Reference to a deposit of biological material

This application contains a reference to a deposit of biological material, which deposit is incorporated herein by reference. For complete information see last paragraph of the description.

FIELD OF THE INVENTION

The present invention relates to formulations able to prevent or reduce infections of Clostridioides (formerly Clostridium) species in particular C. difficile. In more detail, the invention relates to foods, food ingredients, dietary supplements, dietary supplement ingredients, medical foods, foods for special medical purposes, foods for specified health use, foods for special dietary use, health foods, Complementary Medicines; Natural Health Products, Natural Health formulations, Natural Health ingredients, and pharmaceutical products, pharmaceutical preparations, pharmaceutical formulations, and pharmaceutical ingredients comprising one or more microorganisms capable of preventing or reducing Clostridioides in particular Clostridioides difficile infections in the gastrointestinal tract of humans.

BACKGROUND OF THE INVENTION

C. difficile infection (CDI) is a nosocomial infection mainly affecting the elderly and the young. Flowever, studies have shown an increasing rate of CDI in young people and healthy individuals without a history of antibiotic use. Clindamycin resistance has historically been one of the largest contributing factors in the development of CDI in humans and animals. CDI rates are higher in developed countries, such as the US and UK, although antibiotics are more heavily used in developing countries. Perhaps, the distribution of hyper-virulent strains and variations in diets and hygiene contribute to this difference in rates of CDI.

The human gut microbiota contains anywhere from 100-1000 bacteria species with considerable diversity between individuals. This population is dominated by strict anaerobes, and so an important question has been how they transfer between individuals. This can now be partly explained by the remarkable finding that about 60% of genera found in the human Gl-tract are spore-forming bacteria representing 30% of the total intestinal microbiota. In this study, spore- forming bacteria isolated from human faeces were cultured anaerobically and then identified using analysis of the 16S rRNA. Clearly, spores (endospores) have the ability to survive outside of the host for decades and so are well-suited for transfer to other humans.

There are two types of spore forming bacteria, aerobic and anaerobic species. Since the Gl- tract is considered anoxic, it has been long assumed that anaerobic bacteria predominate and are therefore likely to be more important than the aerobic counterparts. As described herein, the inventors have appreciated that aerobic spore forming bacteria are present in the Gl-tract ofhumans and animals, and that they are acquired from the environment and therefore form a so-called ‘allochthonous’ population. The aerobic community of spore formers is mostly Bacillus species. These aerobic spore formers are mostly unnoticed using microbiome-based methods for bacterial detection, because they often exist as spores, and thus are refractory to extraction methods. Instead, they are best detected using culture- based methods.

US 2008/0057047 mentions the use of a Bacillus Amyloliquefaciens named PB6 for the prophylaxis or treatment of gastrointestinal and immuno-related diseases. The supernatant of another Bacillus amyloliquefaciens was tested for prophylactic treatment for Clostridium difficile- associated disease in a mouse model by Geeraerts et al. in Journal of Gastroenterol. Hepatol. (2013). In WO 2014/020226 supernatants of Bacillus amyloliquefaciens were tested against Clostridium butyricum, Clostridium perfringens, and Clostridium histolyticum, and a Bacillus amyloliquefaciens strain named H57 was tested against diarrhea in WO 2016/011511. WO 2019/236806 mentions three strains of Bacillus amyloliquefaciens bacteria for use against C. difficile infections or Clostridium difficile- associated disease (CDAD). Lee etal. tested in British J. Nutrition (2002) the inhibition by eight carbohydrates of Lactobacillus rhamnosus GG in a human enterocyte-like Caco-2 cell assay.

SUMMARY OF THE INVENTION

The invention provides a composition comprising one or more microorganisms selected from Bacillus amyloliquefaciens and Bacillus subtilis strains, and/or extracellular material produced by one or more of the microorganisms, and one or more food grade ingredients.

The invention also provides a composition comprising one or more microorganisms selected from Bacillus amyloliquefaciens and Bacillus subtilis strains, and/or extracellular material produced by one or more of the microorganisms, and one or more food grade ingredients, wherein the microorganism has antimicrobial activity against pathogenic strains of Clostridioides difficile and produces two or more non-ribosomal peptides.

Preferably, the one or more microorganisms are selected from the Bacillus amyloliquefaciensstrains deposited as NCIMB 42971 , NCIMB 42972, NCIMB 42973, NCIMB 43392 or NCIMB 43393; and the Bacillus subtilis strain deposited as NCIMB 42974.

The composition according to the invention may be formulated as a food, food ingredient, dietary supplement, dietary supplement ingredient, medical food, food for special medical purposes, food for specified health use, food for special dietary use, health food, Complementary Medicine; Natural Health Product, Natural Health formulation, Natural Health ingredient, and pharmaceutical product, pharmaceutical preparation, pharmaceutical formulation, and pharmaceutical ingredient.

The invention also provides the use of the composition of the invention for the reduction or prevention of C. difficile infection in an individual at risk of obtaining such an infection, or reduction or prevention of C. difficile colonization in asymptomatic individuals, preferably in the gastrointestinal tract of a subject, preferably a human subject.

The invention also provides a method of reducing or preventing a C. difficile infection in an individual at risk of obtaining such an infection, or reducing or preventing C. difficile colonization in an asymptomatic individual, the method comprising administering, to an individual in need of such treatment, a therapeutically effective amount of the composition of the invention.

The invention also extends to a Bacillus strain deposited as NCIMB 42971 , NCIMB 42972, NCIMB 42973, NCIMB 42974, NCIMB 43392 or NCIMB 43393.

SHORT DESCRIPTION OF THE FIGURES

Figure 1 shows the dosing regimen for the experiment disclosed in example 2.

Figure 2 shows the dosing regimen for the experiment disclosed in example 3.

Figure 3 shows the dosing regimen for the experiment disclosed in example 4.

Figure 4 shows the dosing regimen for the experiment disclosed in example 5.

Figure 5 shows the dosing regimen for the experiment disclosed in example 6.

Figure 6 shows internal markers (BSA and lysozyme) run on the same column. This analysis revealed that anti-CD630 activity did not correlate with protein content. Using the in vitro assay for activity the SEC fraction gave an endpoint titre of 1/5120.

Figure 7 shows an HPLC Chromatogram showing four peaks that were separated into four fractions (Sec0, Sec1 ; Sec2 and Sec3) identified as Fengycin, Surfactin, Iturin and Chlorotetaine, respectively.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to pathogenic bacteria, and is particularly concerned with preventing or reducing bacterial infections using novel probiotic formulations, food supplements or food compositions. The invention is especially useful for preventing or reducing infections of Clostridia species, such as Clostridioides difficile.

As used herein, the term “Clostridioides difficile ", interchangeably termed “C. difficile”, describes a Gram-positive species of spore-forming bacteria which are anaerobic, motile bacteria that are human pathogens. Clostridioides difficile was until 2016 designated “Clostridium difficile”, a term that is still often used, and is also known as Peptoclostridium difficile, C. difficile, and C. diff.

The inventors have shown that some Bacillus species produce biologically active components, and are surprisingly able to prevent or reduce bacterial infections caused by C. difficile. Further, it has been discovered that foods, food ingredients, dietary supplements, dietary supplement ingredients, medical foods, foods for special medical purposes, foods for specified health use, foods for special dietary use, health foods, Complementary Medicines, Natural Health Products, Natural Health formulations, Natural Health ingredients, and pharmaceutical products, pharmaceutical preparations, pharmaceutical formulations, and pharmaceutical ingredients comprising one or more of such Bacillus species or biologically active components produced by these Bacillus species may be used to prevent or reduce C. difficile infections in an individual at risk of obtaining such an infection, or prevent or reduce C. difficile colonization in asymptomatic individuals.

Hence, in a first aspect of the invention, there are provided foods, food ingredients, dietary supplements, dietary supplement ingredients, medical foods, foods for special medical purposes, foods for specified health use, foods for special dietary use, health foods, Complementary Medicines, Natural Health Products, Natural Health formulations, Natural Health ingredients, and pharmaceutical products, pharmaceutical preparations, pharmaceutical formulations, and pharmaceutical ingredients comprising a live spore and/or a live vegetative cell of Bacillus amyloliquefaciens and/or Bacillus subtilis, or extracellular material produced by the live cell, or disrupted cell homogenate, for use in preventing or ameliorating a bacterial infection caused by C. difficile. The inventors have, surprisingly, shown that these bacteria can be used prophylactically, to prevent C. difficile in non-infected individuals, and/or to prevent or delay a sub-clinical infection of C. difficile from developing into a clinical infection requiring medical therapy. Surprisingly, and preferably, the use of allochthonous bacteria (rather than anaerobic, autochthonous bacteria) can be used to effectively prevent or ameliorate bacterial infections.

