Field of the invention

The present invention relates to a method for the construction of a bacteriophage insensitive mutant of a microorganism parent strain suitable for food and feed fermentation. Further, the present invention relates to a method for the construction of a bacteriophage insensitive Streptococcus thermophiius mutant whereby the phage resistance is conferred by a mechanism other than CRISPR.

Background of the invention

Streptococcus thermophiius is a Gram-positive thermophilic bacterium used globally as a starter culture in dairy fermentations and is widely employed for the production of cheese and yoghurt products. Despite its usefulness in starter cultures, S. thermophiius remains highly susceptible to (bacterio)phage predation which can lead to substandard or failed fermentations and considerable economic losses. Evidenced by these potentially considerable costs, there is a clear advantage to selecting robust starters which are less susceptible to phage attack and yet retain favourable growth and production characteristics. Combined with effective hygiene and sanitation in industrial fermentation plants, unrelated robust starters used in rotation have the potential to reduce the incidence of phage fermentation disruption.

Phages of S. thermophiius are, despite their narrow host ranges, the major cause of fermentation failure, due to their short latent period and large burst sizes. They are generally classified as Siphoviridae (having isometric heads and long, non-contractile tails) and usually fall into two groups (cos- and pac-type), based on their mode of DNA packaging and the number of major structural proteins present (Le Marrec et al., 1997. Applied and Environmental Microbiology 63 (8), p. 3246-3253 - Two groups of bacteriophages infecting Streptococcus thermophiius can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins). More recently, a third group of phages infecting S. thermophiius was identified that represents a novel genetic lineage and highlights the genetic plasticity of these phages (Mills et al., 201 1 . International Dairy Journal 21 , p. 963-969 - A new phage on the 'Mozzarella' block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages). Consequently, phages of S. thermophilus persist in dairy fermentation facilities leading to starter culture infections. In reponse to these infections, microorganisms such as S. thermophilus has evolved several mechanisms of phage resistance, some of which are more effective and stable than others.

Mutants which have become resistant to phages by means of effective and stable mechanisms may be characterised by means of DNA sequencing, morphological analyses and/or adsorption assays.

Bacteriophage resistance systems have evolved in microorganisms such as S. thermophilus in tandem with phage adaptation strategies to overcome these biological barriers. These systems can include those preventing phage adsorption, blocking DNA injection, restriction/modification of DNA (R/M) and abortive infection or Abi (Labrie et al. (2010) Nature reviews 8, p. 317-327 - Bacteriophage resistance mechanisms). To date, the most intensely characterised and the most frequent of these systems in lactic streptococci, are the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems, which are known to provide acquired immunity to phages through an RNA-mediated dsDNA targeting process (Barrangou et al. (2007). Science 315, p. 1709- 1712 - CRISPR provides acquired resistance against viruses in prokaryotes; Garneau et al. (2010). Nature 468, p. 67-71 - The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA).

Three distinct CRISPR systems (CRISPRs 1 , 2 and 3), representing two distinct types (types II and III) are widespread in S. thermophilus and individual strains may contain multiple systems. Diversity was observed across three CRISPR loci between 124 different S. thermophilus strains. Specifically, CRISPR1 was ubiquitous, whereas CRISPR2 was present in 59 of 65 strains, and CRISPR3 was present in 53 of 66 strains. A total of 49 strains (39.5%) carried all three loci. (Horvath et al., 2008. Journal of Bacteriology 190 (4), p. 1401 -1412 - Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus). Recently, a fourth CRISPR system has been described (Sinkunas et al., 2013. The European Molecular Biology Organisation journal 32, p. 385-394 - In vitro reconstitution of cascade-mediated CRISPR immunity in Streptococcus thermophilus) although its prevalence is rare and in vivo activity is not known. Although CRISPR provides effective immunity against phages through acquired spacers which are identical to short regions of the attacking phage genomes (Barrangou et al., 2007, as above), it is known that phages can rapidly evolve to overcome these spacer additions through single nucleotide alterations in the corresponding genomic region (Deveau et a/., 2008. Journal of Bacteriology 190 (4), p. 1390-1400 - Phage response to CRISPR-en coded resistance in Streptococcus thermophilus). Furthermore, since CRISPR mutations are the most frequent mutations involved in phage resistance it is difficult to identify other more desirable mutations which provide phage resistance. Therefore, it is desirable to develop a method to obtain phage-resistant derivatives of microorganism parent strains suitable for food and feed fermentation, and especially S. thermophilus, where such phage resistance is due to the action of alternative phage resistance mechanisms than CRISPR. The present invention provides a method to construct and select for such phage-resistant bacteria.

Detailed description of the invention

In a first aspect, the invention provides a method for the construction of a bacteriophage insensitive mutant (further referred to as BIM) of a microorganism parent strain suitable for food and feed fermentation comprising selecting one or more mutants which, compared to parent strain, has an increased sedimentation rate and/or an increased chain formation to provide the bacteriophage insensitive mutant.

Preferably, the invention provides a method for the construction of a non CRISPR mediated bacteriophage insensitive mutant of a microorganism parent strain, a preferably bacteriophage sensitive S. thermophilus parent strain.

Surprisingly, the present inventors found that an increased sedimentation rate and/or increased chain formation is predictive for the phage robustness of the derived mutants. Further, the inventors found that the frequency of CRISPR mutants is much lower in the population with altered sedimentation rate and/or chain formation compared to the parent strain, and thus selecting on these morphological characteristics provides a selective high throughput screening to generate non CRISPR BIMs.

In the present method the mutations are naturally occurring mutations. In other words, the present method preferably does not comprise mutagenesis.

The term microorganism parent strain suitable for food and feed fermentation within the present context means microorganisms which can safely be used in the fermentative production of food and feed without causing health risk for the consumers of the food or feed. Preferably, the present microorganism parent strain suitable for food and feed fermentation is a lactic acid bacterium. For example a bacterium belonging to the genera Lactococcus, Leuconostoc, Lactobacillus or Streptococcus. More preferably, the present microorganism parent strain suitable for food and feed fermentation is a bacteriophage sensitive S. thermophilus parent strain. In a first embodiment the method for the construction of a bacteriophage insensitive mutant of a bacteriophage sensitive S. thermophilus parent strain is comprised of the following steps:

(a) exposing the parent strain to a bacteriophage,

(b) isolating single colonies of one or more bacteriophage insensitive mutant;

(c) comparing the CRISPR loci of the parent strain with the CRISPR loci of the bacteriophage insensitive mutant and

(d) select the bacteriophage insensitive mutant of which the CRISPR loci is identical to the CRISPR loci of the parent strain.

In order to carry out the method of the invention, the bacteriophage-sensitive S. thermophilus parent strain may be cultured in a suitable medium according to methods known in the art in order to generate biomass to carry out step (a). The bacteriophages to which the bacteriophage sensitive S. thermophilus parent strain is exposed, may be isolated from whey samples obtained from dairy plants by any suitable method, for instance by the method described in the MATERIALS AND METHODS.

Preferably, in the present context, the term CRISPR loci means the loci of the CRISPR system 1 , 2 and 3, i.e. preferably not comprising CRISPR locus 4.

Step (a) - Exposing the parent strain to a bacteriophage, may be carried out in any suitable medium, for instance in an aqueous solution such as a buffered aqueous solution or in a soft agar medium or in milk. In a preferred embodiment, exposing the parent strain to a bacteriophage is carried out in a soft agar medium. In another preferred embodiment, exposing the parent strain to a bacteriophage is carried out in milk. The milk may be incubated overnight or until clotting is observed. The parent strain used in the method of the invention may be pre-treated in order to increase the genetic diversity and to increase the number of the BIMs. This pre-treatment may be carried out by methods known in the art, such as chemical mutagenesis or by irradiation with UV- light. The - optionally pre-treated - parent strain may be exposed to one type of bacteriophage or to multiple different bacteriophages, for instance to 2, 3, 4 or 5 different bacteriophages.

