strains. Each bar represents the porphyrins produced by each strain normalized by the bacterial culture density. Shown is the mean of the data obtained from at least three independent experiments with at least three replicates each. Error bars represent standard error.

Figure 2. Vitamin Bu supplementation significantly increased porphyrin production in acne-associated type IA-2 strains, but not in health-associated type II strains. P. acnes strains were cultured in media with {black bars) or without (white bars) the addition of 10 ^ig/rnL vitamin B12. Each bar represents the porphyrins produced by each strain normalized by the bacterial culture density. Shown is the mean of the data obtained from at least three independent experiments with at least three replicates each. Error bars represent standard error.

Figure 3. Vitami B12 supplementation repressed the expression of a vitamin B12 biosynthesis gene cbiL. The expression level of cbiL was quantified by qRT-PCR from P. acnes strains cultured with or without the addition of 10 μg/mL vitamin B12. Strains of types IA-2 and II and an RT1 strain encoding deoR, HL025PA1, are shown. Each bar represents the fold change in gene expression of cbiL in cultures with vitamin B12 supplementation compared to cultures without supplementation. Shown is the mean of the data obtained from three independent experiments with three replicates each. Error bars represent standard deviation.

Figure 4. 5- ALA increased porphyrin production, which was further enhanced by vitamin Bn supplementation in acne-associated type IA-2 strains. P. acnes strains were cultured in media with (grey bars) or without (white bars) substrate 5 -ALA (0.1 mg/mL), or with both 5 -ALA and vitamin Bi2 (10 ,ug/mL) added (black bars). 5 -ALA significantly increased porphyrin production in acne-associated type IA-2 strains (P 0.0001 ) and in health-associated type II strains (P<0.06, except HLOOlPAl). Vitamin B12 supplementation further increased porphyrin production in the presence of 5 -ALA in acne- associated type IA-2 strains, but not in health-associated type II strains. Each bar represents the porphyrins produced by each strain normalized by the bacteria] culture density. Shown is the mean of the data obtained from at least three independent experiments with at least three replicates each. Error bars represent standard error.

Figure 5. Small molecule inhibitor reduced porphyrin production in . acnes and its inhibition was counteracted by vitamin n supplementation in acne-associated type IA-2 strains. P. acnes strains were cultured in media with (grey bars) or without (white bars) inhibitor LA (0.1 mg/mL), or with both LA and vitamin B12 (10 _, ug/mL) added (black bars). LA significantly reduced porphyrin biosynthesis in all strains except HLOOl PAl (P <0.0001). Vitamin B12 supplementation counteracted the inhibition of porphyrin biosynthesis by LA in acne-associated type IA-2 strains, but not in health-associated type 11 strains. Each bar represents the porphyrins produced by each strain normalized by the bacterial culture density. Shown is the mean of the data obtained from at least three independent experiments with at least three replicates each. Error bars represent standard error.

Figure 6. Health-associated strains encode and expressed deoR, a repressor gene in the porphyrin biosynthesis operon. deoR amplification from the cDNA and genomic DNA (gDNA) samples of multiple strains is shown in the gel image. 16S rRNA gene was used as a positive control. HL045PA1, which is an acne-associated type IA-2 strain and does not encode deoR, is shown as a negative control.

Figure 7. Coproporphyria was the dominant porphyrin isoform produced by P. acnes. Porphyrins secreted by P. acnes have a mass spectrum characteristic of the monoisotopic coproporphyrin isoform ([M + H] ⁺ = ^: 655.3). The doubly charged parent ion was also observed ([M + 2H] ²⁺ = 328.2).

Figure 8. Porphyrin (Hem) gene cluster in P. acnes strains. All health-associated type II strains harbor a deoR transcription repressor (PPA0299, in green) in the porphyrin gene cluster. The number below each box represents the gene ID based on the gene annotation in ΚΡΑΓ71202. The letters in black boxes indicate the names of the hem genes, which are porphyrin biosynthesis genes. PPA0300 and PPA0310 were not assigned a hem gene name.

Figure 9. Presence of deoR in P. acnes lineages. P. acnes strains encoding leoR are colored in green an include each type 1C, IB-3, II, and III strain. Additionally, strain HL025PA1 of type IA-2 P. acnes encodes deoR, but no other type IA-1, IA-2, IB-1, or IB-2 strain was found to encode a deoR gene. Asterisks denote the strains tested in the Examples section.

Figure 10. Similar to health-associated type II strains, HL025PA1 produced a low level of porphyrins and did not respond to vitamin B12 supplementation. HL025PA1 was cultured in the media with (black bars) or without (white bars) vitamin B 12 (10 μg/mL). Health-associated type II strains, HL103PA1 and HL042PA3, are shown for comparison. Each bar represents the ροφΐινπηβ produced by each strain normalized by the bacterial culture density. Shown is the mean of the data obtained from three independent experiments with three replicates each. Error bars represent standard error.

Figure 11. Porphyrin production in type I . acnes strains. Types IA-1 and IA-2 strains produced the highest levels of porphyrins among the tested strains. RT8, RT3, and RT16 strains produced less porphyrins than types IA-1 and IA-2 strains, but more than RT2 and RT6 strains. Each bar represents the porphyrins produced by each strain normalized by the bacterial culture density. Shown is the mean of the data obtained from at least two independent experiments with at least three replicates each. Error bars represent standard error.

Figure 12. P. acnes type 1 strains produce significantly more porphyrins than type II and type III strains. Each bar represents the porphyrins produced by each strain normalized by the bacterial culture density. Type I strains responded to vitamin B 12 supplementation with increased porphyrin production. This was not observed in type II and type III strains (data not shown). Shown is the mean of the data obtained from at least one experiment with at least four replicates each. Error bars represent standard error.

DETAILED DESCRIPTION

Some aspects of the invention are based on the fi nding that vitamin B12

supplementation increases P. acnes production of porphyrins, a group of pro-inflammatory metabolites important in acne development. The porphyrin production and regulation of multiple P. acnes strains from acne- and health-associated lineages were compared. Acne- associated strains inherently produced significantly higher levels of porphyrins, which were further enhanced by vitamin B12 supplementation. On the other hand, health-associated strains produced low levels of porphyrins and did not respond to vitamin B12. Using small molecule substrates and inhibitors, porphyrin biosynthesis can be modulated at the metabolic level. Additionally , the repressor gene (deoR) of porphyrin biosynthesis was encoded in all health-associated strains, but not in acne-associated strains. The expression of deoR suggests additional regulation of porphyrin production at the transcriptional level in health-associated strains. These findings provide a molecular mechanism for the different contributions of P. acnes strains to skin health and disease, and further support the role of vitamin B12 in acne pathogenesis. Specifically, the porphyrin biosynthesis pathway is a drug target for acne and related skin conditions, and health-associated strains of P. acnes may be used as probiotics in skin therapeutics.

The instant disclosure also suggests that health conditions of subjects with P. acnes that produce different levels of porphyrins might be treated differently. Vitamin B12 modulation of porphyrin production is strain-specific, and suggests that the P. acnes strain composition of an individual's skin microbiota contributes to vitamin Bn-induced acne, individuals harboring acne-associated strains are likely to be at increased risk for developing acne in response to high vitamin B12 levels due to the ability of their skin bacteria to produce more porphyrins. On the other hand, individuals whose skin is dominated by health- associated strains may have Sower porphyrin levels produced by the bacterium, leading to a reduced risk for acne development when supplemented with vitamin B12.

Definitions

As used herein the specification, "a" or "an" may mean one or more. As used herein in the claim(s), when used in conjunction with the word "comprising" the words "a" or "an" may mean one or more than one. As used herein "another" may mean at least a second or more.

The term "preventing" is art-recognized, and when used in relation to a condition such as a local recurrence (e.g. , blemish), a disease such as acne, or an injury such as scarring, is well understood in the art, and includes administration of a composition which reduces the frequency of, or delays the onset of, symptoms of a medical condition in a subject relative to a subject which does not receive the composition. Thus, prevention of acne includes, for example, reducing the number of detectable blemishes (e.g., lesions) in a population of patients receiving a prophylactic treatment relative to an untreated control population, and/or delaying the appearance of detectable blemishes in a treated population versus an untreated control population, e.g. , by a statistically and/or clinically significant amount.