In one embodiment, it is preferred that live spores and/or vegetative cells of B. amyloliquefaciens and/or Bacillus subtilis, are used to prevent or ameliorate the bacterial infection. In yet an- other embodiment, spores, dead cells or cell fragments or culture supernatants of B. amyloliquefaciens and/or B. subtilis, are used to prevent or reduce the bacterial infection.

However, in a most preferred embodiment, spores or live vegetative cells of B. amyloliquefaciens and/or B. subtilis, or extracellular material produced by the live cells, are used to prevent or ameliorate the infection. As described in the Examples, the inventors have shown that the supernatant extract (which does not include vegetative cells or spores, i.e., a cell-free sample) surprisingly exhibits antibacterial activity against C. difficile. Thus, in another preferred embodiment, a cell-free sample (e.g., the supernatant) comprising extracellular material produced by the live vegetative cell or disrupted cell homogenate may be used to combat the bacterial infection.

In another embodiment, the microorganism of the invention may have antimicrobial activity against pathogenic strains of Clostridioides difficile and produce one or more non-ribosomal peptides.

As used herein, the term “non-ribosomal peptides” (also known as nonribosomal peptides or NRP) means a class of peptide secondary metabolites that are synthesized by non- ribosomal peptide synthetases. Non-ribosomal peptides of the invention include, but are not limited to, peptides that are members of the Fengycin family, members of the Surfactin family, members of the Iturin family and Chlorotetaine.

The non-ribosomal peptides may be one or more peptides selected from the group consisting of a member of the Fengycin family; a member of the Surfactin family; a member of the Iturin family and Chlorotetaine. Preferably, the non-ribosomal peptides may be one or more peptides selected from the group consisting of: a member of the Fengycin family; a member of the Surfactin family and Chlorotetaine. Most preferably, the microorganism may produce the non-ribosomal peptides: a member of the Fengycin family, a member of the Surfactin family, and Chlorotetaine.

The two or more non-ribosomal peptides may be selected from the group consisting of: a member of the Fengycin family; a member of the Surfactin family; a member of the Iturin family; and Chlorotetaine. The two or more non-ribosomal peptides may be selected from the group consisting of: a member of the Fengycin family; a member of the Surfactin family; and Chlorotetaine. The microorganism may produce three or more non-ribosomal peptides. Preferably, the non-ribosomal peptides are: a member of the Fengycin family; a member of the Surfactin family; and Chlorotetaine.

In one embodiment, the general formula for members of the Fengycin family may be set out in formula I below, wherein R1 to R3 is any amino acid, and preferably R1 is L or D Tyr, R2 is Ala or Val and R3 is L or D Tyr:

The member of the Fengycin family may be selected from a group consisting of: Fengycin A [SEQ ID NO: 11], Fengycin B [SEQ ID NO: 12], Plipastatin A [SEQ ID NO: 13] and Plipastatin B [SEQ ID NO: 14]. Preferably, the member of the Fengycin family comprises Fengycin A, or an active derivative thereof. The Fengycin A, or active derivative thereof, may be the C ₁₅ , C ₁₆ , C17 or C ₁₈ isoform. Most preferably, the Fengycin A is the C ₁₅ Fengycin A isoform. The Fengycin A, or active de rivative thereof, may be acetylated.

In one embodiment, Fengycin A may have an amino acid sequence as set out in SEQ ID NO: 11 :

L-Glu-D-Orn-D-Tyr-D-aThr-L-Glu-D-Ala-L-Pro-L-GIn-L-Tyr-L- lle

[SEQ ID NO 11] Preferably, the member of the Fengycin family comprises Fengycin B, or an active derivative thereof. The Fengycin B, or active derivative thereof, may be the C ₁₃ , C ₁₄ , C ₁₅ or C ₁₆ isoform. Most preferably, the Fengycin B is the C ₁₅ Fengycin B isoform. The Fengycin B, or active derivative thereof, may be acetylated.

In one embodiment, Fengycin B may have an amino acid sequence as set out in SEQ ID NO: 12:

L-Glu-D-Orn-D-Tyr-D-aThr-L-Glu-D-Val-L-Pro-L-GIn-L-Tyr-L- ILe

[SEQ ID NO: 12]

In one embodiment where the peptide is a member of the Surfactin samily, the general formula for the members of the Surfactin family may be set out in formula II below, wherein R1-R4 is any amino acid, and preferably R1 is glutamine or glutamic acid, R2 is leucine or valine, R3 is va- line, leucine or alanine, and R4 is leucine or valine.

The member of the Surfactin family may be selected from a group consisting of: Esperin [SEQ ID NO: 15], Lichenysin [SEQ ID NO: 16], Pumilacidin [SEQ ID NO: 17] and Surfactin [SEQ ID NO: 18].

Wherein XL1 is Gin or Glu; XL2 is Leu or lie; XL4 and XL7 are Val or ILe XP7 is Val or lie XS2 is Val, Leu or ILe; XS4 is Ala, Val, Leu or ILe; XS7 is Val Leu or lie.

Preferably, the member of the Surfactin family is Surfactin, or an active derivative thereof. In one embodiment, Surfactin may have an amino acid sequence as set out in SEQ ID NO: 18: L-Glu-L-XS ₂ -D-Leu-L-XS ₄ -L-ASP-D-Leu-L-XS7

[SEQ ID NO: 18]

Active derivatives of Surfactin may therefore comprise any of the C ₁₂ , C ₁₃ , C ₁₄ , C ₁₅ , C ₁₆ , or C ₁₇ isoforms. Preferably, the Surfactin is the C ₁₆ isoform. The Surfactin, or active derivative thereof, may be the C ₁₂ , C ₁₃ , C ₁₄ , C ₁₅ , C ₁₆ , or C ₁₇ isoform. Most preferably, the Surfactin, or active derivative thereof, is the C ₁₅ isoform.

In one embodiment, a Surfactin may have a structure as set out in formula III:

In one embodiment, the member of the Iturin family, or active derivative thereof may be selected from a group consisting of: Iturin A, Iturin A _L , Iturin C, Mycosubtilin, Bacillomycin D, Bacillomycin F, Bacillomycin L, Bacillomycin LC and Bacillopeptin.

In one embodiment, the general formula for members of the Iturin family or active derivative thereof may be as set out in formula IV below, wherein R1 to R5 is any amino acid, and preferably R1 is Asn or Asp, R2 is Pro, Gin or Ser, R3 is Glu, Pro or Gin, R4 is Ser or Asn and R5 is Thr, Ser or Asn:

The member of the Iturin family, or active derivative thereof, may be Iturin A [SEQ ID NO:19], Iturin A _L [SEQ ID NO:20], Iturin C [SEQ ID NO:21], Mycosubtilin [SEQ ID NO:22], or Bacillomycin D [SEQ ID NO:23], Bacillomycin F [SEQ ID NO:24], Bacillomycin L [SEQ ID NO:25], Bacillomycin LC [SEQ ID NO:26], Bacillopeptin A, Bacillopeptin B or Bacillopeptin C

[SEQ ID NO: 27] the sequences of which are shown below:

Bacillopeptin A, B and C: cyclo [D-Asn-Ser-Glu-D-Ser-Thr- AA-Asn-D-Tyr]

[SEQ ID NO: 27] wherein the bAA for each of Bacillopeptin A, B and C is set out under R in Formula V below:

Preferably, the member of the Iturin family is Iturin A, or active derivative thereof. It will be appreciated that Iturin A is a lipopeptide. The Iturin A, or active derivative thereof, may be the C ₁₄ , C ₁₅ or C ₁₆ isoform. Active derivatives of Iturin A may therefore comprise any of the C ₁₄ , C ₁₅ or C ₁₆ isoforms. Most preferably, the Iturin A, or active derivative thereof, is the C ₁₅ Iturin isoform.

In one embodiment, Iturin A may have an amino acid sequence as set out in SEQ ID NO: 19:

Wherein n- C ₁₄ , i-C ₁₅ , ai-C ₁₅

The skilled person would understand that the Chlorotetaine may also be referred to as Chlorotetain.

In one embodiment Chlorotetaine has a structure as set out in formula VI:

In another preferred embodiment, the microorganism of the invention may comprise a Malonyl CoA-acyl carrier protein transacylase gene from Bacillus amylolique-faciens NCIMB 42971 , which is provided herein as SEQ ID No: 7, as follows:

[SEQ ID No: 7]

Accordingly, preferably the microorganism comprises a nucleotide sequence substantially as set out in SEQ ID No: 7, or a variant or fragment thereof.