Step (b) - The suspension or the incubated (clotted) milk obtained in step (a) of the method of the invention may be plated on agar plates. After incubating the agar plates at a temperature at which S. thermophilus may grow, colonies may appear which represent the BIMs. The colonies may be purified and preferably phenotypically verified to obtain a single strain BIM according to methods known in the art.

Step (c) - In step (c) of the method of the invention, the CRISPR loci of the BIMs obtained in step (b) of the method of the invention are analysed for their length (in base pairs) and/or sequenced and compared with the CRISPR loci of the bacteriophage sensitive parent strain.

Step (d) - In step (d) of the method of the invention only those BIMs are selected of which the CRISPR loci are identical to the CRISPR loci of the parent strain. The advantage of the method of the invention is that the selected BIMs have become phage resistant by means of a mechanism that is different from CRISPR and therefore based on an alternative phage resistance mechanism. As a result, the BIMs obtained by the method of the invention may have a more stable and/or robust phage resistance compared to a CRISPR-mediated BIM of which it it is known that phages can rapidly evolve to overcome these spacer additions through single nucleotide alterations in the appropriate genomic region.

In a second embodiment, the method for the construction of a bacteriophage insensitive mutant of a microorganism parent strain, or of a bacteriophage sensitive S. thermophilus parent strain is comprised of the following steps:

a. exposing the microorganism parent strain and/or the bacteriophage sensitive S. thermophilus parent strain to a bacteriophage;

b. optionally isolating single colonies of one or more bacteriophage insensitive mutant;

c. selecting the bacteriophage insensitive mutant which, compared to the microorganisms parent strain or the bacteriophage sensitive S. thermophilus parent strain, exhibits:

1 . an increased sedimentation rate, preferably in a liquid medium; and/or

2. an increased chain formation; and/or

3. a reduced phage adsorption

d. optionally isolating single colonies of the bacteriophage insensitive mutant. Step (a) and (b) are identical to step (a) and (b) described hereinbefore for the first embodiment of the method for the construction of a bacteriophage insensitive mutant of a bacteriophage sensitive S. thermophilus parent strain. Step (b) is optional because the subsequent step (c) may also be performed on multiple BIMs. In the embodiment of the method of the invention wherein step (b), isolating single colonies of the BIMs, followed by step (c), it is not necessary to perform step (d). In the alternative embodiment wherein step (b) is omitted, step (d) is preferably carried out in order to have single BIMs.

Step (c) - In step (c), BIMs are selected that have acquired one or more of the following properties:

(1 ) an increased sedimentation rate; and/or

(2) an increased chain formation; and/or

(3) a reduced phage adsorption.

Preferably, present step (c) comprises selecting the bacteriophage insensitive mutant which, compared to bacteriophage sensitive parent bacterium, exhibits an increased sedimentation rate and/or an increased chain formation. As a consequence of this selection, the selected BIMs have acquired a phage resistance mechanism that is due to one or more phage resistance or phage insensitivity mechanisms other than that mediated by the CRISPR system. Therefore, BIMs obtained by the method of the invention may have a more stable and/or robust phage resistance compared to the CRISPR mechanism of which it it is known that phages can rapidly evolve to overcome these CRISPR-specific spacer additions through single nucleotide alterations in the corresponding genomic region.

Step c.1 - an increased sedimentation rate.

In one embodiment of the method or product of the invention (step c.1 ), the BIMs may have acquired an increased sedimentation rate. The sedimentation rate can be measured by any suitable method, preferably by the method described in the Materials and Methods. In order to be able to measure the difference between the sedimentation rate of a parent and a BIM, the method is preferably carried out under such conditions that only a minor fraction, for instance between 1 -20%, preferably between 5-10% of the parent cells or biomass present in the suspension is collected in the pellet. The skilled person is very well capable of selecting such conditions for instance by varying the sedimentation time or the g-force, for instance when centrifugation is used. In case of a BIM with an increased sedimentation rate, between 20 and 100% of the cells or biomass present in the suspension may be collected in the pellet. Advantageously, selection based on an increased sedimentation rate provides an efficient method allowing high throughput screening of S. thermophilus strains and mutants thereof. CRISPR mediated BIM's do not provide an increased sedimentation rate, or at least a less increased sedimentation rate than non CRISPR BIM's, and thus could be efficiently removed from a suspension.

Differences between sedimentation rates may be established by measuring the weight of the pellet of the various BIM's after careful removal of the supernatant and then compare the pellet weight of the respective BIM with the pellet weight of the parent. The mean pellet weight increase of the BIM is preferably at least 10% of the pellet weight of the parent, more preferably at least 20%, more preferably at least 50%, more preferably at least 100%, preferably at least 150%, more preferably at least 200%, more preferably at least 250%, even more preferably at least 300% and most preferably at least 350% of the pellet weight of the parent. For instance, in case the pellet weight of the parent is 2 mg and the pellet weight of a BIM 7 mg, then the increase is 5 mg which is a 5/2 ^* 100=250% increase of the pellet weight of the parent.

In an alternative embodiment, step b) of the method of the second aspect of the invention, is not carried out, but instead, the entire suspension comprising the phage sensitive parent strain that has been exposed to the bacteriophage, resulting in a suspension with the phage sensitive parent strain as well as one or more BIMs, is subjected to the sedimentation test. The bacteria with the highest sedimentation rate may be collected and subject to further characterization, for instance via step (d) wherein single colonies of the BIM's are isolated in order to have single strains. Alternatively, the BIMs with the highest sedimentation rate may be collected, cultured in a suitable medium and subjected to step c.1 . This may be repeated once or more.

Step c.2 - an increased chain formation

In another embodiment of the method or product of the invention (step c.2), the BIMs have acquired an increased chain formation. The increased chain formation may be measured by any suitable method, preferably by the microscopic method described in the Materials and Methods. In this method, the chain length or cells per chain (CPC) are determined by counting the individual cells per chain. By counting preferably at least 245 chains, the average number of CPC's is calculated. The average increase in chain length can then be expressed as a percentage using the following formula:

CPCmutant ^— CPCparent

*100%

CPCparent

The percentage increase of the averaged CPC of the BIM is preferably at least 50%, more preferably at least 100%, preferably at least 150%, more preferably at least 200%, more preferably at least 250%, even more preferably at least 300% and most preferably at least 350% of the averaged CPC of the parent. For instance, in case the averaged CPC of the parent is 3 and the averaged CPC of a BIM is 12, then the increase is 9 which is a 9/3 ^* 100=300% increase of the averaged CPC of the parent. Alternatively, the increased chain formation may be measured by a flow cytometer or FACS (fluorescence-activated cell sorter) for example as described in (Ibrahim et al., 2007, Adv Biochem Eng Biotechnol 106: p. 19-39 - Flow cytometry and cell sorting). Using the forward scatter and sideward scatter plot visualization of the FACS, the size of the cells in the suspension becomes evident. Cells with a higher chain length will have a higher forward/sideward scatter plot then the parent bacteria.

In an alternative embodiment, step b) of the method of the second aspect of the invention, is not carried out, but instead, the entire suspension comprising the phage sensitive parent strain that has been exposed to the bacteriophage, resulting in a suspension with the phage sensitive parent strain as well as one or more BIMs, is subjected to the increased chain formation test using the FACS. A subfraction of the bacteria with the highest chain formation rate may be collected by the cell sorter by applying a selection filter and be subject to further characterization, for instance via step (d) wherein single colonies of the BIM's are isolated in order to have single strains. Alternatively, the subfraction of BIMs with the highest chain formation rate may be collected via the cell sorter, cultured in a suitable medium and subjected to step c.2. This may be repeated once or more.