The terms "prophylactic treatment" and "therapeutic treatment ^" are art-recognized and include administration to a subject one or more of compositions. If a composition is administered prior to clinical manifestation of the unwanted condition (e.g., disease or other unwanted state of the host animal) then the treatment is prophylactic (i.e. , it protects the subject against developing the unwanted condition), whereas if it is administered after manifestation of the unwanted condition, the treatment is therapeutic (i.e., it is intended to diminish, ameliorate, or stabilize the existing unwanted condition or side effects thereof).

The term "subject" refers to a mammal, including, but not limited to, a human or non- human mammal, such as a primate, bovine, equine, ovine, porcine, canine, lagomorph, feline, or rodent. In preferred embodiments, the subject is a human.

A "therapeutically effective amount" of a compound with respect to the subject method of treatment refers to an amount of the compound(s) in a preparation which, when administered as part of a desired dosage regimen (to a mammal, preferably a human) alleviates a symptom, ameliorates a condition, or slows the onset of disease conditions according to clinically acceptable standards for the disorder or condition to be treated or the cosmetic purpose, e.g., at a reasonable benefit/risk ratio applicable to any medical treatment.

As used herein, the term "treating" or "treatment" includes reversing, reducing, or arresting the symptoms, clinical signs, and underlying pathology of a condition in a manner to improve or stabilize a subject's condition.

I. COMPOSITIONS

In some aspects, the invention relates to a composition for treating or preventing a condition in a subject. In some aspects, the invention relates to a composition for maintaining skin health. The composition may be a topical composition. The composition may be formulated for oral deliver}'. The condition may be a skin condition. The skin conditions may be acne, skin aging, rosacea, or porphyria cutanea tarda.

A composition may comprise a strain of Propionihacierium acnes. A strain of P. acnes may be selected from, for example, RT1, RT2, and RT6. In some embodiments, the strain of P. acnes is selected from RT3, RT8, RT16, or Type III, The strain may be selected from HL001PA1, HL103PA1, HLG42PA3, HL106PA 1, HL110PA3, HL050PA2, or HL025PA1. In some embodiments, the strain may be selected from HL025PA2, HL046PA1, HL110PA2, HLG53PA2, HL059PA1, HL201PA 1, 17A, or 20C. The stram may be RT2, and the RT2 strain may be HL001PA1, HL103PA1, or HL106PA1. The stram may be RT1 and the RT1 strain may be HL050PA2 or HL025PA 1. The strain may be RT6 and the RT6 strain may be HL042PA3 or HL 1 0PA3. The strain may be a type II strain or a type III strain of P. acnes. The strain may be an RT3 strain, such as HL025PA2 or HL046PA1. The strain may be a RT8, such as HL110PA2 or HL053PA2. The strain may be a RT16 stram, such as

HL059PA1. The strain may be a Type III strain, such as HL201PA1, 17A, or 20C. The composition may be formulated for oral delivery. The composition may be a topical composition. The composition may comprise more than one strain of P. acnes. The composition may comprise at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 strains of P. acnes.

In preferred embodiments, the composition is substantially free from an RT4 strain of P. acnes. In preferred embodiments, the composition is substantially free from an RT5 strain of P. acnes. In preferred embodiments, the composition does not comprise HL045PA1 , HL043PA1, HL043PA2, or HL053PA2. In some embodiments, the composition is substantially free from a type lA-1, IA-2, IB-1, and/or IC strain of P. acnes. In preferred embodiments, the composition is substantially free from a type IA-1, IA-2, and/or IC strain of P. acnes. In some embodiments, the composition is substantially free of strains that does not express, harbor, and/or encode deoR. In certain such embodiments, substantially free indicates that the composition does not comprise the indicated strain to an extent that compromises the therapeutic efficacy of the beneficial strains in the composition. In other such embodiments, a composition is substantially free of a strain if it comprises less than 10%, preferably less than 5%, and most preferably less than 1% of the indicated strain.

A composition may comprise a nucleic acid encoding deoR (i.e. , the nucleic acid may comprise the deoR nucleotide sequence). For example, the composition may comprise a vector and the vector may comprise the nucleic acid. The composition may comprise a strain of P. acnes and the strain of P. acnes may comprise the nucleic acid. The nucleic acid may be DNA or R A.

The vector may be a phage or a plasmid. The vector may be a phage, and the phage may have a tropism for Propionibacterium acnes, e.g., such that the phage can transform a P. acnes ceil with the nucleic acid.

The nucleic acid may comprise a promoter, and the promoter and deoR may be operably linked, e.g., such that a cell comprising the nucleic acid can transcribe RNA from the nucleic acid. The nucleic acid may be a recombinant nucleic acid. For example, deoR may be operabiy linked to a promoter other than a native deoR promoter. Similarly, deoR may be present in a vector that is not native to P. acnes, such as a vector comprising an origin of replication of a different species such as E. coli or a vector comprising a packaging signal for a bacteriophage. The nucleic acid may be the P. acnes genome and deoR may be randomly integrated into the genome.

A composition may comprise one or more strains of P. acnes that comprise the nucleic acid, e.g., wherein the nucleic acid is the P. acnes genome, the nucleic acid is a plasmid, or the nucleic acid is R A. A composition may comprise one or more strains of P. acnes that comprise a deoR protein product (e.g. , a transcriptional repressor protein). For example, such strains may express a deoR protein product. A composition may comprise one or more strains of P. acnes that encode or harbor a deoR gene. A composition may comprise one or more strains of P. acnes selected from RT1, RT2, or RT6 strains, and/or strains comprising a recombinant nucleic acid encoding deoR. A composition may comprise a clonal complex 72 (CC72) strain as determined by the Belfast MLSTs classification scheme . A composition may comprise a clonal complex 60 (CC60) strain as determined by the Aarhus MLST9 classification scheme. A composition may comprise one or more strains of P. acnes selected from RT3, RT8, RT16, or Type III, and/or strains comprising a recombinant nucleic acid encoding deoR.

A composition may further comprise ievulmic acid, 4, 6-dioxoheptanoic acid, and/or isonicotinic acid hydrazide.

Compositions described herein may be used for oral administration to the

gastrointestinal

tract. The formulation for a composition (e.g., a probiotic composition) of the present invention may also include other probiotic agents or nutrients which promote spore germination and/or bacterial growth. An exemplary material is a bifidogenic oligosaccharide, which promotes the growth of beneficial probiotic bacteria. In some embodiments, the probiotic bacterial composition is administered with a therapeutically-effective dose of an

(preferably, broad spectrum) antibiotic, or an anti-fungal agent. In some embodiments, the compositions described herein are encapsulated into an enterically-coated, time-released capsule or tablet.

The composition may be a food product, such as, but not limited to, a daisy product.

The diary product may be cultured or a non-cultured (e.g., milk) dairy product. Non-limiting examples of cultured dairy products include yogurt, cottage cheese, sour cream, kefir, buttermilk, etc. Dairy products also often contain various specialty dairy ingredients, e.g. whey, non-fat dry milk, whey protein concentrate solids, etc. The dairy product may be processed in any way known in the art to achieve desirable qualities such as flavor, thickening power, nutrition, specific microorganisms and other properties such as mold growth control. The compositions of the present invention may also include known antioxidants, buffering agents, and other agents such as coloring agents, flavorings, vitamins, or minerals.