In one embodiment, the Malonyl CoA-acyl carrier protein transacylase gene from Bacillus amyloliquefaciens NCIMB 42971 may encode an amino acid sequence provided herein as SEQ ID No:9, as follows:

[SEQ ID No:9]

Accordingly, preferably the microorganism comprises a gene encoding the amino acid sequence substantially as set out in SEQ ID No: 9, or a variant or fragment thereof.

In another preferred embodiment, the microorganism of the invention may comprise a Malonyl CoA-acyl carrier protein transacylase gene from Bacillus amyloliquefaciens NCIMB 42971 , which is provided herein as SEQ ID No: 8, as follows:

[SEQ ID No: 8]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 8, or a variant or fragment thereof.

Therefore, the microorganism may comprise a gene with at least 90% sequence identity to SEQ ID NO: 7 or at least 90% sequence identity to SEQ ID NO: 8, such as at least 95% sequence identity to SEQ ID NO: 7, at least 95% sequence identity to SEQ ID NO: 8, at least 98% sequence identity to SEQ ID NO: 7, at least 98% sequence identity to SEQ ID NO: 8, at least 99% sequence identity to SEQ ID NO: 7, at least 99% sequence identity to SEQ ID NO: 8, 100% sequence identity to SEQ ID NO: 7 or 100% sequence identity to SEQ ID NO: 8.

In one embodiment, Malonyl CoA-acyl carrier protein transacylase gene from Bacillus amyloliquefaciens NCIMB 42971 may encode an amino acid sequence provided herein as SEQ ID No:10, as follows:

[SEQ ID No: 10] Accordingly, preferably the microorganism comprises a gene encoding the amino acid sequence substantially as set out in SEQ ID No: 10, or a variant or fragment thereof.

The microorganism may comprise a gene coding for a protein sequence with at least 90% sequence identity to SEQ ID NO: 9 or at least 90% sequence identity to SEQ ID NO: 10, such as at least 95% sequence identity to SEQ ID NO: 9, at least 95% sequence identity to SEQ ID NO: 10, at least 98% sequence identity to SEQ ID NO: 9, at least 98% sequence identity to SEQ ID NO: 10, at least 99% sequence identity to SEQ ID NO: 9, at least 99% sequence identity to SEQ ID NO: 10, 100% sequence identity to SEQ ID NO: 9 or 100% sequence identity to SEQ ID NO: 10.

In another embodiment, the microorganism of the invention may comprise 16S rDNA.

Thus, in another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 42971 , which is provided herein as SEQ ID No: 1 , as follows:

[SEQ ID No: 1]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 1 , or a variant or fragment thereof. In another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 42972, which is provided herein as SEQ ID No: 2, as follows:

[SEQ ID No: 2]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 2, or a variant or fragment thereof.

Thus, in another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 42973, which is provided herein as SEQ ID No: 3, as follows:

[SEQ ID No: 3]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 3, or a variant or fragment thereof.

In another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 42974, which is provided herein as SEQ ID No: 4, as follows:

[SEQ ID No: 4]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 4, or a variant or fragment thereof. In another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 43393, which is provided herein as SEQ ID No: 5, as follows:

[SEQ ID No: 5]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 5, or a variant or fragment thereof.

In another preferred embodiment, the microorganism may comprise 16S rDNA of NCIMB 43392, which is provided herein as SEQ ID No: 6, as follows:

[SEQ ID No: 6]

Accordingly, preferably the microorganism comprises the nucleotide sequence substantially as set out in SEQ ID No: 6, or a variant or fragment thereof.

The microorganism may comprise 16S rDNA that is more than 98% sequence identity, such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 1 and/or more than 98% sequence identity such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 2 and/or more than 98% sequence identity such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 3 and/or more than 98% sequence identity such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 4 and/or more than 98% sequence identity such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 5 and/or more than 98% sequence identity such as more than 98% sequence identity or 100% sequence identity, to SEQ ID NO: 6.

In one embodiment, the microorganism may comprise one or more of the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

In one embodiment, the microorganism may comprise two or more of the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

In one embodiment, the microorganism may comprise three or more of the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

In one embodiment, the microorganism may comprise four or more of the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

In one embodiment, the microorganism may comprise five or more of the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

In one embodiment, the microorganism may comprise the nucleotide sequences selected from the group consisting of: SEQ ID No: 1 to 6, or variants or fragments thereof.

Strains

The B. amyloliquefaciens strain that is used is selected from a group consisting of: SG57, SG137, SG185, SG277 and SG297. Most preferably, the B. amyloliquefaciens strain is SG277 or SG297. The B. subtilis strain is SG140.

In one embodiment, one or more strains of B. amyloliquefaciens, or extracellular material produced by the cell or disrupted cell homogenate, is used. In other words, any B. amyloliquefaciens strain selected from a group consisting of: SG57, SG137, SG185, SG277 and SG297, may be used. Alternatively, in another embodiment, more than one B. amyloliquefaciens strain selected from a group consisting of: SG57, SG137, SG185, SG277 and SG297, may be used. For example, SG277 and SG297 could be used simultaneously, or SG137 and SG57 could be used simultaneously, and so on.

In yet another embodiment, one or more strains of B. amyloliquefaciens may be used in combination with B. subtilis, or extracellular material produced by the corresponding cell or disrupted cell homogenate therefrom. For example, B. amyloliquefaciens strain SG277 may be used with B. subtilis strain SG140.

The most preferred strains are strains deposited under the Budapest treaty at the NCIMB, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, AB21 9YA on 15 February 2018 and 10 May 2019.

Designation number: NCIMB 42971 - Referred to herein as: B. amyloliquefaciens SG277.

Designation number: NCIMB 42972 - Referred to herein as: B. amyloliquefaciens SG297.

Designation number: NCIMB 42973 - Referred to herein as: B. amyloliquefaciens SG185.

Designation number: NCIMB 42974 - Referred to herein as: B. subtilis SG140.

Designation number: NCIMB 43392 - Referred to herein as B. amyloliquefaciens SG57. Designation number: NCIMB 43393 - Referred to herein as B. amyloliquefaciens SG137. Recent changes in the bacterial taxonomy include the reclassification of Bacillus amyloliquefaciens strains as Bacillus velezensis. The present application discloses stains designated SG57, SG137, SG185, SG277 and SG297, and these strains have been designated Bacillus amyloliquefaciens without taking recent changes in the taxonomy into account. It should therefore be understood that the species designation Bacillus amyloliquefaciens as used in the present description and claims includes strains that a taxonomy expert would designate as Bacillus velezensis strains.

In yet another embodiment, one or more strains of B. amyloliquefaciens may be used in combination with one or more strains of B. subtilis, or extracellular material produced by the corresponding cell or disrupted cell homogenate therefrom. For example in compositions of the invention comprising two strains, B. amyloliquefaciens strain NCIMB 42971 may be used with B. amyloliquefaciens NCIMB 42972, B. amyloliquefaciens NCIMB 42973, B. subtilis NCIMB 42974,

B. amyloliquefaciens NCIMB 43392 or B. amyloliquefaciens NCIMB 43393; B. amyloliquefaciens strain NCIMB 42972 may be used with B. amyloliquefaciens NCIMB 42973, B. subtilis NCIMB 42974, B. amyloliquefaciens NCIMB 43392 or B. amyloliquefaciens NCIMB 43393; B. amyloliquefaciens strain NCIMB 42973 may be used with B. subtilis NCIMB 42974, B. amyloliquefaciens NCIMB 43392 or B. amyloliquefaciens NCIMB 43393; B. subtilis NCIMB 42974 may be used with B. amyloliquefaciens NCIMB 43392 or B. amyloliquefaciens NCIMB 43393; or B. amyloliquefaciens NCIMB 43392 may be used with B. amyloliquefaciens NCIMB 43393.

The composition may comprise a Bacillus amyloliquefaciens strain, and the Bacillus amyloliquefaciens strain is selected from the strains deposited as NCIMB 42971 , NCIMB 42972, NCIMB 42973, NCIMB 43392 or NCIMB 43393. The composition may comprise a Bacillus subtilis strain, and the Bacillus subtilis strain is the strain deposited as NCIMB 42974. All of the one or more microorganisms may be selected from the Bacillus amyloliquefaciens strains deposited as NCIMB 42971 , NCIMB 42972, NCIMB 42973, NCIMB 43392 or NCIMB 43393; and the Bacillus subtilis strain deposited as NCIMB 42974.