Step c.3 - a reduced phage adsorption

In a further embodiment of the method or productc of the invention (step c.3), the BIMs have acquired a reduced phage adsorption. The reduced phage adsorption may be measured by any suitable method, preferably by the method described in the Materials and Methods. In this method, a suspension of the parent strains or the BIM's was incubated for a certain time with a solution comprising phages at a certain titre (the Initial Phage Titre). Subsequently the suspension was centrifuged to give a pellet and a supernatant comprising a lower titre of phages (the Phage Titre in Supernatant), the difference being adsorbed to the bacterial cells. The phage adsorption may be expressed as the percentage of phages that are exposed to the bacterial cells which is binding to the bacterial cells. This can be calculated using the following formula:

[Initial Phage Titre] - [Phage Titre in Supernatant]

*100%

[Initial Phage Titre]

The phage sensitive parent usually has a high phage adsorption percentage under the experimental conditions chosen, e.g. 80% or more, preferably 85% or more, more preferably 90% or more, more preferably 95% or more, more preferably 97% or more, preferably 98% or more, more preferably 99% or more or even 100% of the phages are binding to the phage sensitive parent. The BIMs that exhibit a reduced phage adsorption have consequently a much lower phage adsorption percentage, for example 60% or less, 55% or less, more preferably 50% or less, more preferably 45% or less, more preferably 40% or less, more preferably 30% or less, more preferably 25% or less, more preferably 20% or less, more preferably 15% or less, more preferably 10% or less and most preferably 0%, which means that the BIM completely lost the ability to bind the phage, while that is still capable of binding to the parent from which the BIM had been derived. Alternatively, the reduced phage absorption may be measured by a fluorescent scanner or plate reader using fluorescently labelled phages. This method differentiates in that of the one described in the Materials and Methods in that the phages are pre labelled with a fluorescent label (for example by incubation with a fluorescent label) and that initial phage tire and phage titre in supernatant is a function of the fluorescence.

In yet an alternative embodiment, step c.3 of the method of the second aspect of the invention, is not carried out, but instead, the entire suspension comprising the phage sensitive parent strain that has been exposed to a fluorecently labbeled bacteriophage, resulting in a suspension with the phage sensitive parent strain as well as one or more BIMs, is subjected to the reduced phage absorption test using a fluorescent cell sorter (FACS). A subfraction of the bacteria with the lowest absorption rate may be collected by the cell sorter by applying a fluoresence selection filter and be subject to further characterization, for instance via step (d) wherein single colonies of the BIMs are isolated in order to have single strains. Alternatively, the subfraction of BIMs with the lowest absorption rate may be collected via the cell sorter, cultured in a suitable medium and exposed to freshly labbeled phage and subjected to step c.3. This may be repeated once or more.

Preferably, the one or more BIMs which, compared to bacteriophage sensitive parent bacterium, has an increased sedimentation rate and/or an increased chain formation and/or a reduced phage adsorption is further subjected to comparing the CRISPR loci of the parent strain with the CRISPR loci of the bacteriophage insensitive mutant and selecting one or more BIMs of which the CRISPR loci is identical to the CRISPR loci of the parent strain. The advantage of comparing the CRISPR loci of the selected BIM which, compared to bacteriophage sensitive parent bacterium has an increased sedimentation rate and/or an increased chain formation, with the parent loci is that BIMs are provided having a phage resistance mechanism other than CRISPR.

In a third embodiment, the method of the invention combines the steps a-d of the first embodiment of the method of the invention followed by the steps c.1 -c.3 of the second embodiment of the method of the invention. In this third embodiment, the one or more BIMs of which the CRISPR loci are identical to the CRISPR loci of the parent strain, are further subjected to selecting the bacteriophage insensitive mutant which, compared to bacteriophage sensitive parent bacterium, has an increased sedimentation rate and/or an increased chain formation; and/or a reduced phage adsorption.

In a fourth embodiment, the method of the invention combines the steps a-c of the second embodiment of the method of the invention followed by the steps c and d of the first embodiment of the method of the invention. In this fourth embodiment, the one or more BIMs which, compared to bacteriophage sensitive parent bacterium, has an increased sedimentation rate and/or an increased chain formation and/or a reduced phage adsorption is further subjected to comparing the CRISPR loci of the parent strain with the CRISPR loci of the bacteriophage insensitive mutant and selecting one or more BIMs of which the CRISPR loci is identical to the CRISPR loci of the parent strain. Preferably, the present method, including the disclosed embodiments, further comprises culturing the one or more selected bacteriophage insensitive mutant in a culture medium, and/or recovering the bacteriophage insensitive mutant from the culture medium to provide a starter culture composition. "Starter culture" is defined herein as a preparation containing microbial cells that is intended for, or suitable for, inoculating a medium to be fermented. Such Starter cultures are generally referred to as direct vat set (DVS) or direct-to-vat inoculation (DVI) cultures or bulk starter cultures. The provision of a starter culture is advantageous since starter cultures can be inoculated directly into milk without intermediate transfer and/or propagation. Preferably, culturing is carried out at conditions such as temperature and pH control conducive to the growth of the microorganisms, or preferably S. thermophilus for a period of time until the desired cell concentration and activity of the culture are reached. The skilled person is able to determine the correct conditions for culturing S. thermophilus, or the desired microorganism.

Preferably, to the present bacteriophage insensitive mutant, or to the starter culture composition, an additive is added. For example a cryoprotectant is added. A "cryoprotectant" is defined herein as a substance used to protect cells or tissues from damage during freezing and thawing. The cryoprotectant may be any additive as long as it protects cells or tissues from damage during freezing and thawing.

Examples of cryoprotectants include, but are not limited to, sugars (e.g. sucrose, fructose, trehalose), polyalcohols (e.g. glycerol, sorbitol, mannitol), polysaccharides (e.g. celluloses, starch, gums, maltodextrin), polyethers (e.g. polypropylene glycol, polyethylene glycol, polybutylene glycol), antioxidants (e.g. natural antioxidants such as ascorbic acid, beta-carotene, vitamin E, glutathione, chemical antioxidants), oils (e.g. rapeseed oil, sunflower oil, olive oil), surfactants (e.g. Tween ^® 20, Tween ^® 80, fatty acids), peptones (e.g. soy peptones, wheat peptone, whey peptone), tryptones, vitamins, minerals (e.g. iron, manganese, zinc), hydrolysates (e.g. protein hydrolysates such as whey powder, malt extract, soy), amino acids, peptides, proteins, nucleic acids, nucleotides, nucleobases (e.g. cytosine, guanine, adenine, thymine, uracil, xanthine, hypoxanthine, inosine), yeast extracts (e.g. yeast extracts of Saccharomyces spp., Kluyvermomycesa spp., or Torula spp.), beef extract, growth factors, and lipids.

Preferably, the present method further comprises a step of freeze drying or freezing the present bacteriophage insensitive mutant. More preferably freeze drying to provide a dry powder. Alternatively freezing to provide a frozen matrix, such as frozen pellets. Freeze-drying is a technique well known in the art and may comprise the steps of freezing microorganisms to get frozen material and subsequently reducing the surrounding pressure while adding enough heat to allow the frozen water in the frozen material to sublime directly from the solid phase into the gas phase. Freeze-drying equipment that can be used includes, but is not limited to, rotary evaporator freeze- driers, manifold freeze-driers and tray freeze-driers. If necessary, a secondary step can be performed that aims to remove unfrozen water molecules. It is well within the experience of the person skilled in the art to establish a suitable temperature and pressure profile to achieve satisfactory freeze-drying. The freeze-dried material can be a powder or a granule.

In a second aspect, the invention provides a bacteriophage insensitive mutant of a microorganism parent strain, obtainable by the present method. Preferably the bacteriophage insensitive mutant has an increased sedimentation rate and/or an increased chain formation compared to the microorganisms parent strain. Surprisingly, the present inventors found that the BIMs provided by the present method have an increased phage robustness than CRISPR BIMs.

Preferably, the invention provides a BIM derived from a bacteriophage sensitive S. thermophilus parent strain. This bacteriophage insensitive mutant may be

• obtainable by the first, third or fourth embodiment of the method of the invention and wherein the CRISPR loci of the BIM are identical to the CRISPR loci of the parent S. thermophilus strain.

• obtainable by the second, third or fourth embodiment of the method of the invention and wherein the BIM has an increased sedimentation rate and/or an increased chain formation and/or a reduced phage adsorption compared to the phage sensitive parent S. thermophilus strain.

• obtainable by the third or fourth embodiment of the method of the invention and wherein the CRISPR loci of the BIM are identical to the CRISPR loci of the parent S. thermophilus strain and wherein the BIM has an increased sedimentation rate and/or an increased chain formation and/or a reduced phage adsorption compared to the phage sensitive parent S. thermophilus strain.