In some embodiments, the compositions of the present invention are combined with a carrier (e.g., a pharmaceutically acceptable carrier) which is physiologically compatible with the gastrointestinal tissue of the subject(s) to which it is administered. Carriers can be comprised of solid-based, dry- materials for formulation into tablet, capsule or powdered form; or the carrier can be comprised of liquid or gel-based materials for formulations into liquid or gel forms. The specific type of carrier, as well as the final formulation depends, in part, upon the selected route(s) of administration. The therapeutic composition of the present invention may also include a variety of earners and/or binders. In some embodiments, the carrier is micro-crystalline cellulose (MCC) added in an amount sufficient to complete the one gram dosage total weight. Carriers can be solid-based dry materials for formulations in tablet, capsule or powdered form, and can be liquid or gel-based materials for formulations in liquid or gel forms, which forms depend, in part, upon the routes of administration. Typical carriers for dry formulations include, but are not limited to: trehalose, maito-dextrin, rice flour, microcrystalline cellulose (MCC) magnesium sterate, inositol, FOS, GOS, dextrose, sucrose, and like carriers. Suitable liquid or gel-based carriers include but are not limited to: water and physiological salt solutions; urea; alcohols and derivatives (e.g., methanol, ethanol, propanol, butanol); glycols (e.g., ethylene glycol, propylene glycol, and the like). Preferably, water-based carriers possess a neutral pH value (i.e., pH 7.0). Other carriers or agents for administering the compositions described herein are known in the art, e.g., in U.S. Patent No. 6,461,607.

A, Vehicles, Solvents, and Diluents

A composition may comprise a vehicle, solvent, and/or dilutent. Suitable topical vehicles and vehicle components for use with the formulations of the invention are well known in the cosmetic and pharmaceutical arts, and include such vehicles (or vehicle components) as water; organic solvents such as alcohols (particularly lower alcohols readily- capable of evaporating from the skin such as ethanol), glycols (such as propylene glycol, butylene glycol, and glycerol (glycerin)), aliphatic alcohols (such as lanolin); mixtures of water and organic solvents (such as water and alcohol), and mixtures of organic solvents such as alcohol and glycerol (optionally also with water): lipid-based materials such as fatty acids, acylglycerols (including oils, such as mineral oil, and fats of natural or synthetic origin), phosphoglycerides, sphingolipids and waxes; protein-based materials such as collagen and gelatin; silicone -based materials (both non-volatile and volatile) such as cyclomethicone, dimethiconoi, dimethicone, and dimethicone copoiyoi; hydrocarbon-based materials such as petrolatum and squalane; and other vehicles and vehicle components that are suitable for administration to the skin, as well as mixtures of topical vehicle components as identified above or otherwise known to the art.

In one em bodiment, the compositions of the present invention are oil-in-water emulsions. Liquids suitable for use in formulating compositions of the present invention include water, and water-miscible solvents such as glycols (e.g. , ethylene glycol, butylene glycol, isoprene glycol, propylene glycol), glycerol, liquid poiyols, dimethyl sulfoxide, and isopropyl alcohol. One or more aqueous vehicles may be present.

In one embodiment, formulations without methanol, ethanol, propanols, or butanols are desirable.

B. Surfactants and Emulsifiers

A composition may comprise a surfactant and/or emulsifier. Many topical formulations contain chemical emulsions which use surface active ingredients (emulsifiers and surfactants) to disperse dissimilar chemicals in a particular solvent sy stem. For example, most lipid-like (oily or fatty) or lipophilic ingredients do not uniformly disperse in aqueous solvents unless they are first combined with emulsifiers, which form microscopic aqueous soluble structures (droplets) that contain a lipophilic interior and a hydrophilic exterior, resulting in an oil-in-water emulsion. In order to be soluble in aqueous media, a molecule must be polar or charged so as to favorably interact with water molecules, which are also polar. Similarly, to dissolve an aqueous-soluble polar or charged ingredient in a largely lipid or oil-based solvent, an emulsifier is typically used which forms stable structures that contain the hydrophilic components in the interior of the structure while the exterior is lipophilic so that it can dissolve in the lipophilic solvent to form a water-in-oil emulsion. It is well known that such emulsions can be destabilized by the addition of salts or other charged ingredients which can interact with the polar or charged portions of the emulsifier within an emulsion droplet. Emulsion destabilization results in the aqueous and lipophilic ingredients separating into two layers, potentially destroying the commercial value of a topical product. Surfactants suitable for use in the present invention may be ionic or non-ionic. These include, but are not limited to: cetyl alcohol, polysorbates (Polysorbate 20, Polvsorbate 40, Polvsorbate 60, Polysorbate 80), steareth-10 (Brij 76), sodium dodecyl sulfate (sodium lauryl sulfate), lauryl dimethyl amine oxide, cetyltrimethylammonium bromide (CTAB), polyethoxylated alcohols, polyoxyethylene sorbitan, octoxynol, N,N-dimethyldodecylamine- N-oxide, hexadecyltrimethylammonium bromide (HTAB), poiyoxyl 10 lauryl ether, bile salts (such as sodium deoxycholate or sodium choiate), poiyoxyl castor oil, nonylphenol ethoxylate, cyclodextrins, lecithin, dimethicone copolyol, lauramide DEA, cocamide DEA, cocamide MEA, oleyl betaine, cocamidopropyl betaine, cocamidopropyl phosphatidyl PG- dimonium chloride, dicetyl phosphate (dihexadecyl phosphate), ceteareth-10 phosphate, methylbenzethonium chloride, dicetyl phosphate, ceteth-10 phosphate (ceteth-10 is the polyethylene glycol ether of cetyl alcohol where n has an average value of 10; ceteth-10 phosphate is a mixture of phosphoric acid esters of ceteth-10), ceteth-20, Brij S 10

(polyethylene glycol octadecyl ether, average Mn ~ 711), and Poloxamers (including, but not limited to, Poloxamer 188 ( ! !( ⁾ !( :H i()),(C! Ι(( Ή >)Π ))>.(( ^' ·Η :ΟΜ i. average mol ecular weight 8400) and Poloxamer 407 (HO(C2H40)a(CH(C¾)CH_OMC2H40)aH, wherein a is about 101 and b is about 56)). Appropriate combinations or mixtures of such surfactants may also be used according to the present invention.

Many of these surfactants may also serve as emulsifiers in formulations of the present invention.

Other suitable emulsifiers for use in the formulations of the present invention include, but are not limited to, behentrimonium methosulfate-cetearyl alcohol, non-ionic emulsifiers like emulsifying wax, polyoxyethylene oleyl ether, PEG-40 stearate, cetostearyl alcohol (cetearyl alcohol), ceteareth-12, ceteareth-20, cetearetli-30, ceteareth alcohol, Cetetli-20 (Ceteth-20 is the polyethylene glycol ether of cetyl alcohol where n has an average value of 20), oleic acid, oleyl alcohol, glyceryl stearate, PEG-75 stearate, PEG- 100 stearate, and PEG- 100 stearate, ceramide 2, ceramide 3, stearic acid, cholesterol, steareth-2, and steareth-20, or combinations/mixtures thereof, as well as cationic emulsifiers like stearamidopropyl dimethylamine and behentrimonium methosulfate, or combinations/mixtures thereof.

C. Moisturizers, Emollients, and Humectants

A composition may comprise a moisturizer, emollient, and/or humectant. One of the most important aspects of topical products in general, and cosmetic products in particular, is the consumer's perception of the aesthetic qualities of a product. For example, while white petrolatum is an excellent moisturizer and skin protectant, it is rarely used alone, especially on the face, because it is greasy, sticky, does not rub easily into the skin and may soil clothing. Consumers highly value products which are aesthetically elegant and have an acceptable tactile feel and performance on their skin.

Suitable moisturizers for use in the formulations of the present invention include, but are not limited to, lactic acid and other hydroxy acids and their salts, glycerol, propylene glycol, butylene glycol, sodium PCA, sodium hyaluronate, Carbowax 200, Carbowax 400, and Carbowax 800.