Compositions

The compositions of the invention comprise one or more of the B. amyloliquefaciens strains selected from a group consisting of: NCIMB 42971 , NCIMB 42972 NCIMB 42973, NCIMB 43392, NCIMB 43393 and/or the B. subtilis strain NCIMB 42974, and/or extracellular material produced by the live cells, and further one or more food grade ingredients. A composition according to the invention may for instance be characterized by that it contains 10 ² to 10 ¹⁵ , preferably 10 ⁶ or 10 ⁸ to 10 ¹² , in particular 10 ⁸ to 10 ¹⁰ , Bacillus cells (either in the form of vegetative cells or spores or a mixture thereof). Reference value is a unit of administration, for instance a tablet, a capsule or a sachet. Preferably, the composition is prepared for oral ad- ministration. The Bacillus cells are suitably lyophilized or spray dried.

The preparation of a composition according to the invention can be made in a way being usual in these technologies. Suitable solid or liquid preparation forms are for instance granulates, powders, dragees, tablets, (micro) capsules, suppositories, syrups, juices, suspensions or emulsions, for the production of which usual means are used, such as carrier substances, binding, coating, swelling, sliding or lubricating agents, tasting agents, sweeteners and solution mediators. As auxiliary substances are named here sodium aluminosilicate, magnesium carbonate, titanium dioxide, lactose, mannite and other sugars, talcum, milk protein, gelatin, starch, cellulose and derivatives, animal and vegetable oils such as cod-liver oil, sunflower oil, peanut oil or sesame oil, polyethylene glycols and solvents, such as sterile water and mono- or multi-valent alcohols, for instance glycerine. A composition according to the invention can be produced such that cells of at least one Bacillus strain used according to the invention is mixed in a defined dose with a pharmaceutically suitable and physiologically well tolerated carrier and possibly further suitable active, additional or auxiliary substances, and is prepared in the desired form of administration. Carriers are in particular substances, which are selected from the group comprising "maltodextrin, microcrystalline cellulose, starch, in particular corn starch, levulose, lactose, dextrose, and mixtures of such substances". The composition may contain 0.1 to 95 per- cent by weight carrier and 5 to 99.9 percent by weight Bacillus cells (either in the form of vegetative cells or spores or a mixture thereof), relative to the total amount of cells and carriers, or consist thereof.

In the case of the food composition, it may be provided that the composition contains 10 ² to 10 ¹⁵ , preferably 10 ⁶ to 10 ⁹ , in particular 10 ⁷ to 10 ⁹ , Bacillus cells (either in the form of vegetative cells or spores or a mixture thereof). Reference value is a unit of administration, for instance a packing unit of a food material to be sold to an end user. The physiologically tolerated carrier will normally be a food material, which in particular is selected from the group comprising "milk products, fermented milk products, milk, yogurt, cheese, cereals, muesli bars, and children’s food preparations".

The invention further concerns a method for the production of a pharmaceutical and/or dietetic composition according to the invention, wherein the lyophilized or not lyophilized, preferably vi- able Bacillus cells or spores are mixed with the physiologically tolerated carrier and prepared for oral administration.

The composition may further comprise further ingredients known from the art of preparing foods and food supplements, e.g. selected among fillers, nutrients, minerals (especially calcium may by advantageously administered to diarrheal patients); preservatives, stabilizing agents, flavouring and colouring agents.

The composition may be a food supplement, or in the form of a food or food composition.

When the preparation of the invention is in the form of a food supplement, it can be in a form for separate administration, such as a capsule, a tablet, a powder or a similar form, containing preferably a unit dose of the micro-organisms, containing 10 ² -10 ¹⁵ cells/dose, preferably 10 ⁸ - 10 ¹¹ cells/dose (where cells are either in the form of vegetative cells or spores or a mixture thereof).

The food supplement can also be in the form of a powder or a similar form, which is added to, or mixed with, a suitable food (composition) or a suitable liquid or solid carrier, for the preparation of a food which is ready for consumption.

For instance, the food supplement can be in the form of a dried powder, which is reconstituted using a suitable liquid, such as water, oral rehydration solution, milk, fruit juice, or similar drink- able liquids. It can also be in the form of a powder which is mixed with solid foods, or foods with a high water-content, such as fermented milk products, for example yoghurt.

The composition of the invention can also be in the form of a food which is ready for consumption. Such a food can for instance be prepared by adding a supplement of the invention as de- scribed above to a food or food base known per se; adding the micro organisms (separately or as a mixture) in the amounts required for administration to a food or food base known per se; or by cultivating the required bacteria in a food medium until a food containing the amount of bacteria required for administration is obtained. The food medium is preferably such that it already forms part of the food, or will form part of the food after fermentation.

In this respect, food or food base can be either fermented or non-fermented.

The composition of the invention can be foods for oral consumption, for instance a total food or an infant formula. The composition can further contain prebiotic compounds, in particular fibres that lead to the production butyrate/butyric acid, propionate/propionic acid or acetate/acetic acid upon fermentation; nitrogen donors such as proteins; and specific vitamins, minerals and/or trace elements. With respect to the latter, and as can be seen from the examples, the presence of increased or moderately high amounts of vitamin A, K, B ₁₂ , biotin, Mg, Ca and Zn can be advantageous, as can the presence of folic acid in preparations intended for the treatment of chronic diarrhoea.

The food supplement may further comprise fibres e.g. an amount of at least 0.5 g fibre per 100 g of the total preparation.

As the fibres, the preparation preferably contains a resistant starch or another butyrate generator, as well as a suitable propionate generator such as gums or soy polysaccharides, in the amounts indicated above. Short-chain fatty acids such as butyric acid and propionic acid can also be used as such, preferably in a suitably encapsulated form, or as a physiological equivalent thereof, such as sodium propionate, in an amount of at least 0.1 g per 100 g of the total composition.

Nitrogen, vitamins, minerals and trace elements may also be included e.g. in form of yeast extract.

The composition of the invention can further contain one or more substances that inhibit bacterial adhesion to the epithelial wall of the gastrointestinal tract. Preferably, these compounds are selected from lectins, glycoproteins, mannans, glucans, chitosan and/or derivatives thereof, charged proteins, charged carbohydrates, sialylated compounds and/or adhesion-inhibiting immunoglobulins, galacto-oliogasaccharides, as well as modified carbohydrates and modified chi- tin, the latter in amounts of 1-10 % w/v, preferably 2-5 % w/v of the composition.

Preferred adherence-inhibiting substances are chitosan, carob flour, as well as extracts which are rich in condensed tannin and tannin-derivatives, such as cranberry extract; the amount of tannin in the final product preferably being 10-600 mg/ml.

The composition, in particular if the composition is in the form of a total food, may also contain peptides and/or proteins, in particular proteins that are rich in glutamate and glutamine, lipids, carbohydrates, vitamins, minerals and trace elements. The use of glutamine/glutamate precursors, in amounts corresponding to 0,6-3 g glutamine/100g product, as well as of small polypeptides that have a high content of glutamines, is preferred. Alternatively, proteins that are rich in glutamine, such as milk proteins, wheat proteins or hydrolysates thereof, can be added.

In one preferred embodiment the composition further comprise glucosamine. Glucosamine is typically included in amounts corresponding to a daily intake in the range of 10-2000 mg, e.g., in the range of 100-2000 mg, e.g., in the range of 250-1500 mg e.g., in the range of 500-1000 mg. In particular preferred embodiments the compositions of the invention is formulated in unit dos- age forms, where 1-5 unit dosage forms correspond to a daily dosage of 10 ² to 10 ¹⁵ , preferably 10 ⁶ to 10 ¹² , in particular 10 ⁸ to 10 ¹¹ , Bacillus cells and glucosamine in amounts in the range of 10-2000 mg, e.g., in the range of 100-2000 mg, e.g. in the range of 250-1500 mg e.g., in the range of 500-1000 mg. The glucosamine may be glucosamine hydrochloride or glucosamine phosphate. The skilled person would understand that glucosamine may also be referred to as chitosamine.

The compositions of the invention may be lactose-free. In some embodiments the compositions have a high osmolality (preferably less than 400 mosm/l, more preferably less than 300 mosm/l), in other embodiments the compositions have a lower osmolality e.g. as the compositions disclosed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1717650/. In some embodiments the compositions of the invention are kosher, vegetarian or vegan.

In some embodiments the composition of the invention is a pharmaceutical composition comprising a strain of the invention and one or more pharmaceutically acceptable excipients.

