OA20538A

OA20538A - Compositions comprising bacterial strains.

Info

Publication number: OA20538A
Application number: OA1202100153
Authority: OA
Inventors: Imke Elisabeth MULDER; Ian JEFFERY; Alexander Stevenson
Original assignee: 4D Pharma Research Limited
Priority date: 2018-10-09
Filing date: 2019-10-09
Publication date: 2022-10-27

Abstract

Provided are compositions comprising a bacterial strain of the genus Bacteroides, for use in a method of increasing the microbiota diversity and/or inducing stability of the microbiota of a subject.

Description

COMPOSITIONS COMPRISING BACTERIAL STRAINS

TECHNICAL FIELD

This invention is in the field of compositions comprising bacterial strains isolated from the mammalian digestive tract and the use of such compositions in the treatment of disease.

BACKGROUND TO THE INVENTION

The human intestine is thought to be stérile in utero, but it is exposed to a large variety of maternai and environmental microbes immediately after birth. Thereafter, a dynamic period of microbîal colonîzation and succession occurs, which is influenced by factors such as delivery mode, environment, dîet and host génotype, ail of which impact upon the composition of the gut microbiota, particularly during early life. Subsequently, the microbiota stabilizes and becomes adult-like [I]. The human gut microbiota contains more than 1500 different phylotypes dominated in abundance levels by two major bacterial divisions (phyla), the Bacteroidetes and the Firmicutes [2], The successful symbiotic relationships arising from bacterial colonîzation of the human gut hâve yielded a wide variety of metabolic, structural, protective and other bénéficiai functions. The enhanced metabolic actîvities of the colonized gut ensure that otherwise indigestible dietary components are degraded with release of by-products providing an important nutrient source for the host and additional health benefits. Similarly, the immunological importance of the gut microbiota is well-recognized and is exemplified in germfree animais which hâve an impaired immune System that is functionally reconstituted following the introduction of commensal bacteria [3-5].

Dramatic changes in microbiota composition hâve been documented in gastrointestinal disorders such as inflammatory bowel disease (IBD). For example, the levels of Clostridium cluster XIVa bacteria are reduced in IBD subjects whilst numbers of E. coli are increased, suggesting a shift in the balance of symbionts and pathobionts within the gut [6-9, 16],

In récognition of the potential positive effect that certain bacterial strains may hâve on the animal gut, various strains hâve been proposed for use in the treatment of various diseases (see, for example, [10-13]). A number of strains, including mostly Lactobacillus and Bifidobacterium strains, bave been proposed for use in treating various bowel disorders (see [14] for a review and see [15]).

The relationship between different bacterial strains and different diseases, and the précisé effects of particular bacterial strains on the gut and at a systemic level and on any parti cular types of diseases, are poorly characterised and results to date are variable and pose more questions than provide answers [16],

While the tenu ‘dysbiosis’ has been used in the literature to generically define deleterious fluctuations in the microbiome, there is no universal définition of what does or does not constitute ‘dysbiosis’. A more accurate and vérifiable metric to assess perturbations in the microbiome is ‘microbiota diversity’ Loss of diversity is also measured by réductions in the Shannon Diversity Index. As those skilled in the art will be aware, the Shannon Diversity Index accounts for both the abondance (i.e. changes in the the populations of different OTUs présent) and evenness (i.e. how numerically similar the populations of different OTUs présent in the microbiome are) of species présent in the microbiome. A significant variation in either abondance or evenness from the ‘healthy’ or ‘normal’ microbiome in a popolation eqoates to dysbiosis.

Reduced microbiota diversity is reported in recent studîes of obesity, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), type 2 diabètes and frailer older people [20]. In particular, references [17] and [18] teach that a reduced microbiota diversity is strongly associated with IBD and reference [17] furthers sommarises studies concluding that inereasing the microbiota diversity has curative effects on IBDs.

Re-establîshing the healthy microbiota can be difficult, however, as the bacteria in the gut are résistant to colonisation. This poses a challenge when trying to treat the microbiota of unhealthy subjects by inereasing the diversity of the microbiota [19]. The accompanying loss of microbial metabolic fonction is assumed to be a contributory factor to the symptoms of these pathophysiologies. In contrast to healthy adults in whom the microbiota is stable, the microbiota of unhealthy subjects such as those suffering from IBD, IBS and frail elderly subjects is unstable [16,20].

There is a requirement for the profile effects of gut bacteria to be positively modified to permit the treatment of diseases or conditions characterised by reduced microbiota diversity and / or evenness.

SUMMARY OF THE INVENTION

The inventons hâve developed new thérapies for treating and preventing diseases and disorders by inereasing or maintaining the intestinal microbiota diversity in a subject. In particular, the inventons hâve unexpectedly identified that bacterial strains from the genus Bacteroides eau be effective in increasing or maintaining the diversity and/or evenness of different types of bacteria in the distal gut of a subject.

As described in the examples, an IBD patient population treated with an organism from the species Bacteroides thetaiotaomicron experienced a statîstically significant increase in their microbiome diversity and evenness. Additîonally, the examples show that treatment with compositions comprising Bacteroides thetaiotaomicron increased the stability of the microbiota in IBD subjects throughout the course of the study.

Therefore, in a first embodiment, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron, for use in a method of increasing or maintaining the microbiota diversity. Similarly, there is also provided a method of increasing or maintaining the microbiota diversity in a subject comprising use of a bacterial strain of the species Bacteroides thetaiotaomicron. Preferably, the subject has reduced microbiota diversity and/or stability.