Suitable emollients or humectants for use in the formulations of the present invention include, but are not limited to, panthenoi, cetyi palmitate, glycerol (glycerin), PPG- 15 stearyl ether, lanolin alcohol, lanolin, lanolin derivatives, cholesterol, petrolatum., isostearyl neopentanoate, octyl stearate, mineral oil, isocetyl stearate, myristyl myri state, octyl dodecanol, 2-ethylhexyl palmitate (octyl palmitate), dimethicone, phenyl trimethicone, cyciomethicone, C12-C13 alkyi benzoates, dimethiconoi, propylene glycol, Theobroma grandiflorum seed butter, ceramides {e.g., ceramide 2 or ceramide 3), hydroxypropyl bispalmitamide MEA, hydroxypropyl bislauramide MEA, hydroxypropyl bisisostearaniide MEA, l,3-bis(N-2-(hydroxyetliyl)stearoylamino)-2 -hydroxy propane, bis-hydroxyethyl tocopheiylsuccinoylamido hydroxypropane, urea, aloe, allantoin, glycyrrhetinic acid, safflower oil, oleyl alcohol, oleic acid, stearic acid, dicaprylate/dicaprate, diethyl sebacate, isostearyl alcohol, pentylene glycol, isononyl isononanoate, and l,3-bis(N-2- (hydroxy ethyl)palmitoyiamino)-2 -hydroxypropane .

In addition, appropriate combinations and mixtures of any of these moisturizing agents and emollients may be used in accordance with the present invention.

D. Preservatives and Antioxidants

A composition may comprise components adapted to improve the stability or effectiveness of the applied formulation, such as a preservative and/or antioxidant. Suitable preservatives for use in the present invention include, but are not limited to: ureas, such as imidazolidinyl urea and diazolidinyi urea; phenoxyethanol; sodium methyl paraben, methylparaben, ethylparaben, and propylparaben; potassium sorbate; sodium benzoate; sorbic acid; benzoic acid; formaldehyde; citric acid; sodium citrate; chlorine dioxide; quaternary ammonium compounds, such as benzalkoniurn chloride, benzethonium chloride, cetrirnide, dequalinium chloride, and cetylpyridinium chloride; mercurial agents, such as

phenylmercuric nitrate, phenylmercuric acetate, and thimerosal: piroctone olamine; Vitis vinifera seed oil; and alcoholic agents, for example, chlorobutanol, dichlorobenzyl alcohol, phenylethyl alcohol, and benzyl alcohol.

Suitable antioxidants include, but are not limited to, ascorbic acid and its esters, sodium bisulfite, butylated hydroxytoluene, butylated hydroxyanisole, tocopherols, tocopheryl acetate, sodium ascorbate/ascorbic acid, ascorbyl palmiiate, propyl gallate, and chelating agents like EDTA {e.g. , disodmm EDTA), citric acid, and sodium citrate.

In certain embodiments, the antioxidant or preservative comprises (3-(4~

chlorophenoxy)-2-hydroxypropyl)carbamaie.

In certain embodiments, antioxidants or preservatives of the present invention may also function as a moisturizer or emollient, for example.

In addition, combinations or mixtures of these preservatives or anti-oxidants may also be used in the formulations of the present invention.

E. Combination agents

A composition can also contain any other agent that has a desired effect when applied topically to a mammal, particularly a human. Suitable classes of active agents include, but are not limited to, antibiotic agents, antimicrobial agents, anti-acne agents, antibacterial agents, antifungal agents, antiviral agents, steroidal anti-inflammatory agents, non-steroidal anti -inflammatory agents, anesthetic agents, antipruriginous agents, antiprotozoal agents, anti-oxidants, antihistamines, vitamins, and hormones. Mixtures of any of these active agents may also be employed. Additionally, dermatologically -acceptable salts and esters of any of these agents may be employed.

It is known that antimicrobials such as antibiotics can be bactericidal or bacteriostatic, limiting and reducing the quantity of bacteria in our bodies. Retinoids also reduce the amount of bacteria in pilosebacous units and microcomedones. Light based therapies work via photothermal heating, photochemical inactivation of bacteria, and various

photoimmunological reactions to improve clinical skin outcomes. In general, the above therapies directly act to reduce the amount of pathogenic bacteria in a patient. Thus, the invention proposes that any such therapy that achieves the same goal of reducing the number of pathogenic organisms, when used in combination with subsequent topical probiotic treatment, would lead to replacement of the pathogenic microflora involved in the diseased state with natural microflora enriched in healthy skin or mucous membranes, or less pathogenic species occupying the same ecological niche as the type causing a disease state.

Suitable antibacterial compounds include capreomycins, including capreomycin IA, capreomycin IB, capreomycin ΠΑ and capreomycin IIB: carbomycins, including carbomycin A; carumonam; cefaclor, cefadroxii, cefamandole, cefatrizine, cefazedone, cefazolin, cefbuperazone, cefcapene pivoxil, cefclidin, cefdinir, cefditoren, cefime, ceftamet, cefinenoxime, cefmetzole, cefininox, cefodizime, cefonicid, cefoperazone, ceforanide, cefotaxime, cefotetan, cefotiam, cefoxitin, cefpimizole, cefpiramide, cefpirome, cefprozil, cefroxadine, cefsulodin, ceftazidime, cefteram, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftriaxone, cefuroxime, cefuzonam, cephalexin, cephalogycin, cephaloridine, cephalosporin C, cephaiothin, eephapirm, eephamycins, such as eephamycin C, cephradine,

chlortetracycline; chlarithromycin, clindamycin, clometocillin, clomocycline, cloxacillin, cyciacillin, danofloxacm, demeclocyclin, destomycin A, dicloxacillin, dirithromycin, doxycyclin, epiciilin, erythromycin A, ethanbutol, fenbenicillin, flomoxef, florfenicol, floxacillin, flumequine, fortimicin A, fortimicin B, forfomycin, foraltadone, fusidic acid, gentamycin, glyconiazide, guamecycline, hetaciilin, idarubicin, imipenem, isepamicin, josamycin, kanamycin, leumycins such as leumycin Al, lincomycin, lomefloxacin, loracarbef, lymecycline, meropenam, metampiciilin, methacycime, methicillin, mezlocillin, micronomicin, midecamycms such as midecamycin Al , mikamycin, minocycline, mitomycins such as mitomycin C, moxalactam, mupirocin, nafcillin, netiiicin, norcardians such as norcardian A, oleandomycin, oxytetracycline, panipenam, pazufloxacin,

penamecillin, penicillins such as penicillin G, penicillin N and penicillin O, penillic acid, pentylpenicillin, peplomycin, phenethicillin, pipacyclin, piperacilin, pirlimycin,

pivampicillin, pivcefalexin, porfiromycin, propiailin, quinacillin, ribostamycin, rifabutin, ri f amide, rifampin, rifamycin SV, rifapentine, rifaximin, ritipenem, rekitamycin,

rolitetracycline, rosaramicin, roxithromycin, sancycline, sisomicin, sparfloxacin, spectinomycin, streptozocin, sulbenicillin, sultamicillin, talampicillin, teicoplanin, temocillin, tetracyclin, thostrepton, tiamulin, ticarcillm, tigemonam, tiimicosin, tobramycin,

tropospectromycin, trovafloxacin, tylosin, and vancomycin, and analogs, derivatives, pharmaceutically acceptable salts, esters, prodrugs, and protected forms thereof.

Suitable anti-fungal compounds include ketoconazole, miconazole, fluconazole, clotrimazole, undecvlenic acid, sertaconazole, terbinafine, butenafine, clioquinol, haloprogin, nystatin, naftifme, tolnaftate, ciclopirox, amphotericin B, or tea tree oil and analogs, derivatives, pharmaceutically acceptable salts, esters, prodrugs, and protected forms thereof.

Suitable antiviral agents include acyclovir, azidouridine, anismoycin, amantadine, bromovinyldeoxusidine, chlorovinyldeoxusidine, c\ iar:¾bine. delavirdine, didanosine, deoxynojirimycin, dideoxycytidine, dideoxyinosine, dideoxynucleoside, desciclovir, deoxyacyclovir, efavirenz, enviroxime, fiacitabine, foscamet, fiaiuridine, fluorothymidine, floxuridine, ganciclovir, hypericin, idoxuridine, interferon, interleukin, isethionate, nevirapme, pentamidine, ribavirin, rimantadine, stavudine, sargramostin, suramin, trichosanthin, tribromotliymidine, trichlorothymidine, trifluorothymidine, trisodium phosphomonoformate, vidarabine, zidoviridine, zalcitabine and 3-azido-3-deoxythymidine and analogs, derivatives, pharmaceutically acceptable salts, esters, prodrugs, and protected forms thereof.