The inventors have prepared novel foods, food ingredients, dietary supplements, dietary supplement ingredients, medical foods, foods for special medical purposes, foods for specified health use, foods for special dietary use, health foods, Complementary Medicines Natural Health Products, Natural Health formulations, Natural Health ingredients, and pharmaceutical products, pharmaceutical preparations, pharmaceutical formulations, and pharmaceutical ingredients comprising one of the various B. amyloliquefaciens and B. subtilis strains or any combi- nation of such strains.

Accordingly, there is provided a composition comprising a live or dead spore, or a live or dead vegetative cell, or mixture thereof, of one or more B. amyloliquefaciens strains and/or one or more B. subtilis strains, or extracellular material produced by the live cell, or disrupted cell homogenate; and, one or more food grade ingredients preferably selected among: carrier or vehicle, fillers, stabilizers, nutrients, flavourings, colourings.

The carriers or vehicles are selected among any food grade materials that are inert under the conditions applied during storing and use. Examples of carriers or vehicles includes minerals, such as CaC0 ₃ , NaCI, KCI, CaHPO ₄ ; polymers such as natural or modified starch, pectin, cellu- lose; sugar such as lactose, sucrose or glucose; flour and skimmed milk powder.

The fillers are selected among ingredients that are inert under the conditions applied. Fillers are typically added to the compositions of the invention to secure that the composition obtain the desired volume.

The stabilizers are selected among food grade ingredients having the ability to stabilize and/or protect the one or more B. amyloliquefaciens strains and/or one or more B. subtilis strains, during production and/or storage. Examples of suitable stabilizers include ascorbic acid and vitamin E.

The nutrients can in principle be selected among any nutrients, provided that the composition does not support growth of the one or more B. amyloliquefaciens strains and/or one or more B. subtilis strains. Typically this means that the composition is dry or at least that the water activity is so low that microbial growth is prevented. Example of nutrients includes minerals, vitamins, sugars, proteins, milk or fractions thereof including milk powders, flour, honey and juice.

The flavourings and colorants are selected among food grade flavourings and colorants as known in the area.

The composition may be a food, food ingredient, dietary supplement, dietary supplement ingredient, medical food, food for special medical purposes, food for specified health use, food for special dietary use, health food, Complementary Medicine; Natural Health Product, Natural Health formulation, Natural Health ingredient, pharmaceutical product, pharmaceutical preparation, pharmaceutical formulation, or a pharmaceutical ingredient.

The composition may be a probiotic composition comprising or consisting of live or dead cells, or spores, or compounds originating from the cells or spores. The composition may comprise one or more food grade ingredients selected from fillers and stabilizing agents. The composition may be provided in a unit dosage formulation, such as a capsule, tablet or sachet. Each unit dosage formulation may comprise 10 ⁸ to 10 ¹⁰ CFU of the one or more microorganisms. The composition may be a food composition, comprising at least one nutrient and/or vitamin in addition to the one or more microbial strains. The food composition may comprise a CFU count corresponding to 10 ⁸ to 10 ¹⁰ CFU per serving.

The one or more microorganisms may be provided in lyophilized or spray-dried form. The composition may further comprise glucosamine. The composition may comprise glucosamine corresponding to a daily dosage of 10-2000 mg, optionally in the range of 100- 2000 mg, or in the range of 250-1500 mg, or in the range of 500-1000 mg. The glucosamine may be glucosamine hydrochloride or glucosamine phosphate.

Preparation

The one or more Bacillus strains used in the compositions of the invention may be obtained in any manner known per se, such as cultivating them in suitable media, preferably in such a way and using such media that the microbial preparations thus obtained are suitable for administration to humans and/or animals.

Cultivation of the one or more Bacillus strains used in the compositions of the invention may be performed in standard fermentation equipment suitable for fermenting Bacilli, as will be known in the art.

After cultivation, the one or more Bacillus strains used in the compositions of the invention are recovered from the fermentation broth and turned into a composition of the invention using techniques known in the art, or alternatively the complete fermentation broth may be turned into the composition according to the invention.

The one or more Bacillus strains may be freeze-dried. When microorganisms are freeze- dried it is important that methods that secure a satisfactory high viable cell number and anti- pathogenic activity is used. Such techniques are known in the art and such methods known in the art are also applicable in the present invention.

Freeze dried preparations may contain suitable adjuvants known per se, for example cryoprotectants such as nutriose, maltose or prebiotics (e.g. galactooligosaccharides).

The one or more Bacillus strains used in the compositions of the invention may be spray dried meaning that the Bacillus cells are dried using a spray drying or atomizing method (synonymous), wherein a suspension of one or more Bacillus strains used in the compositions of the invention is dispersed into fine mist-like droplets, for example, and a powder can be obtained.

During spray drying according to the invention, a solution or suspension containing one or more Bacillus strains used in the compositions of the invention cells is sprayed into a hot drying medi- um, whereby it is dried. The mixture to be sprayed can be present in the form of a solution, an emulsion, a suspension or dispersion. It is atomized into millions of individual droplets with the aid of a nozzle or a spraying wheel, drastically increasing the surface. The solvent, such as water, is immediately evaporated by the hot air and is discharged. Moreover, the one or more Bacillus strains used in the compositions of the invention may be spray-dried alone.

The spray drying or atomization method can be distinguished from other drying methods since the use of a nozzle or similarly acting means is required, such as a unary nozzle, hollow cone nozzle, pressure nozzle, binary nozzle externally mixing, pneumatic nozzle, binary nozzle internally mixing, atomizing disk or ultrasonic atomizer.

Spray drying methods are described in the prior art and are familiar to the person skilled in the art (see Gardiner et al., Teixeira et al. (supra) or EP74050 and EP285682). Devices are known and described as relevant, such as the mini spray dryer B-191 or B-290 by Buechi Labortechnik AG (Germany) or SD-6.3-R by GEA Niro (Denmark). It is further known that arbitrary adjuvants and additives can be used. WO2012/168468 describes preferred methods for spray drying bacterial such as the one or more Bacillus strains used in the compositions of the invention.

Dosage and administration

The compositions according to the invention are administered to individuals at risk of obtaining an infection with Clostridioides difficile or at risk of obtaining asymptomatic colonization of C. difficile.

Individuals at risk of obtaining an infection with Clostridioides difficile include healthy individuals such as young people, elderly people or individuals having a reduced immune defense e.g., as a result of other diseases, medical treatment or because they have been exposed to severe conditions e.g., stress, fatigue or malnutrition. The compositions according to the invention may be administered to this group of individuals in order to prevent an infection with Clostridioides difficile, or reduce the duration or severity of an infection with C. difficile, or prevent or reduce asymptomatic C. difficile colonization.

The compositions of the invention are administered to the above-mentioned individuals in amounts so that the individuals receive a daily dose of 10 ² to 10 ¹⁵ , preferably 10 ⁶ or 10 ⁸ to 10 ¹² , in particular 10 ⁸ to 10 ¹⁰ , Bacillus cells.

In one preferred embodiment, the compositions are formulated as discrete dosage forms e.g. as tablets, capsules or sachets. Each dosage form is formulated so it comprises 10 ⁸ to 10 ¹⁰ , Bacillus cells. It is preferred that 1-2 of such discrete dosage forms are administered daily to each individual.

In another preferred embodiment, the compositions are formulated as food compositions, which composition is formulated so that one serving comprises 10 ⁸ to 10 ¹⁰ , Bacillus cells, and that each individual receiving one serving per day.

Administered in this way the composition of the invention can prevent C. difficile infection, or reduce the duration and severity of C. difficile infection, or prevent or reduce asymptomatic colonization of C. difficile.

In an aspect, there is provided a use of the composition described herein for the prevention of C. difficile infection in an individual at risk of obtaining such an infection, or reduction of duration or severity of a C. difficile infection, or prevention or reduction of asymptomatic C. difficile colonization.

10 ⁸ to 10 ¹⁰ CFU Bacillus cells may be administered daily. The composition may prevent or reduce C. difficile infection in the gastrointestinal tract of a subject, preferably a human subject.

In another aspect, there is provided the composition described herein for use in the prevention of C. difficile infection in an individual at risk of obtaining such an infection, or reduction of duration or severity of a C. difficile infection, or prevention or reduction of asymptomatic C. difficile colonization.