The term “increasing or maintaining the microbiota diversity” is used herein to mean increasing or maintaining the number of different types of bacteria and/or the evenness of the different types of bacteria in the microbiota of a subject. In some embodiments, the microbiota diversity is increased. In some embodiments, the number of different généra of bacteria in the microbiota is increased. In some embodiments, the number of different species of bacteria in the microbiota is increased. In some embodiments, the number of different strains of bacteria in the microbiota is increased. In some embodiments, the microbiota diversity is maintained. In some embodiments, the number of different généra of bacteria in the microbiota is maintained. In some embodiments, the number of different species of bacteria in the microbiota is maintained. In some embodiments, the number of different strains of bacteria in the microbiota is maintained. In some embodiments, the number of généra, species and strains in the microbiota is increased or maintained.

The increase in microbiotia diversity may be for non-acetogenic bacteria. It may also be for both acetogenic and non-acetogenic bacteria. Such bacteria are well known in the art. Briefly, acetogenic bacteria produce acetate as an end product of anaérobie respiration or fermentation.

In some embodiments, loss, increase or maintenance of microbiota diversity may be quantified by a measurable réduction, increase or maintenance, respectively, in the number of the sequencebased bacterial classifications or Operational Taxonomie Units (OTUs) in a sample, typically determined by 16S rRNA amplicon sequencing methods. In some embodiments, loss of diversity may be measured by réductions in the Shannon Diversity Index. Conversely, in some embodiments, an increase of diversity may be measured by an încrease in the Shannon Diversity Index. Similarly, in some embodiments, maintenance of diversity may be measured by the same resuit in the Shannon Diversity Index.

In some embodiments, the evenness of the different types of bacteria is increased. in some embodiments, the relative abundance of the different types of bacteria in the microbiota becomes more even following administration of a composition of the invention.

The inventors hâve also developed new thérapies for treating and preventing diseases and dîsorders by indticing stability of the intestinal microbiota. In parti cular, the inventors hâve identifîed that bacterîal strains from the genus Bacteroides induce stability of the intestinal microbiota. By “induce stability is meant that the microbiota diversity remains stable and also the relative numbers of the different généra in the microbiota romains stable. Thus, the relative numbers may fluctuate by less than 10%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2% or less than 1%.

Stability of the intestinal microbiota is important as a number of diseases and disorders, including IBS and IBD, are characterised by reduced stability of the microbiota. As described in the examples, oral administration of compositions comprising Bacteroides ihetaiotaomicron induces stability of the microbiota in stool. Therefore, in a further embodiment, the invention pro vides a composition comprising a bacterîal straîn of the species Bacteroides thetaiotaomicron, for use in a method of inducing stability of the microbiota in a subject. Similarly, there is also provided a method of inducing stability of the microbiota in a subject comprising use of a bacterîal strain of the species Bacteroides thetaiotaomicron.

In some embodiments, the relative numbers of the different bacterîal species in the microbiota of a subject becomes more stable following treatment or prévention with a composition of the invention, for example in a subject diagnosed with a disease or disorder characterised by a réduction in the diversity of microbiota. In some embodiments, the relative numbers of the different bacterîal généra in the microbiota of a subject becomes more stable following treatment or prévention with a composition of the invention, for example in a subject diagnosed with a disease or disorder characterised by a réduction in the diversity of microbiota. The stability of a subject’s microbiota can be assessed by comparing the microbiome from the subject at two different time points. If there is a différence in the microbiome, this can be indicative of disease or of a disorder being présent. In some embodiments, the two different time points are at least three days apart (e.g. at least 1 week, 2 weeks, I month, 3 months, 6 months, l year, 2 years apart). In some embodiments, the two different time points are 3-7 days apart, 1-2 weeks apart, 2-4 weeks apart, 4-S weeks apart, 8-24 weeks apart, 24-40 weeks apart, 40-52 weeks apart or more than 52 weeks apart. In some embodiments, more than two different time points are used, e.g. three, four, five or more than five time points. Suitable intervals are chosen between the various time points, for example, as set out above.

The bacterial strain may be Bacteroides thetaiotaomicron and is preferably the strain deposited under accession number NC1MB 42341. This strain was deposited with the international depositary authority NCIMB, Ltd. (Ferguson Building, Aberdeen, AB21 9YA, Scotland) on 3rd December 2014.

Further Bacteroides thetaiotaomicron strains for use in the invention is the type strain ATCC 29148. The 16S rRNA gene sequences for these strains are disclosed as SEQ 1D NOs 2. A further preferred Bacteroides thetaiotaomicron strain for use in the invention is the strain described in EPI448995. The accession number for the 16S rRNA gene sequence of Bacteroides thetaiotaomicron strain WAL 2926 is M58763 (disclosed herein as SEQ ID NO:3). Other suitable Bacteroides thetaiotaomicron strains hâve the 16S rRNA sequences of SEQ ID NOs 412.

In some embodiments, the microbiota diversity, evenness and/or the stability of the microbiota refers to the microbiota diversity, evenness and/or the stability in a stool sample from the subject. In some embodiments, the microbiota diversity, evenness and/or the stability of the microbiota refers to the microbiota diversity and/or the stability in the distal gut of the subject. In some embodiments, the microbiota diversity, evenness and/or the stability of the microbiota refers to the microbiota diversity, evenness and/or the stability in the gastrointestinal tract of the subject. In some embodiments, the microbiota diversity, evenness and/or the stability of the microbiota refers to the microbiota diversity, evenness and/or the stability in the caecum. In some embodiments, the microbiota diversity, evenness and/or the stability of the microbiota refers to the microbiota diversity, evenness and/or the stability în the colon.