Other suitable antiviral agents include 2',3'-dideoxyadenosine (ddA), 2 ^! ,3'~ dideoxyguanosine (ddG), 2',3'-dideoxycytidine (ddC), 2',3'-dideoxythymidine (ddT), 2'3'- dideoxy-dideoxythymidine (d4T), 2'-deoxy-3'-thia-cytosine (3TC or lamivudmie), 2',3'- dideoxy-2'-fluoroadenosine, 2',3'-dideoxy~2'-fluoroinosine, 2 ^! ,3'~dideoxy-2'-fiuorothymidine, 2',3'-dideoxy-2 ^f -fluorocytosine, 2'3'-dideoxy-2',3'-didehydro-2'-f!uorothymidine (Fd4T), 2*3'- dideoxy-2'-beta-fluoroadenosine (F-ddA), 2'3'-dideoxy-2'-beta-fluoro-inosine (F-ddl), and 2',3'-dideoxy-2'-beta-flurocytosine (F-ddC). In some embodiments, the antiviral agent is selected from trisodium phosphomonoformate, ganciclovir, trifluorothymidine, acyclovir, 3'- azido-3 '-thymidine (AZT), dideoxyinosine (ddl), and idoxuridine and analogs, derivatives, pharmaceutically acceptable salts, esters, prodrugs, and protected forms thereof.

F. Buffer Salts

A composition may comprise a buffer or salt. Suitable buffer salts are well-known in the art. Examples of suitable buffer salts include, but are not limited to sodium citrate, citric acid, sodium phosphate monobasic, sodium phosphate dibasic, sodium phosphate tribasic, potassium phosphate monobasic, potassium phosphate dibasic, and potassium phosphate tribasic.

G. Viscosity Modifiers

A composition may comprise a viscosity modifier. Suitable viscosity adjusting agents {i.e. , thickening and thinning agents or viscosity modifying agents) for use in the

formulations of the present invention include, but are not limited to, protective colloids or non-ionic gums such as hydroxyethylcellulose, xanthan gum, and sclerotium gum, as well as magnesium aluminum silicate, silica, microcry stall ine wax, beeswax, paraffin, and cetyl palmitate. In addition, appropriate combinations or mixtures of these viscosity adjusters may be utilized according to the present invention.

H. Additional constituents

Additional constituents suitable for incorporation into the emulsions of the present invention include, but are not limited to: skin protectants, adsorbents, demulcents, emollients, moisturizers, sustained release materials, solubilizmg agents, skin-penetration agents, skin soothing agents, deodorant agents, antiperspirants, sun screening agents, sunless tanning agents, vitamins, hair conditioning agents, anti-irritants, anti-aging agents, abrasi ves, absorbents, anti-caking agents, anti-static agents, astringents (e.g., witch hazel, alcohol, and herbal extracts such as chamomile extract), binders/excipients, buffering agents, chelating agents, film forming agents, conditioning agents, opacifying agents, lipids,

immunomoduiators, and pH adjusters (e.g. , citric acid, sodium hydroxide, and sodium phosphate).

For example, lipids normally found in healthy skin (or their functional equivalents) may be incorporated into the emulsions of the present invention. In certain embodiments, the lipid is selected from the group consisting of ceramides, cholesterol, and free fatty acids. Examples of lipids include, but are not limited to, ceramide 1 , ceramide 2, ceramide 3, ceramide 4, ceramide 5, ceramide 6, hydroxypropyl bispalmitamide MEA, and

hydroxy-propyl bisiauramide MEA, and combinations thereof.

Examples of peptides that interact with protein structures of the dermal-epidermal junction include palmitoyl dipeptide-5 diaminobutyloyl hydroxy-threonine and palmitoyl dipeptide-6 diaminohydroxybutyrate.

Examples of skin soothing agents include, but are not limited to algae extract, mugwort extract, stearyl glycyrrhetinate, bisabolol, allantoin, aloe, avocado oil, green tea extract, hops extract, chamomile extract, colloidal oatmeal, calamine, cucumber extract, and combinations thereof.

In certain embodiments, the compositions comprise bergamot or bergamot oil.

Bergamot oil is a natural skin toner and detoxifier. In certain embodiments, it may prevent premature aging of skin and may have excellent effects on oily skin conditions and acne.

Examples of vitamins include, but are not limited to, vitamins A, D, E, K, and combinations thereof. Vitamin analogues are also contemplated; for example, the vitamin D analogues calcipotriene or calcipotriol.

In certain embodiments, the vitamin may be present as tetrahexyldecyl ascorbate . This compound exhibits anti-oxidant activity, inhibiting lipid peroxidation. In certain

embodiments, use can mi tigate the damaging effects of UV exposure. Studies have shown it to stimulate collagen production as well as clarifying and brightening the skin by inhibiting melanogenesis (the production of pigment) thereby promoting a more even skm tone.

Examples of sunscreens include, but are not limited to, p-aminobenzoic acid, avobenzone, cinoxate, dioxvbenzone, homosalate, rnenthyl anthranilate, octociylene, octyl methoxycmnamate, octyl salicylate, oxybenzone, padimate O, phenyibenzimidazole sulfonic acid, sulisobenzone, titanium dioxide, trolamme salicylate, zinc oxide, 4-methylbenzylidene camphor, methylene bis-benzotriazolyl tetramethylbutyiphenoi, bis-ethylhexyloxyphenol methoxyphenyl triazine, terephthalyiidene dicamphor sulfonic acid, drometrizole trisiloxane, disodium phenyl dibenzimidazole tetrasulfonate, diethylamino hydroxy-benzoyl hexyl benzoate, octyl triazone, diethylhexyl butamido triazone, polysiiicone-15, and combinations thereof.

Suitable fragrances and colors may be used in the formulations of the present invention. Examples of fragrances and colors suitable for use in topical products are known m the art.

Suitable immunomoduiators include, but are not limited to, tetrachlorodecaoxide, deoxycholic acid, tacrolimus, pimecrolimus, and beta-glucan.

In certain embodiments, palmitoyl-lysyl-valyl-lysine bistrifluoroacetate is added. This peptide stimulates collagen synthesis in human fibroblasts.

Often, one constituent of a composition may accomplish several functions. In one embodiment, the present invention relates to constituents that may act as a lubricant, an emollient, or a skin-penetrating agent. In one embodiment, the multi-functional constituent is socetyl stearate, isopropyl isostearate, isopropyl palmitate, or isopropyl myristate.

II. METHODS OF PREVENTING OR TREATING A CONDITION IN A SUBJECT

In some aspects, the invention relates to a method of preventing or treating a condition in a subject, comprising administering a composition to the subject. The condition may be a skin condition. The composition may be any composition described herein.

Administration may comprise topical administration. Administration may comprise oral administration. For example, the method may comprise administering to the subject a composition comprising an RT1, RT2, and/or RT6 strain of Propionihacterium acnes. In oilier embodiments, the method may comprise administering to the subject a composition disclosed herein comprising an RT3, RT8, RT16, or Type III strain of Propionibactemim acnes. In some embodiments, the method may comprise administering a strain expressing, encoding, or harboring deoR.

In some embodiments, the skin condition may be acne, skin aging, rosacea, or porphyria cutanea tarda.