It will be appreciated that the invention extends to any nucleic acid or peptide or variant, derivative or analogue thereof, which comprises substantially the amino acid or nucleic acid sequences of any of the sequences referred to herein, including variants or fragments thereof. The terms “substantially the amino acid/nucleotide/peptide sequence”, “variant” and “fragment”, can be a sequence that has at least 40% sequence identity with the amino acid/nucleotide/peptide sequences of any one of the sequences referred to herein, for example 40% identity with the sequence identified as SEQ ID Nos: 1-27 and so on.

Amino acid/polynucleotide/polypeptide sequences with a sequence identity which is greater than 65%, more preferably greater than 70%, even more preferably greater than 75%, and still more preferably greater than 80% sequence identity to any of the sequences referred to are al- so envisaged. Preferably, the amino acid/polynucleotide/polypeptide sequence has at least 85% identity with any of the sequences referred to, more preferably at least 90% identity, even more preferably at least 92% identity, even more preferably at least 95% identity, even more preferably at least 97% identity, even more preferably at least 98% identity and, most preferably at least 99% identity with any of the sequences referred to herein. The skilled technician will appreciate how to calculate the percentage identity between two amino acid/polynucleotide/polypeptide sequences. In order to calculate the percentage identity be- tween two amino acid/polynucleotide/polypeptide sequences, an alignment of the two sequences must first be prepared, followed by calculation of the sequence identity value. The percent- age identity for two sequences may take different values depending on:- (i) the method used to align the sequences, for example, ClustalW, BLAST, FASTA, Smith- Waterman (implemented in different programs), or structural alignment from 3D comparison; and (ii) the parameters used by the alignment method, for example, local vs global alignment, the pair-score matrix used (e.g. BLOSUM62, PAM250, Gonnet etc.), and gap- penalty, e.g. functional form and constants.

Having made the alignment, there are many different ways of calculating percentage identity between the two sequences. For example, one may divide the number of identities by: (i) the length of shortest sequence; (ii) the length of alignment; (iii) the mean length of sequence; (iv) the number of non-gap positions; or (v) the number of equivalenced positions excluding over- hangs. Furthermore, it will be appreciated that percentage identity is also strongly length de- pendent. Therefore, the shorter a pair of sequences is, the higher the sequence identity one may expect to occur by chance.

Hence, it will be appreciated that the accurate alignment of protein or DNA sequences is a complex process. The popular multiple alignment program ClustalW (Thompson et al., 1994, Nucleic Acids Research, 22, 4673-4680; Thompson et al., 1997, Nucleic Acids Research, 24, 4876-4882) is a preferred way for generating multiple alignments of proteins or DNA in accordance with the invention. Suitable parameters for ClustalW may be as follows: For DNA alignments: Gap Open Penalty = 15.0, Gap Extension Penalty = 6.66, and Matrix = Identity. For protein alignments: Gap Open Penalty = 10.0, Gap Extension Penalty = 0.2, and Matrix = Gonnet. For DNA and Protein alignments: ENDGAP = -1 , and GAPDIST = 4. Those skilled in the art will be aware that it may be necessary to vary these and other parameters for optimal sequence alignment.

Preferably, calculation of percentage identities between two amino ac- id/polynucleotide/polypeptide sequences may then be calculated from such an alignment as (N/T)*100, where N is the number of positions at which the sequences share an identical residue, and T is the total number of positions compared including gaps and either including or excluding overhangs. Preferably, overhangs are included in the calculation. Hence, a most preferred method for calculating percentage identity between two sequences comprises (i) preparing a sequence alignment using the ClustalW program using a suitable set of parameters, for example, as set out above; and (ii) inserting the values of N and T into the following formula:- Sequence Identity = (N/T)*100.

Alternative methods for identifying similar sequences will be known to those skilled in the art. For example, a substantially similar nucleotide sequence will be encoded by a sequence which hybridizes to DNA sequences or their complements under stringent conditions. By stringent conditions, the inventors mean the nucleotide hybridises to filter-bound DNA or RNA in 3x sodium chloride/sodium citrate (SSC) at approximately 45ºC followed by at least one wash in 0.2x SSC/0.1% SDS at approximately 20-65ºC. Alternatively, a substantially similar polypeptide may differ by at least 1 , but less than 5, 10, 20, 50 or 100 amino acids from the sequences shown in, for example, any of SEQ ID Nos: 1 -27 that correspond to amino acid sequences.

Due to the degeneracy of the genetic code, it is clear that any nucleic acid sequence described herein could be varied or changed without substantially affecting the sequence of the protein encoded thereby, to provide a functional variant thereof. Suitable nucleotide variants are those having a sequence altered by the substitution of different codons that encode the same amino acid within the sequence, thus producing a silent (synonymous) change. Other suitable variants are those having homologous nucleotide sequences but comprising all, or portions of, sequence, which are altered by the substitution of different codons that encode an amino acid with a side chain of similar biophysical properties to the amino acid it substitutes, to produce a conservative change. For example small non-polar, hydrophobic amino acids include glycine, alanine, leucine, isoleucine, valine, proline, and methionine. Large non-polar, hydrophobic amino acids include phenylalanine, tryptophan and tyrosine. The polar neutral amino acids include serine, threonine, cysteine, asparagine and glutamine. The positively charged (basic) amino acids include lysine, arginine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. It will therefore be appreciated which amino acids may be re- placed with an amino acid having similar biophysical properties, and the skilled technician will know the nucleotide sequences encoding these amino acids.

EXAMPLES

Example 1

To evaluate the ability of B. amyloliquefaciens (SG277) to suppress or inhibit C. difficile infection (CDI) in vivo a mouse trial was conducted.

Mouse C57 BL/6 (females, age 10-11 weeks) Source: Charles River Housing: Animals were housed in groups (n = 5) until the start of the study. After which they were housed individually in IVCs (independently ventilated cages). Food: Irradiated food pellets and sterile drinking water.

Test products (TPs):

TP1 SG2775 X 10 ⁹ CFU/dose

SG277 grown 16h at 37°C in 25ml BHIB (>90% spores)

TP2 SG2775 X 10 ⁹ CFU + germinant (1 OmM glucose+ L-alanine)

TP3 SG2772 X 10 ⁸ CFU (<4% spores)

Dose: 0.2ml of the TP by intra-gastric (i.g.) gavage.

TP1 and TP2 were prepared by growth of SG277 (16h, 37°C) in 250ml Bellco flasks with 25ml BHIB. Using these conditions >90% of culture = spores. The cells were pelleted and suspended in 0.5ml of supernatant. TP3 was SG277 grown in a test tube in a roller drum (16h, 37°C) and under these conditions produced low levels of spore formation. 1 ml of culture was pelleted and suspended in 0.2ml of supernatant.

Groups: n = 5

A TP1

B TP2

C TP3

D placebo

Analysis: Toxin A in caecum at 48h

CFU of C. difficile spores in caecum at 48h

Protocol:

The animals were treated with 30 mg/kg Clindamycin 24 hours before C. difficile challenge. 4 and 1 hours before C. difficile challenge and 1 , 7, 13, 25, 31 and 37 hours after the C. difficile challenge the animals were treated with Test products. At 0 hours the animals were give a C. difficile challenge consisting of 100 CFU C. difficile strain CD 630. After 48 hours the Toxin A concentration and CFU C. difficile in caecum of the animals were determined Results

Table 1: Toxin A analysis Table 2: C. difficile CFU

Summary This experiment showed that SG277 could successfully prevent colonization of C. difficile using caecum CFU and toxins for defining colonization.

Example 2

This mouse trial was conducted to evaluate the ability of B. amyloliquefaciens (Ba) strains (SG57, SG137, SG277) to suppress or inhibit C. difficile infection (CDI) in vivo.

Species: Mouse C57 BL/6 (females, age 12-13 weeks) Source: Charles River. Housing: Animals were housed in groups (n=5) until the start of the study. After which they were housed individually in IVCs (independently ventilated cages). Food: Irradiated food pellets and sterile drinking water. Test products (TPs):

B. amyloliquefaciens SG57, SG137, SG277 in three forms: i) SP+VC in SUP

Cells of each of the 3 strains was grown for 16h at 37°C in 25ml BHIB The cells were harvested from 50ml culture and the pellet resuspended in 0.5ml of supernatant. I dose = 0.1 ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-90%) ii) SP+VC in PBS As above but the pellet was suspended in PBS

I dose = 0.1ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-90%) iii) SUP 0.1 ml of supernatant only

C. difficile challenge, administration of the test composition and sampling were made as indicated in figure 1.

Challenge: C. difficile strain CD630 (Wust et al.1982 J. Clin Microbiol (16)

1096- 1101) Groups: n = 4

Gp A SG277 SP+VC in SUP Gp B SG277 SP+VC in PBS Gp C SG277 SUP Gp D SG57 SP+VC in SUP Gp E SG57 SP+VC in PBS Gp F SG57 SUP Gp G SG137 SP+VC in SUP Gp H SG137 SP+VC in PBS Gp I SG137 SUP Gp J PBS (0.1ml) Analysis: CFU of C. difficile spores in caecum at 24h

Results

Table 3: CFU in caecum

Summary

The experiment shows that colonization was abolished in groups dosed with cells (SP+VC) suspended in supernatant or PBS. SG57, SG137 and SG277 appeared to have similar efficacy. Example 3 Objective

To evaluate the ability of B. amyloliquefaciens (Ba) strain SG277 to suppress or inhibit C. difficile infection (CDI) in vivo.