Preferably, the present bacteriophage insensitive mutant has a pellet weight increase of least 10% of the pellet weight of the parent, more preferably at least 20%, more preferably at least 50%, more preferably at least 100%, preferably at least 150%, more preferably at least 200%, more preferably at least 250%, even more preferably at least 300% and most preferably at least 350% of the pellet weight of the parent.

Preferably, the present bacteriophage insensitive mutant has a percentage increase of average chain length or average cells per chain (CPC) of at least 50%, more preferably at least 100%, preferably at least 150%, more preferably at least 200%, more preferably at least 250%, even more preferably at least 300% and most preferably at least 350% of the averaged CPC of the parent.

Preferably, the present bacteriophage insensitive mutant has a phage adsorption percentage of 60% or less, preferably 55% or less, more preferably 50% or less as compared to the phage adsorption of the parent.

Preferably, the present bacteriophage insensitive mutant has a reduced susceptibility to, or is insensitive for, one or more phages comprising a nucleotide sequence selected from the group consisting of SEQ ID NO 1 , SEQ ID NO 2, SEQ ID NO 3, SEQ ID NO 4 and SEQ ID NO 5 or comprising a nucleotide sequence having 80%, preferably 85%, more preferably 90%, most preferably 95% or even 96%, 97%, 98% or 99% sequence identity with the nucleotide sequence selected from the group consisting of SEQ ID NO 1 , SEQ ID NO 2, SEQ ID NO 3, SEQ ID NO 4 and SEQ ID NO 5. The term sequence identity is defined as the number of corresponding positions in an alignment showing an identical nucleic acid in both sequences divided by the total length of the alignment after subtraction of the total number of gaps in the alignment.

Preferably, the present bacteriophage insensitive mutant is as deposited in deposit numbers CBS136256, CBS136255 or CBS138555, or bacteriophage insensitive mutant derived from deposit CBS136256, CBS136255 or CBS138555. In other words, the present bacteriophage insensitive has preferably a sedimentation rate, an increased chain formation; and/or a reduced phage adsorption as found in CBS136256, CBS136255 or CBS138555.

In a third aspect, the invention relates to a starter culture composition comprising the present bacteriophage insensitive mutant. Preferably, the present starter culture composition is suitable for inoculation of a medium to be fermented on an industrial scale. Preferably the present starter culture composition is suitable for inoculation of milk for the production of fermented milk products. More preferably the starter culture composition comprises an additive. An example of an additive is a cryoprotectant. Additionally the starter culture composition may comprise other microorganisms or other lactic acid bacteria such as lactic acid bacteria belonging to the genera Lactococcus, Leuconostoc or Lactobacillus. More preferably the starter culture composition comprises a combination of the present bacteriophage insensitive mutant with L. bulgaricus, or Lactobacillus delbrueckii subsp. bulgaricus. Such a mixed starter culture is advantageous for the provision of yoghurt. Alternatively, for the provision of cheese, the present starter culture composition comprises a combination of the present bacteriophage insensitive mutant with Lactococcus lactis.

Preferably, the starter culture composition is frozen, preferably in the form of frozen pellets such as individual frozen pellets. Preferably the frozen pellets comprises as additive formate, such as sodium formate. Preferably the present frozen pellets have an average diameter within the range of 0.1 to 10 mm. The advantage of frozen pellets is that they will not stick and flow freely which allows a convenient dosing of the frozen pellets. Preferably the frozen pellets comprises a content of viable bacteria, preferably S. thermophilus, of at least 10 ⁹ colony forming units (CFU) per gram frozen pellets. The advantage of such concentrated frozen material is that only low amounts of frozen material is necessary to inoculate milk in industrial milk fermentation processes.

Alternatively the starter culture composition is freeze-dried. A freeze-dried starter composition may be in the form of a pellet, granule, tablet or a powder. Most preferably as a powder. The freeze-dried culture compositions can be stored and transported without refrigeration for extended periods of time under dry conditions. However, storage below 0°C is recommended, more preferably below 15°C.

Alternatively, the present starter culture composition may be in liquid form.

In a fourth aspect, the invention relates to a container comprising the present bacteriophage insensitive mutant or comprising the present starter culture composition. The advantage of packing the present bacteriophage insensitive mutant or starter culture composition in a container is the ease of storage and transport. Preferably the present container is a commercial relevant package. An example of a commercial relevant package is a container comprising at least 50 or 500 gram frozen material when formulated in a frozen form, or comprising at least 50, 200 or at least 500 U when formulated in a freeze-dried form.

In a fifth aspect, the invention provides a process for the production of a dairy product such as a fermented milk product or cheese comprising the use of one or more of the BIM of a bacteriophage sensitive S. thermophilus parent strain as disclosed hereinbefore.

In a sixth aspect, the invention provides the use of the BIM of a bacteriophage sensitive S. thermophilus parent strain as disclosed hereinbefore in a process for the production of a dairy product, such as a fermented milk or cheese.

Figure Legends

Figure 1 : Observed sedimentation of S. thermophilus strain ST802 parent (tube A) and its derived BIMs BIMST802-D1 B-L-3 (non-CRISPR BIM; tube B) and BIMST802-D1 B-L- 6 (non-CRISPR BIM; tube C) and BIMST802-D3A-S/L-1 a (CRISPR BIM; tube D).

Figure 2: Observed sedimentation of S. thermophilus strain ST23 parent (tube A) and its derived BIMs BIMST23-D1A-L-4 (non-CRISPR BIM; tube B).

Figure 3: Observed sedimentation of S. thermophilus strain 100-E parent (tube A) and its derived BIMs BIM100-E-D1A-L-7 (CRISPR BIM, tube B) and BIM100-E-D1A-L-5 (non- CRISPR BIM, tube C).

Figure 4: Light microscope images of S. thermophilus strain ST802 parent (photograph A) and its derived BIMs BIMST802-D1 B-L-3 (non-CRISPR BIM; photograph B), BIMST802-D1 B-L-6 (non-CRISPR BIM; photograph C) and BIMST802-D3A-S/L-1 a (CRISPR BIM; photograph D).

Figure 5: Light microscope images of S. thermophilus strain ST23 parent (photograph A) and its derived BIMST23-D1A-L-4 (non-CRISPR BIM; photograph B).

Figure 6. Light microscopic analysis of S. thermophilus strain 100-E parent (photograph A) and derived BIMs BIM100-E-D1A-L-7 (CRISPR BIM, photograph B) and BIM100-E- D1A-L-5 (non-CRISPR BIM, photograph C).

Figure 7: PCR profiling of strains ST802, ST23 and derived BIMs. Lanes 1 and 6: Molecular weight marker X (Roche, Switzerland); lane 2: ST802 parent; lane 3: BIMST802-D1 B-L-3; lane 4: BIMST802-D1 B-L-6; lane 5: BIMST802-D3A-S/L-1 a, lane 7: ST23 parent, lane 8: BIMST23-D1A-L-4.

Figure 8: PCR profiles of strain 100-E and its derived BIMs. Lanes 1 and 6: 1 kb Full Scale DNA Ladder (Fisher Scientific, U.S.A); Lane 2: S. thermophilus 100-E parent; Lane 3: BIM100-E-D1A-L-5 (non-CRISPR BIM); Lane 4: BIM100-E-D1A-L-7 (CRISPR BIM); Lane 5: Negative control.

Figure 9: Representative photograph showing phage 100-E-D1A-L plaque sizes on S. thermophilus 100-E parent, and its derived BIMs BIM100-E-D1A-L-7 and BIM100-E- D1A-L-5 which are labelled as 100-E-D1A-L-B7 and 100-E-D1A-L-B5, respectively.