The subject may be receiving at least 2 \% of vitamin Bi2 per day, such as at least 3

^ig, 4 ^ig, 5 g, 6 μg, 7 .ug, 8 μg, 9 μg, or at least 10 ^ig of vitamin B12 per day. A subject may be receiving about 2 ^ig to about 10 mg of vitamin B12 per day, such as about 2 ,ug to about 1 mg of vitamin B12 per day, about 3 μg to about 1 rng, about 4 μg to about 1 mg, about 5 μg to about 1 mg, about 6 μg to about 1 mg, about 7 ,ug to about 1 mg, about 8 ^ig to about 1 mg, about 9 to about 1 mg, or about 10 ug to about 1 mg of vitamin B12 per day.

In some aspects, the invention relates to a method for determining the risk that a subject will develop vitamin Bn-induced acne. The method may comprise calculating the porphyrin concentration of a cell suspension comprising P. acnes obtained from the subject. The method may comprise identifying a strain of P. acnes obtained from, the subject. The method may comprise identifying the proportion of P. acnes obtained from the subject that belong to a particular ribotype, that comprise a gene encoding deoR, or that are otherwise associated with acne or healthy skin.

Calculating porphyrin concentration may comprise measuring a concentration of coproporphyrin III or∞propoiphyrin I, e.g., in a cell suspension of P. acnes obtained from a subject. Calculating porphyrin concentration may comprise measuring an absorbance of light, e.g. , wherein the light has a wavelength of about 380 nm to about 430 nm, such as about 400 nm, about 405 nm, or about 410 nm. Calculating a porphyrin concentration may comprise measuring the cell suspension density, e.g. , to normalize the porphyrin

concentration measurement. Measuring the cell suspension density may comprise measuring light transmittance through the cell suspension at a wavelength of about 580 nm to about 620 nm, such as a wavelength of about 590 nrn, about 595 nm, about 600 nm, or about 605 nm. The method may or may not comprise culturing P. acnes obtained from a subject, e.g. , prior to calculating a porphyrin concentration.

A method may comprise diagnosing a subject with an elevated risk of developing vitamin Bn-induced acne if the porphyrin concentration of a suspension of P. acnes obtained from the subject is higher than about 2 μΜ, such as higher than about 3 μΜ. A method may comprise diagnosing a subject with a low risk of developing vitamin Bn-induced acne if the porphyrin concentration of a suspension of P. acnes obtained from the subject is less than about 2 μΜ.

The method may comprise identifying a strain of P. acnes obtained from the subject, and diagnosing the subject with an elevated risk of developing vitamin Bu-mduced acne if the strain of P. acnes is sensitive to vitamin B12. For example, the subject may be diagnosed as having an elevated risk of developing vitamin Bn-induced acne if the strain of P. acnes is RT4 or RT5. The subject may be diagnosed as hav ing an elevated risk of developing vitamin Bi2-induced acne if the strain of P. acnes is RT3 strain HL063PA2 or RT8 strain HL082PA1. The subject may be diagnosed as having an elevated risk of developing vitamin Bn-induced acne if the strain of P. acnes is RT1 strain HL005PA2 or HL083PA1.

The method may comprise identifying a strain of P. acnes obtained from the subject and diagnosing the subject with a low risk of developing vitamin Bn-induced acne if the strain of P. acnes is not sensitive to vitamin B12. For example, a subject may be diagnosed as having a low risk of developing vitamin Bn-induced acne if the strain of P. acnes is RT2 or RT6. Similarly, a subject may be diagnosed as not having an elevated risk of developing vitamin Bn-induced acne if the strain of P. acnes is RT2 or RT6. A subject may be diagnosed as not having an elevated risk of developing vitamin Bn-induced acne if the strain of P. acnes is RT3 (i .e., an RT3 strain that is not HL063PA2), RT8 (i.e., an RT8 strain that is not HL082PA 1 or HL053PA2), or RT16. The subject may be diagnosed as not having an elevated risk of developing vitamin Bn-induced acne if the strain of P. acnes is Type II and Ty pe III. In some embodiments, the subject may be diagnosed with a low risk of developmg vitamin Bn-induced acne if the subject has one or more strains of ^' P. acnes, but the majority of P. cnes strains are RT2, RT6, RT3 (i .e., an RT3 strain that is not HL063PA2), RT8 (i .e., an RT8 strain that is not HL082PA 1 or HL053PA2), RT16, or Type III.

Identifying a strain of P. acnes may comprise sequencing a nucleic acid of the strain of P. acnes. For example, identifying a strain of P. acnes may comprise sequencing a nucleotide sequence encoding the 16S rRNA of the strain, or identifying a strain of P. acnes may comprise sequencing a nucleotide sequence encoding all or part of the porphyrin biosynthesis gene operon of the strain.

A method may comprise treating a subject with photodynamic therapy if the subject has an elevated risk of developing vitamin Bn-induced acne. A method may comprise treating a subject with a treatment other than photodynamic therapy [e.g., with antibiotics, such as topical or oral antibiotics) if the subject has a low risk of developing vitamin Bn- induced acne.

A method may comprise administering vitamin Bn to a subject if the subject is not diagnosed with an elevated risk of developing vitamin Bn-induced acne. A method may comprise administering vitamin Bn to a subject if the subject is diagnosed with a low risk of developing vitamin Bn-induced acne.

In some aspects, the invention relates to a method for treating a skin condition in a subject, comprising treating the subject with photodynamic therapy. For example, the method may comprise treating a subject with photodynamic therapy if a P. acnes strain of the subject is either an RT4 strain or an RT5 strain. Similarly, the method may comprise treating a subject with photodynamic therapy if the poiphyrin concentration of a cell suspension of P. acnes obtained from the subject is above a threshold value, such as above about 1 μΜ, about 2 μΜ, about 3 μΜ, about 4 μΜ, about 5 μΜ, or about 6 μΜ.

A method may comprise treating a subject with a treatment other than photodynamic tiierapy if no P. acnes strain of the subject is either an RT4 strain or an RT5 strain. Similarly, the method may comprise treating a subject with a treatment other than photodynamic therapy if the poiphyrin concentration of a ceil suspension of P. acnes obtained from the subject is lower than a threshold value, such as lower than about 1 μΜ, about 2 μ.Μ, about 3 μΜ, about 4 μΜ, about 5 μΜ, or about 6 μΜ. The method may comprise not treating a subject with photodynamic therapy if the strain of P. acnes is RT2 or RT6. In some embodiments, the subject is not treated with photodynamic therapy if the strain of P. acnes is Type HI.

The method may comprise calculating the porphyrin concentration of a cell suspension comprising P. acnes obtained from the subject as described herein, e.g., with or without culturing the P. acnes prior to measuring the porphyrin concentration.

In some aspects, the method comprises reducing the amount of porphyrins on the skin of a subject by administering a composition (e.g., an. oral or topical composition disclosed herein) comprising one or more strains of Propianibacterium acnes disclosed herein to the subject.

The method may comprise determining whether a subject is at risk for a skin condition, the method by obtaining a skin sample from the subject, optionally isolating bacterial DNA from the skin sample, sequencing the bacterial DNA in the skin sample, and if deoR transcriptional repressor is not expressed, expressed at low levels, or is not present in the bacterial DNA, the subject is considered at risk for a skm disease.

The invention now being generally described, it will be more readily understood by reference to the following examples which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention. EXEMPLIFICATION

MATERIALS AND METHODS

P. acnes strains and cultures. P. acnes strains used in this study (Table 1) were isolated from the facial skin of acne patients and healthy individuals as described by Fitz-

Gibbon et al. (J Invest Dermatol 133:2152-2160 (2013)). Briefly, each strain was isolated from the content collected from multiple hair follicles on the nose of an acne patient or healthy individual. The sampled skin site of acne patients may or may not have visible acne lesions; therefore, the strains do not necessarily correspond to the diseased or healthy state. Four RT4 and RT5 P. acnes strains, HL053PA1 , HL045PA1 , HL043PA 1, and HL043PA2, were selected to represent type IA-2 strains, which were associated with the disease based on a 16S metagenomic study (J Invest Dermatol 133:2152-2160 (2013)). Common to most of the RT4 and RT5 strains, these strains harbor mutations in their 16S and 23 S rRNA genes, which confer antibiotic resistance. Tliree RT2 and RT6 strains, HLOOIPA I, HL103PA1, and HL042PA3, were selected to represent type 11 strains that were associated with healthy skin. To confirm, the findings, an additional three type II strains, I II ! 10PA3, HL106PA1 , and HL050PA2, were also tested. The genome sequences of these ten strains were reported previously (Fitz-Gibbon, J Invest Dermatol 133:2152-2160 (2013); Tomida, MBio 4:e00003- 00013 (2013 )). For each experiment, 5 mL of reinforced clostridial broth was inoculated with 5 X 10 ^s P. acnes cells per mL of culture. Cultures were grown to stationary phase anaerobically at 37°C in a light-protected box. Cultures were supplemented on day 0 with vitamin Bi j. (10 μg/mL), 5 -ALA (0.1 mg/mL), and/or LA (0.1 mg/mL). As controls, P. acnes strains were also cultured without supplementation. Three to five independent experiments with at least three replicates per experiment were performed for each strain, except strains HL110PA3, HL106PA 1, and HL050PA2, which were tested in only one experiment with tliree replicates.