Study plan

Species: Mouse C57 BL/6 (females, age 17-18 weeks) Source: Charles River. Housing: Animals were housed in groups (n = 5) until the start of the study. After which they were housed individually in IVCs (independently ventilated cages). Food: Irradiated food pellets and sterile drinking water.

Test products (TPs):

B. amyloliquefaciens SG277 in four forms or SG378 (negative control): i) SG277 SP+VC in SUP

Cells were grown for 16h at 37°C in 25ml BHIB. The cells were harvested from 100ml culture (4 flasks) and the pellet resuspended in 2ml of super-natant.

I dose = 0.2ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-90%) ii) SG277 SP+VC in PBS

As above but the pellet was suspended in PBS

I dose = 0.2ml and ~ 5 X 10 ⁹ CFU consisting of spores ( ~70-90% )

Nil SG277 SUP

0.2 ml of supernatant from 16h BHIB culture of SG277 supernatant was filter sterilised (0.45 mm) and used with 2h iv) SG277 spores

SG277 was grown on DSM agar trays for 72h at 37°C. Spores crops (~100% spores) were harvested and washed 3 times with sterile water and CFU of heat-resistant spores determined by serial dilutions and plating. Aliquots were prepared and stored at 4°C till use.

I dose = 0.2ml and ~ 5 X 10 ⁹ spores v) SG378 SP+VC in SUP

Cells were grown for 16h at 37°C in 100ml BHIB. The cells were harvest- ed from 100ml culture and the pellet resuspended in 2ml of supernatant.

I dose = 0.2ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-90%)

B. difficile challenge, administration of the test composition and sampling were made as indicated in figure 2.

Challenge: CD630

Groups: n = 10

Gp A SG277 SP+VC in SUP Gp B SG277 SP+VC in PBS Gp C SG277 SUP Gp D SG277 spores Gp E SG378 SP+VC in SUP Gp F 0.2ml of PBS Analysis: Toxin A and B in caecum at 24h CFU of C. difficile spores in caecum at 24h

Results

Table 4: Toxin A and B (ng/g) in caecum)

Table 5: CFU in caecum

^* Mouse sick and had to be culled

Summary

These data provide strong evidence that a combination of spores and vegetative cells of Ba strain SG277 can provide protection against CDI. Example 4 Objective

To evaluate the ability of SG137 to suppress or inhibit Clostridioides difficile infection (CDI) in vivo.

Study plan s: Hamster (males, age 24 weeks) Source: Charles River. Housing: Animals were housed in groups until the start of the study, after which they were housed individually in IVCs (independently ventilated cages). Food: Irradiated food pellets and sterile drinking water.

Test products (TPs):

B. amyloliquefaciens SG137 grown 16h at 37°C in BHIB (25ml) and pellet suspended in 0.6ml of cell free supernatant. The suspension comprises spores (70-90%) and vegetative cells and is thus namedSP+VC Total CFU of 3 X 10 ¹⁰ in 0.2ml/dose

Challenge: CD630 spores Regimen: Figure 3 Dose: 0.2ml i.g. Groups: n = 3 Gp A SG137 SP+VC in SUP Gp B Placebo (PBS buffer) Analysis: Survival only Results

Table 6: Survival data

Summary

The experiment shows that administration of SG137 delayed symptoms in hamsters. Example 5 Objective

To evaluate the ability of SG137 and SG277 to suppress or inhibit Clostridioides difficile infection (CDI) in vivo.

Study plan

Basically, the same as example 4 except :

(i) animals challenged 72h post-clindamycin treatment rather than 24h.

(ii) the cell pellet (SP+VC) was suspended in 6ml of supernatant

(iii) 2ml (3 X 10 ¹⁰ CFU) was used to dose each animal

(iv) hamsters at age ~26 weeks

Dose: 2ml i.g.

Group size: n = 3

Dosing regime is shown in figure 4.

Table 7: Survival data

Summary

SG277 showed clear evidence of protection and was superior to SG137.

Example 6 Objective To evaluate the ability of Bacillus amyloliquefaciens strain SG277 to suppress or inhibit Clostridioides difficile infection (CD I) in vivo.

Study plan

Species: Mouse C57 BL/6 (females, age 10 weeks) Source: Envigo. Housing: Animals were housed in groups (n=5) until the start of the study. After which they were housed individually in IVCs (independently ventilated cages). Food: Irradiated food pellets and sterile drinking water.

Test products (TPs):

B. amyloliquefaciens SG277 in four forms or PBS:

Gp.1. SG277 SP+VC Cells were grown for 16h at 37°C in 25ml BHIB. The cells were harvested from 100ml culture (4 flasks) and the pellet resuspended in 2ml of PBS.

1 dose = 0.2ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-100%)

Gp.2. Freeze-dried SG277 SP+VC (SG277 SP+VC ^FD )

Cells were grown for 16h at 37°C in 25ml BHIB. Cells pellet was then frozen at -20°C o/n. The next day tubes containing frozen pellet from 25ml culture were covered with perforated parafilm and lyophilized o/n. When ready, stored at -20°C (lids on, parafilmed). On the day of use, pellet from 4 flasks was harvested and resuspended in 2ml of PBS. 1 dose = 0.2ml and ~ 5 X 10 ⁹ CFU consisting of spores (~70-100%)

Gp.3. SG277 SUP

1 dose = 0.2ml of filtered supernatant from 16h BHIB culture of SG277

Gp.4. SG277 SEC Supernatant from a 16h BHIB culture of SG277 was filtered and then processed first by Ammonium sulphate precipitation and then by size exclusion chromatography (SEC). By SEC, the "active" fractions were assessed and isolated for use in this experiment. According to the purification protocol and water was used as final vehicle. Samples aliquots were stored at -20 °C and thawed on the day of use. 1 dose = 0.2ml of SEC sample

Gp.5. Placebo

1 dose = 0.2ml of PBS

Challenge: 1 x 10 ² of CD630 spores

Regimen: Figure 5 Groups: n = 8

Gp 1 SG277 SP+VC Gp 2 SG277 SP+VC ^FD Gp 3 SG277 SUP Gp 4 SG277 SEC Gp 5 Placebo (PBS)

Analysis: Toxin A and B in cecum at 24h (SOP27) CFU of C. difficile spores in cecum at 24h (SOP26).

Results

Table 8: Toxin A and B (ng/q) in cecum

Table 9: CFU in cecum

Summary

Administration of ~ 5 X 10 ⁹ CFU of freeze-dried cells of B. amyloliquefaciens SG277 (Gp.2.) was efficient in suppressing CDI in a murine model. No toxin A and B levels were detected in caeca of mice infected with CD630. Bacteria remain viable after lyophilisation process and they retain their antimicrobial activity.

Administration of SG277 supernatant active compound purified through liquid chromatography (Gp.4.) significantly decreased toxins levels in caeca detected at 24h post challenge. In 3/8 samples toxins were not detected.

Example 7 Objective

To evaluate the ability of N-acetyl-glucosamine (GlcNAc) or glucosamine to suppress or inhibit Clostridioides difficile infection (CDI) in animals.

Study

Design: Holloway model of CDI. C57BL/6 (age 9 weeks). Six (6) mice per group were housed in independently ventilated cages. Animals were dosed with test products (TPs) ad libitum starting 2 days before clindamycin treatment and then for the duration of the study. Infection started at hour 0 with oral dosing (intra-gastric gavage) of clindamycin (30 mg/kg) and then at 24h animals were challenged with 100 pure spores of CD strain 630. Animals were monitored for 24h post challenge after which caeca were removed and examined for levels of Toxin A and Toxin B. · Groups Gp1 GlcNAc 20 mg/ml in drinking water Gp2 GlcNAc 50 mg/ml in drinking water Gp3 GlcNAc 100 mg/ml in drinking water Gp4 Glucosamine 20 mg/ml in drinking water Gp5 Glucosamine 50 mg/ml in drinking water

Gp6 Glucosamine 100 mg/ml in drinking water Gp7 water only

GlcNAc (Sigma A4106). Glucosamine hydrochloride (Sigma G4875) Table 10: Water consumption ¹

Observations: Animals in Gp6 appeared dehydrated and drank less water (Table 10). Other animals looked healthy.