In some embodiments, the invention provides a composition comprising a bacterial strain ofthe species Bacteroides thetaiotaomicron, for use in a method of treating or preventing a disease or disorder assocîated with a level of microbiota dîversity that is reduced relative to the microbiota diversity of a healthy subject, or a population of healthy subjects. Such diseases are well known in the art and include, for example, IBS, IBD (such as Crohn’s disease and ulceratîve colitis) [21], cancer (for example colorectal cancer, or other cancers for example where a réduction in microbiota diversity is observed with concomitant cancer therapy treatment incîuding chemotherapy), obesity [22], autism, allergy, celiac disease, infectious diseases, and graft versus host disease amongst others [23], The invention is useful for treating these diseases. Preferably, the compositions of the invention are for use în treating IBD, in particular Crohn’s disease, or cancer. Whilst these conditions may be associated with reduced microbiota diversity and/or stability this is not an inhérent feature of these diseases as patients can suffer from these even if their microbîome diversity/stability is unaffeced. A skilled person can easily ascertain whether a patient suffering from any of these conditions has reduced microbiota diversity and/or stability relative to the levels in a healthy individual, or a population of healthy indîviduals as explained in further detail below. Thus, in embodiments of the invention, the subject to be treated, who may be diagnosed with one or more of the diseases discussed therein has reduced microbiota diversity and / or stability.

In some embodiments, the treatment or prévention using a composition of the invention results in the microbiota diversity, evenness and / or stability increasing to the levels corresponding to or greater than those présent in a healthy individual, or a population of healthy indîviduals. A healthy individual in this context may be someone who does not suffer from a disease which is associated with réductions in microbîome diversity. A healthy individual may be the subject being treated prior to the onset or diagnosis of their disease; administration of the compositions of the invention may cause the diversity, evenness or stability of their microbîome to revert to their former, pre-disease levels.

In some embodiments, treatment or prévention using a composition of the invention results in the microbiota diversity, evenness and / or stability increasing to levels corresponding to or greater than those présent in a population of healthy indîviduals.

In embodiments of the invention in which changes in microbîome diversity are determined with reference to a healthy individual or a population of healthy indîviduals, the healthy individual/s is/are résident in the same geographîcal région (e.g. résides withîn a 200km radius, within a 100km radius, or within a 50km radius) as the subject, is of a similar/same âge to the subject and/or is of a similar/same race to the subject. Similarly, the invention also provides a method of treatment or prévention of a disease or disorder associated with a level of microbiota diversity that is reduced relative to the microbiota diversity of a healthy individual or population of healthy individuals wherein the method comprises administering a composition comprising a bacterial strain of the genus Bacteroides.

The levels of microbiota diversity in a healthy individual are well known in the art and can be determîned by a skilled person using methods known in the art (see, for example, reference [24]).

In some embodiments, the subject is an infant or child with a reduced microbiota diversity compared to a healthy infant or child (or population thereof), respectively. It has been observed that some children who develop a disease associated with a reduced microbiota diversity later in life hâve a reduced diversity of faecal microbiota as 1 week old infants [25]. Thus, in some embodiments, the infant is less than 1 week old, is less than 2 weeks old, is less than one month old, is less than two months old or is less than four months old. In some embodiments, the subject is an infant who has not been delivered via a vaginal birth. For example, in some embodiments, the subject is an infant who has been delivered by Caesarean section. Reduced microbiota diversity has also been reported in frail elderly subjects. In some embodiments, therefore, the subject is an elderly subject, for example, a frai! elderly subject. In some embodiments, the subject is 65 or more years in âge (e.g. 70 or more, 75 or more, 80 or more, 85 or more or 90 or more years in âge) [20]. The subject may also be an adolescent. For example, the subject may be between 10 and 19 years of âge.

It has been estimated that a healthy human individual has approximately 101 different bacterial specîes and 195 different bacterial strains in its microbiota [26], Accordingly, in some embodiments, the composition is for use in treating a subject having fewer than 101 different bacterial specîes (e.g. fewer than 100, 99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 85, 80, 75 or 70 bacterial specîes) and/or fewer than 195 different strains (e.g. less than 194, 193, 192, 191, 190, 189, 188, 187, 186, 185, 183, 180, 175, 170, 165, 160, 150, 140 bacterial strains) in its microbiota. In some embodiments, the treatment or prévention results in the microbiota diversity increasing to more than 80 bacterial species (e.g. more than 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100 bacterial species) or to 101 bacterial species. For example, in some embodiments, the treatment or prévention results in the microbiota diversity increasing to more than 90 bacterial species. For example, in some embodiments, the treatment or prévention results in the microbiota diversity increasing to more than 95 bacterial species. For example, in some embodiments, the treatment or prévention results in the microbiota dîversity increasing to more than 97 bacterial species. For example, in some embodiments, the treatment or prévention results in the microbiota diversîty increasing to more than 99 bacterial species. In some embodiments, the treatment or prévention results in the microbiota diversîty increasing to more than 160 bacterial strains (e.g. more than 165, 170, 185, 186, 187, 188, 189, 190, 191, 192, 193 or 194 bacterial species) or to 195 bacterial strains. For example, in some embodiments, the treatment or prévention results in the microbiota diversîty increasing to more than 175 bacterial strains. For example, in some embodiments, the treatment or prévention results in the microbiota diversîty increasing to more than 185 bacterial strains. For example, in some embodiments, the treatment or prévention results in the microbiota dîversity increasing to more than 190 bacterial strains.