1. P. acnes strains

Health- CC6 CC60

II II HL103PA1 RT2

associated (ST25 (ST60)

CC6 CC60

HL042PA3 RT6

(ST7) ST73)

Type I CC4 CC28

I ΙΑ( HL025PA1 RTI

with deoR (ST4) ( S i 27) ^a - ^c as described by Fitz-Gibbon et al. (I Invest Dermatol 133 :2152-2160 (2013))

b- ^d as descnbed by McDowell et al. (J Clin Microbiol 43 :326-334 (20i

s as described by Lomholt and Kilian (PloS One 5 :312277 (2010)),

Extraction, identification, and quantification of extracellular porphyrins. For each strain, porphyrins were extracted using the method described by Kang et a/. (Sci Trans] Med 7:293ral03 (2015)). Briefly, 500 μί, of bacterial culture was extracted in ethyl acetate and acetic acid (4: 1, v/v), and solubilized in 1.5M HC1. The absorbance at 405 nm was measured from 200 \iL of the soluble phase using a Tecan Genios Spectrophotometer Ml 000 (Tecan US Tnc, Morrisville, NC), The standard cun/e to convert absorbance to concentration was generated using coproporphyrin III standards of known concentration (C654-3, Frontier Sci). Porphyrin levels were measured in P. acnes strain KPA171202 using the quantification method descnbed by Wollenberg et al. (MBio 5:e01286-01214 (2014)). The measurement, which was 206 pmol/mg, is consistent with the reported value of 220 pmol/mg by

Wollenberg et al. This indicates that the method is comparable to previous studies.

Porphyrins were extracted from cultures at stationary phase. The results from cultures at mid-log phase displayed a consistent trend found in cultures at stationary phase. Bacterial culture density was measured at OD595 for normalization of ροφΗ)^ levels. For mass spectrometry experiments, extracted porphyrins were directly injected onto an Agilent 6460 Triple Quad LC/MS system and each strain's m/z in the negative ion mode was identified.

Statistical analysis for porphyrin production comparisons. The average amount of porphyrins produced by each strain under each culture condition was calculated based on the data from at least three independent experiments, with at least three replicates for each. The porphyrin levels between strains, groups (acne-associated vs. health-associated), and culture conditions (with treatment vs. without treatment) were estimated in a linear mixed effect model, with random intercepts by trial to account for trial effects, /'-values for specific comparisons among groups were corrected using Tukey ^" s method. Ail statistical analysis was performed using R software (version 3.1.3).

Identification of deoR transcription repressor. The sequences of the porphyrin gene clusters from 82 P. acnes genomes (Tomida, MBio 4:e00003-00013 (2013)) were aligned using the multiple sequence alignment software (CiustalW2). The deoR transcription repressor (PPA0299) was identified as an extra genomic element found in all health- associated type II strains and a few type I strains.

RNA extraction and cDNA synthesis. For cbiL and deoR gene expression analysis, cells were !ysed with bead beating. Total RNA was extracted using the standard phenol- chloroform method and purified using RNeasy kit (Qiagen). DNA was removed using the Turbo DNA-free kit (Life Technologies). RNA quality was assessed using gel

electrophoresis. Single-stranded complementary DNA (cD A) was synthesized using Superscript III First-Strand Synthesis SuperMix (Life Technologies).

Analysis of cbiL gene expression. qRT-PCR was performed using the LightCycler 480 High Resolution Melting Master Mix (Roche) on a LightCycler 480 (Roche) with the following primers: cbiL -forward, 5'-GCGCGAGGCAGACGTGATCC-3', and cbiL -reverse, 5'-GACACCGGACCTCTCCCGCA-3' , The following qRT-PCR protocol was used: initial denaturation at 95°C for 5 rnin, followed by 50 cycles of 95°C for 10 sec, 62°C for 30 sec, and 72°C for 30 sec. The fold change in cbiL gene expression between cultures with vitamin Bi2 supplementation and cultures without supplementation was calculated. The gene expression level of chiL in each sample was normalized against the 16S rRNA transcript level. Melting curve analysis was performed using the Light Cycler 480 software Version 1.5

(Roche) to verify the specificity of the amplified products based on their melting

temperatures. All reactions were ran in triplicate.

Analysis of deoR gene expression. deoR was amplified from the cDNA and genomic

DNA of several P. acnes strains using a C 1000 Thermal Cycler (BioRad). The following primers were used in the PC : deoR-£orwaxd, 5 '-CTGGCACGAGAAGGAACAA-3 and deoR-reverse, 5 ' -GAATCGAGCAGAACTAGGTC AC-3 ' . The following PCR protocol was used: initial denaturation at 95°C for 5 min, followed by 35 cycles of 95°C for 10 sec, 62°C for 30 sec, 72°C for 30 sec, followed by one cycle at 72°C for 5 min. Amplified deoR products were visualized on a 2% agarose gel. The amplification of 16S rRNA was included as a positive control. Acne-associated strain HL045PA1 was used as a negative control for deoR expression.

RESULTS

Acne-associated P. acnes strains produced significantly more porphyrins than health-associated strains. To investigate whether different P. acnes strains produce the same porphyrin species, the types of porphyrins secreted by multiple P. acnes strains where characterized using mass spectrometry. Four acne-associated type IA-2 strains, HL053PA1 (RT4), HL045PA1 (RT4), HL043PA1 (RT5), and HL043PA2 (RT5), and three health- associated type II strains, HL001PA1 (RT2), HL103PA i (RT2), and HL042P 3 (RT6), were examined (Table 1). No difference in the porphyrin species produced by these P. acnes strains was observed. Coproporphyrin III was the dominant porphyrin isomer produced by all strains ([M+H] ^" = 655.3). Minimal amounts of coproporphyrin I were also detected. Porphyrin levels are measured with the following method. Bacterial cells are collected, and porphyrins are extracted. The concentration of porphyrins is measured spectrophotometrically and normalized to the optical density (also measured spectrophotometrically). Porphyrin levels are therefore measured per bacterial unit.

To determine whether P. acnes strains produce different amounts of porphyrins, the secreted porphyrins in the seven P. acnes strains were quantified (Fig. I ). The average porphyrin level produced by acne-associated type IA-2 strains was 6,5μΜ (5.6 - 8.8 μΜ), which was significantly greater than that produced by health-associated type II strains, 1.1 μΜ (0 - 2.1 μΜ, O.OUO i (Figure I)). Notably, the RT2 strain HL001PA1 produced no detectable porphyrins in all experiments. This strain belongs to clonal complex 72 (CC72) based on the Belfast MLST8 scheme (Table 1), and the strain was isolated from healthy skin.