Table 11: Toxins raw data

Table 12: Ethanol resistant CFU Raw data

Summary

Administration of GlcNAc or glucosamine at levels as low as 20 mg/ml in drinking water could suppress CD colonisation.

Conclusion

Water containing 20 mg/ml of GlcNAc or glucosamine hydrochloride prevented CD infections (CDI) in mice. This equates to a mouse consuming approximately 3g/kg/day.

Example 8

Objective

Characterization of the antimicrobial activity of bacterial strains

Study

Preparation of Cell free filtrates

Bacillus strains were grown in BHIB (Brain heart infusion broth, Oxoid CM1135) medium grown at 37°C O/N under aerobic condition (by agitation). The cultures were centrifuged (8,000g for 15min.) and the supernatant filter-sterilized using 0.45 mm filters. The filtrates were stored on ice and used the day they were produced. Alternatively, Aerobic Bacillus strains were grown in LB medium at 37°C for 16-18h and supernatants filter-sterilized (0.20 mm syringe filter) and stored on ice till use. For Clostridioides difficile TGY agar plates were pre-reduced (4h in an anaerobic chamber) (TGY agar is, per litre, tryptic soy broth (30g), glucose (20g), yeast extract (1 Og), L-cysteine (1 g), Resazurin (1 mg) and agar (15g)). Plates were then spread with an overnight C. difficile culture (~ 100mI) and allowed to dry for 30 min. after which 4-6 wells (5mm) were cut per plate. 50 mI of Bacillus supernatants was applied to labelled wells and the plates incubated at 37°C for 48h in an anaerobic chamber and zones of inhibition measured (diameter), typically 9-20mm.

Preparation of Indicator culture

A single colony of the relevant C. difficile strain was inoculated into 10ml of BHIS and incubated overnight at 37°C in an anaerobic chamber.The overnight culture was then sub cultured 1 :100 into BHIS (typically 0.1 ml into 10ml BHIS) and incubated at 37°C for 6h after which the culture was ready for use. BHIS (Brain Heart Infusion supplemented with yeast extract and L-cysteine) broth: 37g Brain heart infusion (Oxoid CM1135), 5g Yeast extract (Oxoid LP0021 ), 1g L-cysteine (Sigma-Aldrich C7352) 1000mI 1000x Resazurin

(Sigma-Aldrich R7017) dH ₂ 0 to 1000ml

Plate set up 180mI of sterile BHIS was pipetted into the first row of a 96-well U-bottom microplate (Sigma) and 100mI into each subsequent row. 20mI of the sample to be tested was pipetted into the first row (1 :10 dilution factor) and serially diluted in a 2-fold dilution series until the last row (1 :1280 dilution factor) on the microplate. For one serial dilution a media-only control was also pipetted into a single well on the first column. 10mI of the 6h C. difficile ‘indicator culture’ was pipetted into each well and the plate was incubated overnight at 37°C in an anaerobic chamber. After overnight growth the microplate contents were agitated on a rotary plate shaker at 200rpm for 2 min. after which the OD ₆ oo was measured using a microplate plate reader. Positive inhibitory activity was defined as an ODeoo increase of <50% of the media- only control. Antimicrobial activity measured with the microdilution assay to quantify the level of extracellular inhibitory activity against C. difficile strain CD630:

B. subtilis PY79 B. subtilis and B. amyloliquefaciens 10A1 were control strains obtained from the Bacillus Genetic Stock Centre (BGSC).

C. difficile cultures were grown in BHIS for 10h at 37 °C. 180 mI of the C. difficile culture was added to a microplate well followed by 20 mI of a sterile SG277 filtrate. Plates were incubated anaerobically 18h at 37°C after which the OD600 was read. The SG277 filtrate was also incu- bated overnight as a control and showed no growth.

Isolation and characterization of bioactive compounds Bacterial growth

SG277 was streaked on DSM agar, incubated O/N at 37°C and a single colony used to inoculate 25ml of BHIB broth. The culture was allowed to grow for 16h at 37°C. The culture was centrifuged to pellet bacteria and the supernatant removed after centrifugation and filtered through a 0.45miti membrane. Stored on ice for up to 4h or frozen at -20°C.

Fractionation Using centrifugal concentrators of different molecular weight cut-offs (MWCO) we determined the approximate mwt. of Amycide™ contained within the filter-sterilised (0.45 mm) supernatant from SG277 (Table 13). Activity (determined using the microdilution assay) was found in two fractions: 30-100 kDa and >100kDa, suggesting that Amycide™ might exist as a complex, be physically labile and could dissociate while retaining some activity.

Sterile filtered (0.45mm) culture supernatant were fractionated using Vivaspin 6 centrifugal concentrators at cut-off indicated in the table. Fractions were tested for activity against CD630 measured using microdilution assay.

Table 13 Ammonia sulphate precipitation

AmSO (113g/L) was added to the sterile filtrate to give a 20% w/v solution and incubated O/N at 4°C. The solution was then centrifuged, and the pellet was suspended in PBS at a concentration of 30x (that is, for 30ml of initial culture the ppt would be dissolved in 1 ml of PBS). The Am- SO ₄ ppt was dialysed in PBS O/N (at 4°C) to remove excess AmSO _4. Activity of AmSO ₄ ppt = 1/2560. This method enabled precipitation of the large molecular weight species responsible for the functional activity (as evidenced in MWCO experiments), and to reduce the amount of protein which would be co-purified alongside them.

Preparative SEC ¹ separation

In order to further purify the active species, the AmSO ₄ precipitate was separated using a Superdex 200 column (10,000Da - 600,000Da) in PBS + 0.1% SDS (w/v). This allowed a preparative separation of high MW species. SDS was added to denature/linearize unwanted proteins resulting in a purer separation. Fractions were tested for activity against CD630 (using dilution factor or endpoint titre) using a microplate assay and active fractions were combined and washed to remove excess SDS. This analysis revealed that anti-CD630 activity did not correlate with protein content. Using the in vitro assay for activity the SEC fraction gave an endpoint titre of 1/5120 (as illustrated in figure 6: internal markers (BSA and lysozyme) run on the same column).

HPLC analysis

To examine further the constituent species of the preparative SEC active fraction, separation was performed using HPLC using a column that separated molecules in the range of 200- 3,000 Da. Acetonitrile was used as the isocratic buffer (Figure 7). The four HPLC fractions were tested for activity against CD630, all four fractions showed activity

Bioinformatics analysis

By Bioinformatics analysis of the whole genome sequence genes encoding enzymes involved in the biosynthesis of the non- ribosomal peptides fengycin, surfactin and chlorotetaine were found in all six strains tested 297. For example, the Malonyl CoA-acyl carrier protein trans-acylase from SG277 gene (Seq ID NO 9 and Seq ID NO 10) encoded by the genes Seq ID NO 7 and Seq ID NO 8.

Conclusion

In the Bioinformatics analysis, the genetic basis of fengycin, surfactin and chlorotetaine was demonstrated in all six strains and iturin was found in SG277 and SG297.

Deposit of Biological Material

The following biological material has been deposited under the terms of the Budapest Treaty with the NCIMB, Ferguson Building, Crabstone Estate, Bucksburn, Aberdeen, AB21 9YA, and given the following accession number:

Deposit Accession Number Date of Deposit

B. amyloliquefaciens SG277 NCIMB 42971 15 February 2018

B. amyloliquefaciens SG297 NCIMB 42972 15 February 2018

B. amyloliquefaciens SG185 NCIMB 42973 15 February 2018

B. subtilis SG140 NCIMB 42974 15 February 2018

B. amyloliquefaciens SG57 NCIMB 43392 10 May 2019

B. amyloliquefaciens SG137 NCIMB 43393 10 May 2019

The strains have been deposited under conditions that assure that access to the culture will be available during the pendency of this patent application to one determined by foreign patent laws to be entitled thereto. The deposits represent a substantially pure culture of the deposited strain. The deposits are available as required by foreign patent laws in countries wherein counterparts of the subject application, or its progeny are filed. However, it should be understood that the availability of a deposit does not constitute a license to practice the subject invention in derogation of patent rights granted by governmental action.