In some embodiments, the treatment or prévention results in the microbiota diversîty increasing by at least one bacterial genus (e.g. by at least two, tliree, four, five, six, seven, eight, nine or ten bacterial généra). In some embodiments, the treatment or prévention results in the microbiota dîversity increasing by at least one bacterial species (e.g. by at least two, three, four, five, six, seven, eight, nine, ten, 12, 15, 17 or 20 bacterial species). In some embodiments, the treatment or prévention results in the microbiota diversîty increasing by at least one bacterial strain (e.g. by at least two, three, four, five, six, seven, eight, nine, ten, 12, 15, 17, 20 or 25 bacterial strains).

In some embodiments, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron, for use in a method of treating or preventing a disease or disorder associated with reduced stability of the microbiota compared to the stability of the microbiota in a healthy subject (or compared to a population of healthy subjects). B y “reduced stability of the microbiota” is meant that the microbiota dîversity does not remain as stable and also the relative numbers of the different généra in the microbiota do not remain as stable as the stability observed in a healthy subject or in a population of healthy subjects. In some embodiments, inducing stability of the microbiota results in the stability being induced to a similar level as is présent in a healthy subject, or in a population of healthy subjects. In some embodiments, inducing stability of the microbiota results in the stability being induced to the same level as is présent in a healthy subject, or in a population of healthy subjects.

Similarly, the invention provides a method of treating or preventing a disease or disorder associated with reduced stability of the microbiota wherein the method comprises administering a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron. For example, the pathogenesis of some diseases or disorders is characterised by reduced stability of the microbiota. Examples of such diseases and disorders are IBS, 1BD, diabètes (e.g. type 2 diabètes), allergie diseases, autoimmune diseases and metabolic diseases/disorders. Accordingly, in some embodiments, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron, for use in a method of treating or preventing a dîsease or disorder associated with reduced stability of the microbiota, wherein the treatment or prévention comprises inducing stability of the microbiota. In some embodiments, the dîsease or disorder is selected from IBS, IBD, diabètes (e.g. type 2 diabètes), allergie diseases, autoimmune diseases and metabolic diseases/disorders. In some embodiments, the dîsease or disorder is IBS or IBD. In some embodiments, the disease or disorder is Crohn’s dîsease. Accordingly, in some embodiments, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotciomicron, for use in a method of treating or preventing IBS or IBD (in particular Crohn’s disease), wherein the treatment or prévention comprises inducing stability of the microbiota. In such embodiments, the composition may be adminîstered to a subject having reduced microbiota dîversity and / or stability.

In some embodiments, the invention provides a method of treatment or prévention of a disease or disorder associated with a level of microbiota dîversity and/or evenness that is reduced relative to the microbiota dîversity of a healthy subject or population of healthy subjects wherein the method comprises diagnosing a subject as having a reduced level of microbiota dîversity and then îf a reduced level of dîversity is found to be présent, administering a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron to the subject.

In some embodiments, the invention provides a method of treatment or prévention of a disease or disorder associated with reduced stability of microbiota relative to the stability of microbiota in a healthy subject wherein the method comprises diagnosing a subject as having reduced stability of microbiota and then if reduced stability is found to be présent, administering a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron to the subject.

S trains closely related to the species Bacteroides thetaiotaomicron may also be used. Such bacterial strains may hâve a 16s rRNA sequence that is at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequence of a bacterial strain of Bacteroides thetaiotaomicron. Preferably, the bacterial strain has a 16s rRNA sequence that is at least 95%, 95%, 97%, 98%, 99%, 99.5% or 99.9% identical to any one of SEQ ID NOs:l-12, preferably to SEQ ID NO: I. Preferably, the bacterial strain has the 16s rRNA sequence of SEQ ID NO:1.

Most preferably, the bacterial strain in the composition is the Bacteroides thetaiotaomicron strain deposited under accession number NCÏMB 42341.

In certain embodiments, the composition of the invention is for oral administration. Oral administration of the strains of the invention can be effective for increasing the microbiota 5 diversity and/or inducing the stability of the microbiota. Also, oral administration is convenient for subjects and practitioners and allows delivery to and/or partial or total colonisation of the intestine.

In certain embodiments, the composition of the invention comprises one or more pharmaceutically acceptable excipients or carriers.

In certain embodiments, the composition of the invention comprises a bacterial strain that has been lyophilised. Lyophilisation is an effective and convenient technique for preparing stable compositions that allow delivery of bacteria, and is shown to provide effective compositions in the examples.

In certain embodiments, the invention provides a food product comprising the composition as 15 described above.

In certain embodiments, the invention provides a vaccine composition comprising the composition as described above.

Additionally, the invention provides a method of increasing the microbiota diversity and/or inducing the stability of the microbiota and thereby treating or preventing diseases or disorders 20 associated with a reduced microbiota diversity and/or with reduced stability of the microbiota, comprising administering a composition comprising a bacterial strain of the genus Bacteroides.

BRIEF DESCRIPTION OF DRAWINGS

Figure 1: Effect of Thetanix treatment on microbiota diversity using Observed Species and Shannon Diversity Metrics

Figure 2: Effect of Thetanix on microbiota evenness

DISCLOSURE OF THE INVENTION

Bacterial strains

The compositions of the invention comprise a bacterial strain of the genus Bacteroides. The examples demonstrate that bacteria of this genus are useful for increasing the microbiota diversity and/or inducing the stability of the microbiota. The preferred bacterial strains are of the species Bacteroides thetaiotaomicron, particularly the bacterium deposited under accession number NCIMB 42341.