MATERIALS AND METHODS

1. Bacterial growth conditions

Streptococcus thermophilus strains were routinely grown from 10% glycerol stocks, 20% Reconstituted Skimmed Milk (RSM) stocks or from single colonies overnight at 42°C in M17 Broth (Oxoid, U.K.) supplemented with 0.5% lactose (LM17) or on plates using LM17 containing 10 g/L technical agar (Merck, Germany). In phage enumeration assays, adapted from D. Lillehaug, 1997 (Journal of applied microbiology 83, (1 ), 85-90 - "An improved plaque assay for poor plaque-producing temperate lactococcal bacteriophages"), LM17 broth was supplemented with 0.25% glycine (Oxoid, U.K.), 10 mM CaCI ₂ (Oxoid, U.K.) and either 10 g/L (solid agar base) or 4 g/L (semi-solid overlay) technical agar. The semi-solid agar was sterilised by autoclaving at 121 °C for 15 minutes whereas the solid agar was boiled for 7 minutes in a microwave.

2. Isolation and selection of (bacterio)phages

Whey samples from dairy plants producing fermented milk products were obtained and analysed for the presence of phages against S. thermophilus ST802, S. thermophilus ST23 and S. thermophilus 100-E using the spot assay described below under "(Bacterio)phage assays". Single plaques were isolated by twice single plaque purification on semi-solid overlays. Phages were then propagated as follows: 10 ml LM17 broth was inoculated with 2 ml of an overnight grown culture of the host strain (S. thermophilus ST802, S. thermophilus ST23 or S. thermophilus 100-E) and allowed to grow for 1.5-2.0 hours. Then, a single plaque was added to the growing culture, mixed well and incubated at 42°C for a further 2-4 hours or at 30°C overnight. The lysed culture was centrifuged and the supernatant filtered (0.45 μηι). The filtered supernatant was used as the phage stock for subsequent assays. Table 1 summarizes the phages that were obtained.

S. thermophilus ST802 = DS67009 (CBS136256) was deposited on 2 October 2013 with the Centraal Bureau for Schimmelcultures, Uppsalalaan 8, 3508 AD in Utrecht, The Netherlands.

S. thermophilus ST23 = DS64987 (CBS 136255) was deposited on 2 October 2013 with the Centraal Bureau for Schimmelcultures, Uppsalalaan 8, 3508 AD in Utrecht, The Netherlands.

S. thermophilus 100-E = DS64990 (CBS138555) was deposited on 15 July 2014 with the Centraal Bureau for Schimmelcultures, Uppsalalaan 8, 3508 AD in Utrecht, The Netherlands.

Table 1. A list of strains and phages used in this study.

3. Generation of BIMs (Bacteriophage Insensitive Mutants)

Spontaneous BIMs of the parent strains mentioned in Table 1 were generated using one of two methods.

3.1 BIMs of Streptococcus thermophilus ST802

BIMs of S. thermophilus ST802 were isolated by one of two methods.

(1 ) BIMs against phage ST802-D1 B-L were generated by adding 400 μΙ fresh overnight culture of S. thermophilus ST802 and 10 μΙ of neat phage lysate (phage ST802-D1 B-L isolated from a single plaque; titre approx. 1 x 10 pfu/ml) to 4 ml of soft LM17 agar, followed by spreading this suspension on solid agar. Colonies, representing potential BIMs, growing in the top layer were twice single colony purified and subjected to phage assays and CRISPR sequencing as described below. Two BIMs were thus obtained and characterized (see below): S. t ermop ilus BIMST802-D1 B-L-3, S. t ermop ilus BIMST802-D1 B-L-6.

(2) A third BIM of S. thermophilus ST802, namely BIMST802-D3AS/L-1A was isolated using a method as described below (to isolate S. thermophilus BIMST23-4) with the addition of 20 overnight passages in 10% RSM and a 1 % lysate containing a mixture of phages <|)D3A-S and <|)D3A-L (titre approx. 1 x 10 ⁸ pfu/ml).

3.2 BIMs of Streptococcus thermophilus ST23

BIMs of S. thermophilus ST23 were isolated by inoculating 1 ml of 10% (w/v) RSM with 1 % of an overnight culture of S. thermophilus ST23 and 1 % of a particular phage lysate (phages ST23 D1A-L and D2A-L, each produced from a single plaque; titer approx. 1 x 10 ⁸ pfu/ml). The milk with the added culture and phage was then incubated at 42°C overnight or until clotting was observed. Potential BIMs were selected on LM17 agar, twice single colony purified and subjected to phage assays and CRISPR sequencing as described below. BIMST23-D1A-L-4 was generated in this manner.

3.3 BIMs of Streptococcus thermophilus 100-E

BIMs of S. thermophilus 100-E against phage 100-E-D1A-L were isolated as described for BIMs BIMST802-D1 B-L-3 and BIMST802-D1 B-L-6 (section 3.1 (1 ) above). Two BIMs were selected for further characterization (see Example 3 below), and were designated BIM100-E-D1A-L-7 (CRISPR BIM) and BIM100-E-D1 A-L-5 (non-CRISPR BIM).

4. (Bacterio)phage assays

Spot assays were performed by seeding the LM17 semi-solid agar overlay with 400 μΙ fresh overnight culture and applying 5-10 μΙ of phage lysate in a grid format, as described by Dupont et al. 2005 (Journal of Applied Microbiology 98, (4), 1001-1009. "Detection of lactococcal 936-species bacteriophages in whey by magnetic capture hybridization PCR targeting a variable region of receptor-binding protein genes). Plates were then allowed to dry and incubated anaerobically overnight at 42°C. A clear zone indicating lysis of the bacterial lawn by the applied phage was recorded as '+', whereas absence of lysis was recorded as

For phage enumeration, plaque assays were performed by adding 500 μΙ culture and 10 μΙ of neat or appropriately diluted phage suspension/lysate to 4 ml soft agar, followed by plating on LM17 agar plates as described above with subsequent overnight incubation at 42°C. Efficiency of plaquing (EOP) was calculated by dividing the obtained titre of a given phage on the test strain by the titre of the same phage on the parent strain.

5. Sedimentation assays

5. thermophilus strains were routinely grown from 10% glycerol stocks, 20% Reconstituted Skimmed Milk (RSM) stocks or from single colonies overnight at 42°C in LM17 broth (as described in section 1 of the MATERIALS AND METHODS). The parent strains and BIMs were treated identically and after overnight incubation at 42°C, visual assessment of the cultures was performed to observe the growth characteristic of the cultures in broth. Only if the cultures were consistently observed to sediment to the base of the tube or along the wall of the tube was the phenotype considered relevant. In all cases, the parent strain was observed to sediment to a markedly reduced degree after overnight growth. In order to measure the increase in pellet weight (and hence relative amount of sedimentation), overnight cultures of each parent and derived BIM were prepared in LM17 as described above and the supernatant carefully removed. The remaining pellet was suspended in 250 μΙ sdH ₂ 0 and transferred to a fresh Eppendorf tube. The mixture was then made up to a volume of 500 μΙ using sdH ₂ 0 and transferred to a section of pre-weighed blotting paper. The paper was then dried at 75°C for 15 minutes and weighed again, with the increase in dry weight of the blotting paper taken as the pellet weight for each sample. The increase in the weight of the pellet of each derived BIM relative to the parent was then calculated. In this and all cases, the unpaired student t-test was used to determine significant differences between the parent and derived BIMs datasets.

6. Adsorption assays

Determination of phage adsorption to parent strains and BIMs was determined as adapted from Garvey et al. 1996 (Applied environmental microbiology 62, (2), 676-679 "The Lactococcal plasmid pNP40 encodes a third bacteriophage resistance mechanism, one which affects phage DNA penetration"): 10 ml LM17 broth was inoculated with the appropriate strain from an overnight culture and grown at 42°C until the OD ₆ oonm reached at least 0.5 but did not surpass 0.53. 700 μΙ of culture was transferred to a micro centrifuge tube and centrifuged at 2000 (for strains ST802 and ST23, and their derivatives) or 5000 (for strain 100-E and derivatives) x g for 10 minutes to pellet the cells. The cells were resuspended in 700 μΙ of ¼ strength Ringers solution (Merck, Germany) and an equal volume of the appropriate phage lysate at a titre of approximately 1 x 10 ⁵ pfu/ml was added to the tube or to 700 μΙ buffer control. The mixture was incubated at 42°C for 12 minutes, centrifuged at 15,000 x g for 3 minutes and 500 μΙ of residual phage was immediately removed. The phage preparations were stored at 4°C until plaque assays were performed on the parent strain, as described above. Calculation of adsorption levels (as a percentage of total number of phages present) was performed as follows: ([Control phage titre - Free phage titre in supernatant] / Control phage titre) ^χ 100%.