Vitamin B12 supplementation significantly increased porphyrin production in acne-associated strains, but not in health-associated strains. To investigate whether vitamin B12 modulates P. acnes porphyrin production in a strain-specific manner, the levels of poiphvrins produced by different P. acnes strains were compared with and without vitamin Bi2 supplementation. Vitamin B12 supplementation led to increased porphyrin production in all tested acne-associated type IA-2 strains (average porphyrin level increasing from 6.5 μΜ to 9.2 μΜ), with statistical significance in three of the four tested strains (P<0.02) (Fig. 2), in contrast vitamin B12 supplementation had no significant effect on porphyrin production in health-associated type II strains (average porphyrin level remaining at 1.1 μΜ, P>0.77). The porphyrin levels in I 11.0 ⁽ 51 PA I remained undetectable. To confirm these results, porphyrin production was measured, with and without the addition of vitamin B 12, in three additional type 11 strains, HLl 10PA3 (RT6), HL106PA1 (RT2), and HL050PA2 (RTl). These strains produced similarly low levels of porphyrins (1.4 ± 1.2 μΜ) and the production level was not significantly affected by vitamin B12 supplementation. This data suggests that vitamin 612 modulates porphyrin production in acne-associated type IA-2 strains, but not in health- associated type II strains, indicating a molecular link between P. acnes strain composition of the skin microbiota and the observation that vitamin B12 induces acne in a subset of individuals.

Vitamin B12 supplementation repressed vitamin B12 biosynthesis gene expression.

To determine whether vitamin B12 affects porphyrin production via repression of its own biosynthesis in P. acnes, qRT-PCR was performed to measure the expression level of cbiL, a gene in the vitamin B12 biosynthesis pathway. The cbiL gene encodes precorrin-2 C20- methyltransferase, one key enzyme involved in comn ring formation in the vitamin B12 biosynthesis pathway. The addition of vitamin B12 to P. acnes cultures resulted in the down- regulation of cbiL gene expression, with an average fold change of 0.74 in acne-associated type IA-2 strains and 0.24 in health-associated type II strains (Figure 3). The down- regulation ofcbiL gene expression is consistent with the previous finding that vitamin B12 supplementation repressed the vitamin B12 biosynthesis pathway, leading to increased porphyrin production. The expression of cbiL was down-regulated in both type IA-2 and type II strains, despite the observation that the porphyrin production in type II strains was unaffected by vitamin B12 supplementation. This suggests that additional mechanisms are involved in inhibiting porphyrin production in health-associated type II strains.

Addition of 5-aminolevulinic acid (5-ALA) increased porphyrin production, which was further enhanced by vitamin B12. The porphyrin and vitamin B12 biosynthesis pathways in P. acnes share the same initial enzymatic steps and a common precursor, 5-ALA, the substrate of the rate-limiting enzyme, porphobilinogen synthase. To investigate whether porphyrin production can be promoted by increasing the availability of 5-ALA, the porphyrin production levels of P. acnes strains was compared with and without the addition of the substrate. Additionally, the effect of vitamin Bu on porphyrin production was assessed in combination with 5 -ALA. Upon substrate addition only, porphyrin production was significantly increased by an average of 2.2 fold in acne-associated type TA-2 strains (P<0.0001) and 3.4 fold in health-associated type II strains (P<0.06, except HLOOIPAI) compared to untreated controls (Fig. 4). HLOOIPAI consistently produced no detectable porphyrins, even upon addition of 5 -ALA. Supplementation of 5-ALA in combination with vitamin Bu further enhanced porphyrin production in acne-associated type IA-2 strains (2.7 fold increase compared to substrate only) with statistical significance in three of the four tested strains (P<0.04), but not in health-associated type II strains (P>0,94). This is consistent with the above finding that health-associated type II strains do not respond to vitamin B 12 in their porphyrin production (Fig. 2). This data suggests that the metabolic influx of substrates influences porphyrin production in P. acnes. The modulation of porphyrin production by vitamin B12 supplementation is specific to acne-associated type IA-2 strains, but not health -associated type Π strains.

Small molecule inhibitor reduced porphyrin production in P. acnes and its inhibition was counteracted by vitamin Bn supplementation. To further demonstrate that porphyrin production can be modulated at the metabolic level, the effect of a small molecule inhibitor, levulinic acid (LA), was assessed on porphyrin biosynthesis in P. acnes strains. Additionally, the effect of vitamin B 12 supplementation on porphyrin production was assessed in combination with LA. L A is an analog of 5-ALA and has been shown in Pseiidomonas aeruginosa to inhibit the enzymatic activity of porphobilinogen synthase, blocking the metabolic influx to the poiphyrin and vitamin B12 biosynthesis pathways. A range of concentrations of LA from 0.1 mg/mL to 1.0 mg/mL was assessed and 0.1 mg/mL LA did not significantly affect the bacterial growth, thus making the measurements of porphyrin production experimentally feasible. LA (0.1 mg/mL) significantly reduced porphyrin production in all strains except HLOOIPAI with an average of 30% reduction compared to untreated cultures (P<0.0001) (Fig. 5). However, in acne-associated type IA-2 strains, there was no significant reduction of porphyrins when supplemented in combination with 10 μg/mL vitamin B12. Vitamin B12 supplementation counteracted the inhibition of porphyrin biosynthesis by LA specifically in acne-associated type IA-2strams, but not in health-associated type ΪΪ strains. This is consistent with our above findings (Figure 2 and

Figure 4) and further supports the conclusions that vitamin B12 modulates poiphyrin production in acne-associated type IA-2 strains and that porphyrin production can be modulated at the metabolic level. This data also suggests that LA is an effective inhibitor of porphyrin biosynthesis in P. acnes and that the porphyrin biosynthesis pathway can be a potential therapeutic target for new acne treatments.

Health-associated strains harbor a porphyrin biosynthesis repressor gene, deoR, To identify potential molecular mechanisms that can explain differences in porphyrin levels produced by acne-and health-associated P. acnes strains, the porphyrin biosynthesis gene operon (Hem) of 82 P. acnes strains were compared, including the strains tested in this study. All health-associated type I! strains and a few type I strains (mainly IB-3 and IC strains) harbor an additional gene in the porphyrin biosynthesis operon, annotated as deoR transcriptional repressor (Figures 8 and 9). The deoR gene is located 13 bp upstream of the porphyrin biosynthesis gene cluster. This gene is absent in all acne-associated type TA-2 strains. To determine whether deoR is functional, gene expression analysis was performed and found to be expressed in two of the three health-associated type 11 strains, HL001PA1 and HL042PA3, but not in HL103PA1 (Figure 6). Characterizations of deoR-likc repressors in multiple other species have revealed their roles in regulating cellular processes such as sugar phosphotransferase activity, daptomycin production, and fatty acid beta-oxidation. The close proximity of deoR to the porphyrin biosynthesis genes in the genome and the presence and expression of deoR in health-associated type II strains suggest that deoR may function as a transcriptional repressor in porphyrin biosynthesis. This may partly explain the low porphyrin levels produced by health-associated type 11 strains and their associations with healthy skin.

Acne-associated type TA-2strains and health-associated type II strains belong to distinct P. acnes lineages. To further investigate whether the low levels of porphyrins produced by health-associated type II strains were potentially due to repression by deoR and not due to other lineage differences, the porphyrin levels produced by a type I P. acnes strain, HL025PA1 were examined. HL025PA1 represents a distinct lineage within type I and is phylogeneticaily more similar to type IA-2strains than to type II strains (Figure 9). Unique from most other type I strains, HL025PA 1 encodes and expresses deoR in its porphyrin biosynthesis operon (Figure 6). HL025PA1 produced porphyrins at a level similar to that of health-associated type II strains (2.7 μΜ, P=0.31), significantly lower than acne-associated type IA-2 strains (1 ^>; =0.0006) (Figure 10). Consistent with the trend observed in health- associated type II strains, vitamin Bi supplementation resulted in its own transcriptional repression in HL025PAI (Figure 3), while its the porphyrin production was unaffected by vitamin Bo supplementation (Figure 10). This finding further supports an inhibitory role for deoR in porphyrin biosynthesis and may potentially explain the health association of type II strains.

INCORPORATION BY REFERENCE

All of the scientific articles, patents, and published patent applications cited herein are hereby incorporated by reference.

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.