Bacteroides is a genus of gram-negative, obligate anaérobie bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species.

Bacteroides thetaiotaomicron was first described in 1912 under the name Bacillus thetaiotaomicron and moved to the genus Bacteroides in 1919. It was originally isolated from adult human feces. Bacteroides thetaiotaomicron triggers the nuclear export of the RelA subunit of nuclear kappa-light-chain-enhancer of actîvated B cells (NK-B), an important nuclear transcription factor, thereby limîting the transcription of downstream pro-inflammafory genes and synthesis of inflammatory factors, including interleukin (IL)-9 and tumor necrosis factor alpha (TNFa).

Bacterial strains closely related to the strain tested in the examples are also expected to be effective for increasing the microbiota diversity and/or inducing the stability of the microbiota. In certain embodiments, the bacterial strain for use in the invention has a 16s rRNA sequence that is at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequence of a bacterial strain of Bacteroides thetaiotaomicron. Preferably, the bacterial strain for use in the invention has a 16s rRNA sequence that is at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% identical to SEQ ID NO:1. Preferably, the bacterial strain for use in the invention has a 16s rRNA sequence that has the sequence of SEQ ID NO:1. Preferably, the bacterial strain for use in the invention belongs to the genus Bacteroides.

Bacterial strains that are biotypes of the bacterium deposited under accession number NCIMB 42341 are also expected to be effective for increasing the microbiota diversity and/or inducing the stability of the microbiota. A biotype is a closely related strain that has the saine or very similar physiological and biochemical characteristics.

Strains that are biotypes of a bacterium deposited under accession number NCIMB 42341 and that are suitable for use in the invention may be identified by sequencing other nucléotide sequences for a bacterium deposited under accession number NCIMB 42341. For example, substantîally the whole genome may be sequenced and a biotype strain for use in the invention may hâve at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% sequence identity across at least 80% of its whole genome (e.g. across at least 85%, 90%, 95% or 99%, or across its whole genome). For example, in some embodiments, a biotype strain has at least 98% sequence identity across at least 98% of its genome or at least 99% sequence identity across 99% of its genome. Other suitable sequences for use in identifying biotype strains may include hsp60 or répétitive sequences such as BOX, ERIC, (GTGfr, or REP or [27], Biotype strains may hâve sequences with at least 97%, 98%, 99%, 99.5% or 99.9% sequence identity to the corresponding sequence of a bacterium deposited under accession number NCIMB 42341. In some embodiments, a biotype strain has a sequence with at least 97%, 98%, 99%, 99.5% or 99.9% sequence identity to the corresponding sequence of the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341 and comprises a 16S rRNA sequence that is at least 99% identical (e.g. at least 99.5% or at least 99.9% identical) to SEQ ID NO:1. In some embodiments, a biotype strain has a sequence with at least 97%, 98%, 99%, 99.5% or 99.9% sequence identity to the corresponding sequence of the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341 and has the 16S rRNA sequence of SEQ ID NO:1.

Altematively, strains that are biotypes of a bacterium deposited under accession number NCIMB 42341 and that are suitable for use in the invention may be identified by using the accession number NCIMB 42341 deposit, and restriction fragment analysis and/or PCR analysis, for example by using fluorescent amplified fragment iength polymorphism (FAFLP) and répétitive DNA element (rep)-PCR fingerprinting, or protein profiling. or partial 16S or 23s rDNA sequencing. In preferred embodiments, such techniques may be used to identify other Bacteroides thetaiotaomicron strains.

In certain embodiments, strains that are biotypes of a bacterium deposited under accession number NCIMB 42341 and that are suitable for use in the invention are strains that provide the same pattern as a bacterium deposited under accession number NCIMB 42341 when analysed by amplified ribosomal DNA restriction analysis (ARDRA), for example when using Sau3AI restriction enzyme (for exemplary methods and guidance see, for example [28]). Altematively, biotype strains are identifîed as strains that hâve the same carbohydrate fermentation patterns as a bacterium deposited under accession number NCIMB 42341.

Other Bacteroides species that are useful in the compositions and methods of the invention, such as biotypes of a bacterium deposited under accession number NCIMB 42341, may be identifîed 5 using any appropriate method or strategy. For instance, strains for use in the invention may be identifîed by cuituring bacteria and administering to rats to test in the distension assay. In particular, bacterial strains that hâve similar growth patterns, metabolic type and/or surface antigens to a bacterium deposited under accession number NCIMB 42341 may be useful in the invention. A useful strain will hâve comparable microbiota modulatory activity to the NCIMB 10 42341 strain. In particular, a biotype strain will elicît comparable effects on the microbiota to the effects shown în tire Examples.

A parti cul arly preferred strain of the invention is the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341. This is the exemplary strain tested in the ex amples and shown to be effective for increasing the microbiota diversity and/or inducîng the 15 stability of the microbiota. Therefore, the invention provides a cell, such as an isolated cell, of the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341, or a dérivative thereof, for use in therapy, in particular for the diseases and disorders described herein.

A dérivative of the strain may be a daughter strain (progeny) or a strain cultured (subcloned) 20 from the original. A dérivative of a strain of the invention may be modified, for example at the genetic level, without ablating the biological activity. In particular, a dérivative strain of the invention is therapeutically active. A dérivative strain will hâve comparable microbiota modulatory activity to the original strain. In particular, a dérivative strain will elicit comparable effects on the microbiota to the effects shown in the Examples, which may be identifîed by using 25 the cuituring and administration protocols described in the Examples. A dérivative of the

NCIMB 42341 strain will general 1 y be a biotype of the NCIMB 42341 strain.