7. Staining & visualisation of cells to determine chain length

Morphological assessment and comparison of the parent strains and derived BIMs was performed via wet mount. A drop of fresh overnight culture was placed on a glass slide and a cover slip immediately placed on top of the sample. Each sample was then visualised under 100X magnification using a light microscope (Leica DM1000, Germany). Images were captured using a mounted Leica DFC290HD camera and processed using Leica Application Suite software. The percentage increase in chain length or cells per chain (CPC) of derived BIMs relative to the parent strains was calculated firstly by determining the average number of individual cells per chain in all samples by counting at least 25 chains. The average increase in length was then expressed as a percentage using the following formula: (CPC _mu tant - CPCparent) CPCparent x 100%).

8. PCR screening & CRISPR locus sequencing

All BIMs generated were subjected to PCR profiling to confirm their relatedness to the parent strains from which they were derived. This was performed on single colonies of each parent strain and BIM using the '(GTG)5' primer (Gevers D., Huys G. and Swing J., 2001 , Applicability of rep-PCR fingerprinting for identification of Lactobacillus species FEMS Microb. Letters 205, 31 -36 (see Table 2)). The PCR conditions were as follows: 95°C x 10 min, followed by 30 cycles of 95 °C x 15 s, 40 °C x 30 s and 72 °C for 8 min with a final extension step of 72 °C for 16 min.

BIMs generated were purified and the CRISPR loci amplified by PCR and sequenced to determine acquisitions or alterations to the spacer content of the BIMs. CRISPR-1 , CRISPR-2 and CRISPR-3 repeat/spacer arrays for each strain were amplified individually using a single colony of the appropriate strain as template material for the PCR and primers described previously by Horvath et al. 2008 (Journal of Bacteriology 190 (4): 1401 -1412 "Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. ")

The PCR conditions were as follows: 95°C x 10 min, followed by 30 cycles of 95°C x 15 s, 55°C x 15 s and 72°C for either 2 min 45 s (CRISPR-1 ) or 1 min (CRISPR-2 and CRISPR-3) with a final extension step of 72 °C for 10 min.

The PCR generated products were visualised on a 1 % agarose (Fisher Scientific, USA) gel and purified using a PCR purification spin kit (Genomed, Germany). Sequencing was performed by MWG Biotech (Eurofins, Germany), firstly using the primers used to amplify the loci, then internally using synthetic primers based on a unique spacer of each repeat/spacer array in order to complete the sequencing of the CRISPR loci, where required. CRISPRs were assembled using the Seqman program (DNAstar) and CRISPR arrays were visualised using the online CRISPR finder program (http://crispr.u-psud.fr).

Table 2. PCR primers used in this study

10. Acidification assay

An acidification experiment was performed using a CINAC pH measurement system. For this purpose, overnight cultures of strains were generated in triplicate using 2 mL of 10% RSM with 20 μΙ_ of stock solution of the strains in 50 mL tubes with subsequent incubation at 42°C. The next day fresh 9.5% Campina QC-Milkbase was added to a final volume of 20 ml, mixed and the entire 20 mL was added to a milk bottle containing 180 mL 9.5% Campina QC-Milkbase, followed by overnight incubation at 42°C. pH was measured online (every 2 minutes) using a pH probe (Mettler Toledo HA405-DXK-08).

11. Demonstration of non-CRISPR BIM robustness

In order to demonstrate the relative robustness of non-CRISPR BIMs relative to CRISPR BIMs of 100-E, a phage plaque measurement and propagation experiment was performed. Firstly, the 100-E parent strain and both BIM100-E-D1A-L-5 and BIM100-E- D1A-L-7 were exposed a second time by standard plaque assay (as described in the MATERIALS AND METHODS) to the phage that was initially used in the challenge. While a high level of resistance to this phage was observed for both BIMs, phage escape mutants were also observed in the overlay agar (Table 13). Wild type and escape mutant plaques were measured using a digital callipers (Workzone, U.K.) on subsequent identical experiments, the results of which are shown in Table 17. A representative image illustrating the differences in plaque sizes on the respective strains is shown in Figure 9. Single plaques each of wild-type phage (exposed to 100-E parent), CRISPR-escape mutant (CEM; exposed to BIM100-E-D1A-L-7) and non-CRISPR escape mutant (NCEM; exposed to BIM100-E-D1A-L-5) were then propagated on their respective host strains. This was performed as described in the MATERIALS AND METHODS, with the following modifications to increase efficiency of propagation: a 1 % inoculum of each strain was added to 10 ml of pre-warmed LM17 broth (supplemented with 10 mM CaCI ₂ (Oxoid)) at 37°C. A single plaque of the appropriate phage was picked using a sterile pipette tip and immediately added to the tube. The propagation was allowed to proceed for 4 hours at 37°C before filtration (0.45 μηι) and plaque assay on the appropriate strain, the results of which are presented in Table 18.

A 'second round' (2°) propagation was then performed in order to confirm the non- CRISPR BIM robustness over a series of cycles. The escape mutant lysates generated from the plaque propagations (described above) were diluted to approximately 10 ⁴ pfu/ml. A 1 % inoculum of the appropriate strain was added from a fresh overnight culture to pre-warmed LM17 broth at 42°C and allowed to grow for 1 hour. CaCI ₂ (Oxoid) was added to a final concentration of 10 mM. 1 % of the appropriate phage lysate was added and the propagation proceeded for 4 hours at 42°C before filtration (0.45 μηι) and plaque assay (as described above) on the appropriate strain, the results of which are shown in Table 18.

EXAMPLES Example 1

Bacteriophage Insensitive Mutants (BIMs) of S. thermophilus ST802 1.1 Phage sensitivity

Bacteriophages against S. thermophilus ST802 were isolated as described in the MATERIALS AND METHODS. BIMs against phage φ5Τ802-ϋ1 Β-ί or against φ5Τ802- D3A-S and <|)ST802-D3A-L were isolated, purified (by picking a single colony and growing in LM17 broth overnight at 42°C), and subjected to spot assays. The BIM phenotype and stability was confirmed by plaque assays as described in the MATERIALS AND METHODS, the results of which are displayed in Table 3. Table 3. Relative efficiencies of plaquing (EOP) of phages of Streptococcus thermophilus strain ST802 and derived BIMs.

BIM was challenged with a phage lysate containing 1 x 10 pfu/ml phages.

Note 2: In derived BIM nomenclature, D1 B-L or D3A-SL denotes the phage(s) against which the BIM was generated.

1.2 CRISPR sequencing

The loci of CRISPR-1 , CRISPR-2 and CRISPR-3 of S. thermophilus ST802 and its BIMs were sequenced as described in paragraph 8 of the Materials and Methods. Table 4 shows that the sizes of the CRISPR-1 , CRISPR-2 and CRISPR-3 (2545 bp, 258 bp and 827 bp, respectively) for BIMST802-D1 B-L-3 and BIMST802-D1 B-L-6, as well as the spacer number and content were identical in the parent and BIMs. No CRISPR locus could be detected using CRISPR-4 repeat GTTTTTCCCGCACACGCGGGGGTGATCC (SEQ ID No. 20) as a consensus signature, nor by using the online CRISPR finder program (http://crispr.u-psud.fr).

The result shows that phage insensitivity was conferred to BIMST802-D1 B-L-3 and BIMST802-D1 B-L-6 by a mechanism other than CRISPR-1 , CRISPR-2 or CRISPR-3. The adsorption results as well as the sedimentation results suggest that these BIMs carry mutations and/or adaptations in the cell envelope and/or phage receptor binding site. In the case of BIMST802-D3A-S/L-1 a, the addition of three new spacers at the leader end of the CRISPR-1 locus and two at the leader end of the CRISPR-3 locus indicate that phage insensitivity was conferred by the CRISPR mechanism.

Table 4. Summary of CRISPR in S. thermophilus strain ST802 and derived BIMs

#

Strain CRISPR Size Direct repeat Terminal repeat spacers

ST802 (parent) 1 2543 bp 5 -GTTTTTGTACTC 38 5 -GTTTTTGTACTC

TCAAGATTTAAGT TCAAGATTTAAGTA

BIMST802-D1 B-L-3 1 2543 bp 38

AACTGTACAAC-3' ACTGTACAGT-3'

BIMST802-D1 B-L-6 1 2543 bp (SEQ ID NO 21 ) 38 (SEQ ID NO 22)

1.3 PCR profiling

PCR profiling using the (GTG)5 primer and method described above was performed on all BIMs and their parent strains to confirm their relatedness to the parent strain from which they were derived. The results were visualised on a 1 % agarose gel (shown in Figure 5) and, taken together with the results of CRISPR locus sequencing (described above), confirm that all BIMST802-D1 B-L-3 and BIMST802-D1 B-L-6 are direct derivatives of the corresponding phage-sensitive S. thermophilus strain ST802.

1.4 Mutant phenotype

All BIMs showed similar acidification activities compared to the parent (data not shown). While the proposed CRISPR-mediated BIM of ST802 did not appear to sediment compared to the parent (Figure 1 , Tubes A and D) proposed non-CRISPR BIMs exhibited a distinctive sedimentation phenotype relative to the parent and to each other (Figures 1 , Tubes A, B and C). The degree to which each BIM sediments relative to the parent strain is indicated by an increase in pellet weight, shown in Table 5 below. It is clear that the proposed non-CRISPR BIMs produce a heavier pellet than both the parent and CRISPR BIM strains. Morphological analysis using simple staining of cells combined with light microscopy revealed that the BIMs form cell aggregates and long chains in comparison with the parent strain (Figures 3A, 3B and 3C). The percentage increase in chain length is indicated in Table 6 below. This increase in chain length may also explain the observed sedimentation phenotype in Figure 1 : BIMST802-D1 B-L-3 and BIMST802- D1 B-L-6 sediment more than the parent strain, while BIMST802-D3A-S/L-1 a does not. Table 5.

Pellet weights of parent and BIMs of S. thermophilus strain ST802.

Table 6.

Relative cells per chain (CPC) of parent and BIMs of S. thermophilus strain ST802.

1.5 Adsorption of phages

Adsorption assays were performed to determine the level of adsorption of phages to both the parent strains and the derived BIMs, the results of which are shown in Table 7. Each of the infecting phages adsorb efficiently to the parent strain (adsorption levels are = 80%). In contrast, phage adsorption to two of the BIMs is markedly reduced which indicates that in two out of three cases the BIMs confer resistance through an adsorption blocking mechanism. able 7: Adsorption of phages to parent and BIMs of S. thermophilus strain ST802.

Long chain

Strain <PST802-D1B-L 4>ST802-D3A-S 4>ST802-D3A-L formation?

ST802 (parent) No 89 ± 3% 89 ± 9% 94 ± 2%

BIMST802-D1 B-L-3 Yes 32 ± 10% 47 ± 15% 25 ± 17%

p-value 0.0013 0.014 0.0009

BIMST802-D1 B-L-6 Yes 6 ± 1 % 29 ± 25% 15 ± 5% p-value 3.12x10 ^"6 0.029 3.22x10 ^"5

BIMST802-D3A-S/L-

No 100 ± 0% 99 ± 0% 99 ± 0% 1 a

p-value 0.006 0.12 0.030

Example 2

Bacteriophage Insensitive Mutants of S. thermophilus ST23

2.1. Phage sensitivity

Bacteriophages against S. thermophilus ST23 were isolated as described in the MATERIALS AND METHODS. A BIM against phage <|)ST23-D1A-L was isolated, purified (by picking a single colony and growing in LM17 broth overnight at 42°C) and subjected to spot assays and confirmatory plaque assays as described in the MATERIALS AND METHODS, the results of which are shown in Table 8.

Table 8. Relative efficiencies of plaquing (EOP) of phages of Streptococcus thermophilus strain ST23 and derived BIM.

Note: < denotes the limit of detection i.e. no plaques were detected when the derived BIM was challenged with a phage lysate containing 1 x 10 ⁹ pfu/ml phages.

* A reduction in plaque size (by approximately 50%) and an increase in plaque haziness was also observed.

2.2 CRISPR sequencing

PCR-generated CRISPR-1 , CRISPR-2 and CRISPR-3 size profiles (1952 bp, 843 bp and 1289 bp respectively) of ST23 and its derivatives indicated that no additions were made to the arrays and this result was confirmed by sequencing: both spacer number and content were identical to those of the parent - see Table 9. No CRISPR locus could be detected using CRISPR-4 repeat GTTTTTCCCGCACACGCGGGGGTGATCC (SEQ ID No. 20) as a consensus signature, nor by using the online CRISPR finder program (http://crispr.u-psud.fr). Table 9. Summary of CR SPR in S. thermophilus strain ST23 and derived BIMs

The result in Example 2 shows that phage resistance was conferred to BIMST23- D1A-L-4 by a mechanism other than CRISPR. The adsorption results (section 2.5) suggest mutations and/or adaptations in the cell wall and/or phage receptor binding site.

2.3 PCR profiling

PCR profiling using the (GTG)5 primer and method described above was performed on all BIMs and their parents to confirm their relatedness to the parent strains from which they were derived. The results were visualised on a 1 % agarose gel (shown in Figure 5) and, taken together with the results of CRISPR locus sequencing (described above), confirm that BIMST23-D1A-L-4 is a direct derivative of the corresponding phage- challenged S. thermophilus strain ST23.

2.4 Mutant phenotype

S. thermophilus BIMST23-D1A-L-4 was shown to exhibit similar acidification activities compared to the parent (data not shown). Furthermore, BIMST23-D1A-L-4 also aggregates and forms longer cell chains than the parent, as shown in Figures 4A and 4B, respectively. The proposed non-CRISPR BIM exhibited a distinctive sedimentation phenotype relative to the parent (Figure 2 - Tubes A and B). The degree to which the BIM sediments relative to the parent strain is indicated by an increase in pellet weight, shown in Table 10 below. The percentage increase in chain length is indicated in Table 1 1 .

Table 10. Pellet weights of parent and BIM of S. thermophilus strain ST23. Pellet weight Mean pellet weight

Strain/BIM p-value

(g) increase in g (%)

ST23 0.0036 ± 0.0001 N/A N/A

BIMST23-D1A-L-

0.0044 ± 0.0002 0.0008 (22%) 0.009 4

Table 11. Relative cells per chain (CPC) of BIM of S. thermophilus strain ST23.

2.5 Adsorption of phages

Adsorption assays were performed to determine the level of adsorption of phages to both the parent strains and the derived BIM, the results of which are shown in Table 7. Each of the infecting phages adsorb optimally to the parent strain (adsorption levels are = 80%). In contrast, phage adsorption to the BIM is markedly reduced and indicates that the BIM confers resistance through an adsorption blocking mechanism.

Table 12. Adsorption of phages to parent and BIM of S. thermophilus strain ST23.

Example 3

Bacteriophage Insensitive Mutants of S. thermophilus 100-E 3.1 Phage sensitivity

Bacteriophages against S. thermophilus 100-E were isolated as described in the MATERIALS AND METHODS section. BIMs against phage φΙ ΟΟ-Ε-DIA-L were isolated, purified (by picking a single colony and growing in LM17 broth overnight at 42°C) and subjected to spot assays and confirmatory plaque assays as described in the MATERIALS AND METHODS, the results of which are shown in Table 13. BIM100-E- D1A-L-7 showed a high level of resistance to the phage that was used in the challenge only, while BIM100-E-D1A-L-5 appeared insensitive to this phage as well as a distinct phage (phage 100-E-D2A-L; Table 13).

Table 13. Relative efficiencies of plaguing (EOP) of phages of Streptococcus thermophilus strain 100-E and derived BIMs.