References to cells of the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341 encompass any cells that hâve the same safety and therapeutic efficacy characteristics as the strains deposited under accession number NCIMB 42341, and such cells 30 are encompassed by the invention.

In preferred embodiments, the bacterial strains in the compositions of the invention are viable and capable of partially or totally colonising the intestine.

Therapeutic uses

In certain embodiments, the compositions of the invention are for use in încreasing the microbiota diversity, eveuness and/or inducing the stability of the microbiota. Reduced diversity or evenness of the microbiota and/or reduced stability of the microbiota are associated with numerous pathological diseases and disorders, as discussed above, and the examples demonstrate that the compositions of the invention may be effective for încreasing the microbiota diversity and evenness and/or inducing the stability of the microbiota. Accordingly, the disease or dîsorder to be treated or prevented using a composition of the invention is preferably a disease or disorder associated with a level of microbiota diversity and / or evenness that is reduced relative to the microbiota diversity and / or evenness of a healthy subject and/or a disease or disorder that is associated with reduced stability of the microbiota. Thus, in some embodiments, the disease or disorder may be associated with a level of microbiota diversity and / or evenness that is reduced relative to the microbiota diversity of a healthy subject and also be associated with reduced stability of the microbiota.

In certain embodiments, the compositions of the invention are for use in încreasing the microbiota diversity, evenness and/or inducing the stability of the microbiota in patients diagnosed with a disease or disorder selected from IBS, IBD (including Crohn’s disease), cancer (including colorectal cancer) optionally in patients receiving concomitant anti-cancer thérapies such as chemotherapy, obesity, type 2 diabètes, one or more infections diseases, one or more allergie diseases, one or more autoimmune diseases and one or more metabolic diseases/disorders. Use of the compositions of the invention to increase the microbiota diversity, evenness and/or induce the stability of the microbiota in patients diagnosed with other diseases and disorders is also envisaged. In certain embodiments, the compositions of the invention are for use in treating or preventîng IBS or IBD. In certain embodiments, the compositions of the invention are for use in treating or preventîng IBS. In certain embodiments, the compositions of the invention are for use in treating or preventîng IBD. In certain embodiments, the compositions of the invention are for use in treating or preventîng one or more allergie diseases. In certain embodiments, the compositions of the invention are for use in treating or preventîng cancer optionally in patients administered concomitant anticancer therapy. In certain embodiments, the compositions of the invention are for use in treating or preventîng obesity. In certain embodiments, the compositions of the invention are for use in treating or preventing one or more infections diseases. In certain embodiments, the compositions of the invention are for use in treating or preventing one or more autoimmune diseases. In certain embodiments, the compositions of the invention are for use in treating or preventing one or more metabolic diseases/disorders. Preferably, the treatment or prévention comprises increasing the microbiota diversity and/or inducing the stability of the microbiota in the subject. Preferably the disease which is treated is Crohn’s disease.

In certain embodiments, the one or more infections diseases is selected from a viral, bacterial or fongal disease. In certain embodiments, the one or more allergie diseases is asthma. In certain embodiments, the one or more metabolic diseases/disorders is selected from diabètes, e.g. type 2 diabètes, and obesity. In certain embodiments, the one or more autoimmune diseases is selected from multiple sclerosis and rheumatoid arthritis.

In certain embodiments, the compositions of the invention are for use in treating or preventing IBS, IBD (including Crohn’s disease), obesity, type 2 diabètes, one of more infectious diseases, one or more allergie diseases, one or more autoimmune diseases or one or more metabolic diseases/disorders by increasing the microbiota diversity in the microbiota. In certain embodiments, the compositions of the invention are for use in treating or preventing IBS or IBD by inducing the stability of the microbiota. In certain embodiments, the compositions of the invention are for use in treating or preventing IBD by inducing the stability of the microbiota

In preferred embodiments, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron , for use in the treatment or prévention of IBD, IBS, obesity, type 2 diabètes, one or more infectious diseases, one or more allergie diseases, one or more autoimmune diseases or one or more metabolic diseases/disorders, wherein the treatment or prévention comprises increasing the microbiota diversity and/or inducing the stability of the microbiota in the subject.

In some embodiments, the invention provides a composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron for use in treating or preventing a disease or disorder selected from IBS, IBD, obesity, type 2 diabètes, one or more infectious diseases, one or more allergie diseases, one or more autoimmune diseases and one or more metabolic diseases/disorders. In some embodiments, the invention provides a method of treating or preventing a disease or disorder selected from IBS, IBD, obesity, type 2 diabètes, one or more infections diseases, one or more allergie dîseases, one or more autoimmune diseases and one or more metabolic diseases/disorders, comprising administering a composition comprising a bacterîal strain of the species Bacteroides thetaïotaomicron.

In preferred embodiments, the compositions of the invention comprise the bacterium deposited 5 under accession number NCIMB 42341 and are for use in increasing the microbiota diversity and/or inducing the stabîlîty of the microbiota in the subject in the treatment of IBD, IBS, obesity, type 2 diabètes, one or more infections diseases, one or more allergie diseases, one or more auto immune diseases or one or more metabolic diseases/disorders. In further preferred embodiments, the compositions of the invention comprise the bacterium deposited under 10 accession number NCIMB 42341 and are for use in treating or preventîng IBD, IBS, obesity, type 2 diabètes, one or more infectious diseases, one or more allergie diseases, one or more autoimmune diseases or one or more metabolic diseases/disorders by increasing the microbiota diversity and/or inducing the stability of the microbiota.

In some embodiments, the pathogenesis of the disease or disorder affects the intestine. In some 15 embodiments, the pathogenesis of the disease or disorder does not affect the intestine. In some embodiments, the pathogenesis of the disease or disorder is not localised at the intestine. In some embodiments, the treating or preventing occurs at a site other than at the intestine. In some embodiments, the treating or preventing occurs at the intestine and also at a site other than at the intestine. In certain embodiments, the disease or disorder is systemic.

In certain embodiments, the compositions are for use in subjects that exhibit, or are expected to exhibit, reduced levels of microbiota diversity, for example, when compared to a healthy subject, or a population of healthy subjects. For example, in some embodiments, the composition is for use in treating a subject having less than 101 different bacterîal species (e.g. less than 100, 99, 98, 97, 96, 95, 93, 90, 85, 80, 75 or 70 bacterîal species) and/or less than 195 different strains 25 (e.g. less than 193, 190, 187, 185, 183, 180, 175, 170, 165, 160, 150, 140 bacterîal strains) in its microbiota. For example, in some embodiments, the composition ts for use in treating a subject that has at least one bacterîal genus (e.g. at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 bacterîal généra) fewer in its intestinal microbiota compared to a healthy subject or compared to a population of healthy subjects. In some embodiments, the treatment or prévention comprises a step of diagnosing a 30 subject as having a reduced level of microbiota diversity and then if a reduced level of diversity is found to be présent, the subject is then treated with a composition according to the invention.

In certain embodiments, the compositions are for use in subjects that exhibit, or are expected to exhibit, reduced stability of the microbiota. In some embodiments, the compositions are for use in subjects that exhibit, or are expected to exhibit, reduced stability in its microbiota, for example, when compared to a healthy subject, or a population of healthy subjects. In some embodiments, the treatment or prévention comprises a step of diagnosing a subject as having a reduced stability in its microbiota and then if reduced stability is found to be présent, the subject îs then treated with a composition according to the invention.

In certain embodiments, the subject îs an infant. In certain embodiments, the subject is a child. In certain embodiments, the subject is an adult. The subject maybe an adolescent, for example a subject with an âge between 10 and 19 years.

In certain embodiments, the subject is a healthy subject. For example, in some embodiments in which the composition is used for preventing a disease or disorder, the subject is a healthy subject, optionally one identified as being at risk of developing a disease or disorder characterised by a réduction in microbiota diversity.

In certain embodiments, the subject has previously received, is receiving, or will be receiving anticancer treatment, for exampie chemotherapy. Accordingly, in some embodiments, the treatment or prévention comprises administering the composition of the invention after, together with, or before anticancer treatment.

In certain embodiments, the subject has previously received, is receiving, or will be receiving antibiotic treatment. Accordingly, in some embodiments, the treatment or prévention comprises administering the composition of the invention after, together with, or before antibiotic treatment. The composition of the invention and the one or more antibiotics may be for separate, sîmultaneous or sequential administration.

Treatment or prévention may refer to, for example, an alleviatîon of the severity of symptoms or a réduction in the frequency of exacerbations or the range of triggers that are a problem for the subject.

Bacteria in the microbiota may be detected in faeces from a subject, using standard techniques, such as the qPCR techniques used in the examples.

Modes of administration

Preferably, the compositions of the invention are to be administered to the gastrointestinal tract in order to enable delivery to and / or partial or total colonisation of the intestine with the bacterial strain of the invention. Generaily, the compositions of the invention are administered orally, but they may be administered rectaily, intranasally, or via buccal or sublingual routes.

In certain embodiments, the compositions of the invention may be administered as a foam, as a spray or a gel.

In certain embodiments, the compositions of the invention may be administered as a suppository, such as a rectal suppository, for example in the form of a theobroma oil (cocoa butter), synthetic hard fat (e.g. suppocire, witepsol), glycero-gelatin, polyethylene glycol, or soap glycerin composition.

In certain embodiments, the composition of the invention îs administered to the gastro intestinal tract via a tube, such as a nasogastric tube, orogastric tube, gastric tube, jejunostomy tube (J tube), percutaneous endoscopie gastrostomy (PEG), or a port, such as a chest wall port that provides access to the stomach, jéjunum and other suitable access ports.

The compositions of the invention may be administered once, or they may be administered sequentially as part of a treatment regimen. In certain embodiments, the compositions of the invention are to be administered daily. The examples demonstrate that daily administration provides successful delivery and clinical benefits.

In certain embodiments, the compositions of the invention are administered regularly, such as daily, every two days, or weekly, for an extended period of time, such as for at least one week, two weeks, one month, two months, six months, or one year.

In certain embodiments of the invention, treatment accordîng to the invention is accompanied b y assessment of the subject’s gut microbiota. Treatment may be repeated if delivery of and / or partial or total colonisation with the strain of the invention is not achieved such that efficacy is not observed, or treatment may be ceased if delivery and / or partial or total colonisation is successful and efficacy is observed.

In certain embodiments, the composition of the invention may be administered to a prégnant animal, for example a mammal such as a human in order to prevent reduced levels of diversity in the microbiota and/or reduced stability of the microbiota developing in her child in utero and / or after it is born.