3.2 CRISPR sequencing

PCR-generated CRISPR-1 , CRISPR-2 and CRISPR-3 size profiles (2409/2476 bp, 1 15 bp and 1358 bp respectively) of 100-E and its derivative BIMs indicated that no additions were made to the arrays of BIM100-E-D1A-L-5. This result was confirmed by sequencing: both spacer number and content were identical to those of the parent - see Table 14. In the case of BIM100-E-D1A-L-7, the addition of a spacer at the leader end of the CRISPR1 locus indicates that the observed phage resistance was conferred by the CRISPR mechanism_No CRISPR locus could be detected using CRISPR-4 repeat GTTTTTCCCGCACACGCGGGGGTGATCC (SEQ ID No. 20) as a consensus signature, nor by using the online CRISPR finder program (http://crispr.u-psud.fr).

Table 14. Summary of CRISPR in S. thermophilus strain 100-E and derived BIMs

Size # Terminal

Parent/BIM CRISPR Direct repeat

(bp) spacers repeat

100-E (parent) 2409 5 - 36 5 -

GTTTTTGTAC GTTTTTGTA TCTCAAGATT CTCTCAAG

BIM100-E-D1A-L5 1 2409 36

TAAGTAACT A I I I AAGTA GTACAAC ACTGTACA

BIM100-E-D1A-L7 2476 -3' 37 GT-3'

100-E (parent) 5 - 5'-

GATATAAAC GATATAAAC

2 1 15 1

CTAATTACCT CTA BIM100-E-D1A-L5

CGAGAGGGG ATTACCTCG ACGGAAAC - AGAG

GGGAC I I I I

BIM100-E-D1A-L7 3'

TT-3'

100-E (parent) 5 -

G I I I I AGAG CTGTGTTGTT As direct BIM100-E-D1A-L5 3 1358 20

TCGAATGGT repeat TCCAAAAC BIM100-E-D1A-L7 -3'

The result in Example 3 shows that phage resistance was conferred to BIM100- E-D1A-L5 by a mechanism other than CRISPR. The adsorption results (section 3.5) suggest that the observed phage resistance or insensitivity is due to an inability of the phage to efficiently recognize and bind to its host.

3.3 PCR profiling

PCR profiling using the (GTG)5 primer method described above was performed on both BIMs and their parent to confirm their relatedness to the parent strain from which they were derived. The results were visualized on a 1 % agarose gel (Figure 8) and, taken together with the results of CRISPR locus sequencing (described above), confirm that both BIM100-E-D1A-L5 and BIM100-E-D1A-L7 are direct derivatives of the corresponding phage-challenged S. thermophilus parent strain 100-E.

3.4 Mutant phenotype

S. thermophilus 100-E and its derived BIMs were examined for sedimentation phenotypes as described in the MATERIALS AND METHODS. While the proposed CRISPR-mediated BIM of 100-E (BIM100-E-D1A-L-7) did not appear to sediment compared to the parent (Figure 3, Tubes A and B), the proposed non-CRISPR BIM (BIM100-E-D1A-L-5) was shown to exhibit a distinctive sedimentation phenotype relative to the parent (Figure 3, Tube C). Morphological analysis using light microscopy revealed that BIM100-E-D1A-L-5 forms cell aggregates and long chains in comparison with the parent strain, while BIM100-E-D1A-L-7 resembles the parent strain in its sedimentation profile (Figure 6A, B and C). The percentage increase in chain lengths are indicated in Table 15 below. This increase in chain length may also explain the observed sedimentation phenotype in Figure 3. Ta jle 15. Relative cells per chain (CPC) of BIMs of S. thermophilus strain 100-E.

% CPC increase versus

Strain CPC p-value parent

100-E parent 6.4 ± 3.9 N/A N/A

BIM100-E-D1A-L-7 6.7 ± 4.5 4.5% 0.72

BIM100-E-D1A-L-5 16.8 ± 9.3 162.7% 1 x 10 ^"11

3.5 Adsorption of phages

Adsorption assays were performed to determine the level of adsorption of both phages to both the parent strains and the derived BIMs of 100-E, the results of which are shown in Table 16. Each of the infecting phages adsorb optimally to the parent strain (adsorption levels are « 80%), and to the CRISPR BIM (BI M100-E-D1A-L-7) In contrast, phage 100-E-D1A-L adsorption to BIM100-E-D1A-L-5 is markedly reduced and indicates that the insensitivity of the BIM to this phage is conferred by an adsorption blocking mechanism.

Table 16. Adsorption of phages to parent and BIM of S. thermophilus strain 100-E

Long chain

Strain <p100-E-D1A-L <p100-E-D2A-L

formation?

100-E (parent) No 79.9 ± 13.6% 91.1 ± 1.0%

BIM100-E-D1A-L-7 No 83.2 ± 1 .8% 92.0 ± 2.2%

p-value 0.76 0.62

BIM100-E-D1A-L-5 Yes 10.2 ± 8.2% 87.4 ± 3.9%

p-value 0.0034 0.26

3.6 Non-CRISPR BIM robustness

In order to demonstrate that non-CRISPR BIMs are more phage robust than CRISPR- mediated BIMs, four parameters were measured: 1 ) efficiency of plaquing of two phages on each BIM, 2) range of phage resistance (i.e. number of non-identical phages to which the BIM is resistant), 3) phage escape mutant plaque size and 4) phage escape mutant propagation ability.

Firstly, it is clear from the results shown in Table 13 that BIM100-E-D1A-L-5 (non- CRISPR) has an approximately equal and high level of resistance to phage 100-E-D1A-L as BIM100-E-D1A-L-7 (CRISPR), and has a broader range of resistance compared to BIM100-E-D1A-L-7, being resistant to both infecting phages of 100-E. The CRISPR- mediated resistance of BIM100-E-D1A-L-7 renders this BIM insensitive to one phage only (i.e. the phage that was used in the challenge to generate the BIM). This trend is also upheld for all four phages infecting 100-E in the DSM collection, with BIM100-E- D1A-L-7 being sensitive to three of four phages and BIM100-E-D1A-L-5 being resistant to all four phages (data not shown).

Secondly, as well as exhibiting a broader phage resistance/insensitivity, phage escape mutants capable of producing plaques on BIM100-E-D1A-L-5 (NCEMs) are less virulent than those obtained on BIM100-E-D1A-L-7 (CEMs), using plaque size and propagation ability as measures of virulence, as shown in table 17.

Table 17. Plaque sizes of wild type phage 100-E-D1A-L and escape mutants on S. thermophilus 100-E parent and derived BIMs.

Table 17 above shows the plaque sizes of wild type phage 100-E-D1A-L and both NCEM and CEM phages. It is clear that CEMs approximately maintain the plaque size of the wild type phage, whereas NCEMs have a markedly reduced plaque size. This phenomenon is also illustrated in Figure 9.

Table 18. Relative EOP of wild type phage 100-E-D1A-L and escape mutants on S. thermophilus 100-E parent and derived BIMs.

Strain Phage EOP (1 ° EOP (2°

propagation) propagation)

100-E (parent) 100-E-D1A-L (wild tvoe) 1 1

BIM100-E-D1A-L-7 100-E-D1A-L (CEM) 3.2 0.5

BIM100-E-D1A-L-5 100-E-D1A-L (NCEM) 1 .2 x 10 ^"4 6.0 x 10 ^"7 Table 18 above details the relative EOP of the wild type phage on 100-E (parent) and phage escape mutants BIM100-E-D1A-L-5 and BIM100-E-D1A-L-7 on their respective hosts, over the course of two phage propagations (as outlined in the MATERIALS AND METHODS). It is clear that while the CEM phage could quickly overcome the CRISPR based resistance to propagate to wild type phage levels, the NCEM phage was unable to do so. In fact, while a relatively low level of propagation was achieved from a plaque in the first round, it appears that none was achieved in the second round, with the reduction in detected phage approximately reflecting the dilution factor in the second propagation. Taken together, these data clearly show the higher level of robustness of non-CRISPR BIMs against phage challenges relative to those utilising CRISPR.

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