The compositions of the invention may be admînistered to a subject that has been diagnosed with reduced microbiota diversity relative to a healthy subject and/or reduced stability of the microbiota or a disease or disorder associated with reduced microbiota diversity relative to a healthy subject and/or reduced stability of the microbiota, or that has been identified as being at risk of reduced microbiota diversity relative to a healthy subject and/or reduced stability of the microbiota. The compositions may also be admînistered as a prophylactic measure to prevent the development of reduced microbiota diversity relative to a healthy subject and/or reduced stability of the microbiota in a healthy subject.

The compositions of the invention may be admînistered to a subject that has been identified as having an abnormal gut microbiota. For example, the subject may hâve reduced or absent colonisation b y Bacteroides, and in particular Bacteroides thetaiotaomicron.

The compositions of the invention may be admînistered as a food product, such as a nutritional supplément.

Generally, the compositions of the invention are for the treatment of humans, although they may be used to treat animais including monogastric mammals such as poultry, pigs, cats, dogs, horses or rabbits. The compositions of the invention may be useful for enhancing the growth and performance of animais. If admînistered to animais, oral gavage may be used.

Compositions

Generally, the composition of the invention comprises bacteria. In preferred embodiments of the invention, the composition is formulated in freeze-dried fonn. For example, the composition of the invention may comprise granules or gelatin capsules, for example hard gelatin capsules, comprising a bacterial strain of the invention.

Preferably, the composition of the invention comprises lyophilîsed bacteria. Lyophilisation of bacteria is a well-established procedure and relevant guidance is available in, for example, references [29-31]. The examples demonstrate that lyophilisate compositions are partîcularly effective.

Altematîvely, the composition of the invention may comprise a live, active bacterial culture.

ln some embodiments, the bacterial strain in the composition of the invention has not been inactivated, for example, has not been heat-inactivated. In some embodiments, the bacterial strain in the composition of the invention has not been killed, for example, has not been heatkilled. In some embodiments, tire bacterial strain in the composition of the invention has not been attenuated, for example, has not been heat-atténuaied. For example, in some embodiments, the bacterial strain in the composition of the invention has not been killed, inactivated and/or attenuated. For ex ample, in some embodiments, the bacterial strain in the composition of the invention is live. For example, in some embodiments, the bacterial strain in the composition of the invention is viable. For example, in some embodiments, the bacterial strain in the composition of the invention is capable of partialiy or totally colonising the intestine. For example, in some embodiments, the bacterial strain in the composition of the invention is viable and capable of partialiy or totally colonising the intestine.

In some embodiments, the composition comprises a mixture of live bacterial strains and bacterial strains that hâve been killed.

In preferred embodiments, the composition of the invention is encapsulated to enable delivery of the bacterial strain to the intestine. Encapsulation protects the composition from dégradation until delivery at the target location through, for example, rupturing with Chemical or physical stîmuli such as pressure, enzymatic activity, or physical disîntegration, which may be triggered by changes in pH. Any appropriate encapsulation method may be used. Exemplary encapsulation techniques include entrapment within a porous matrix, attachment or adsorption on solid carrier surfaces, self-aggregation by flocculation or with cross-linking agents, and mechanical containment behind a microporous membrane or a microcapsule. Guidance on encapsulation that may be useful for preparing compositions of the invention is available in, for example, référencés [32] and [33].

The composition may be administered orally and may be in the form of a tablet, capsule or powder. Encapsulated products are preferred because Blautia are anaerobes. Other ingrédients (such as vitamin C, for ex ample), may be included as oxygen scavengers and prebiotîc substrates to improve the delivery and / or partial or total colonisation and survival in vivo. Altematively, the probiotic composition of the invention may be administered orally as a food or nutritional product, such as mîlk or whey based fermented dairy product, or as a pharmaceutical product.

The composition may be formulated as a probiotic.

A composition of the invention includes a therapeutically effective amount of a bacterial strain of the invention. A therapeutically effective amount of a bacterial strain is sufficient to exert a bénéficiai effect upon a subject. A therapeutically effective amount of a bacterial strain may be sufficient to resuit in deiivery to and / or partial or total colonisation of the subject’s intestine.

A suitable daily dose of the bacteria, for example for an adult human, may be from about 1x10 to about 1 x 10 colony forming units (CFU); for example, from about 1 x 10⁷ to about 1 x 10¹⁰CFU; în another example from about 1 x 10⁷ to about 1 x 10¹¹ CFU; in another example from about 1 x 10⁸ to about 1 x 10¹⁰ CFU; in another example from about 1 x 10^s to about 1 x 10¹¹CFU; în another example from about 1 x 10⁶ to about 1 x 10¹⁰ CFU.

In certain embodiments, the dose of the bacteria is at least 10⁹ cells per day, such as at least 10*°, at least 10¹¹, or at least 10¹² cells per day.

In certain embodiments, the composition contains the bacterial strain in an amount of from about 1 x 10⁶to about 1 x 10¹¹ CFU/g, respect to the weight of the composition; for example, from about 1 x 10⁸ to about 1 x 10¹⁰ CFU/g. The dose may be, for exampie, 1 g, 3g, 5g, and 10g. In preferred embodiments, the composition contains the bacterial strain in an amount from about 1 x 1Û⁶ to about 1 x 10^{9 5}.

Typically, a probiotic, such as the composition of the invention, is optionally combined with at least one suitable prebiotic compound. A prebiotic compound is usually a non-digestible carbohydrate such as an oligo- or polysaccharide, or a sugar alcohol, which is not degraded or absorbed in the upper digestive tract. Known prebiotics include commercial products such as inulin and transgalacto-oligosaccharides.

In certain embodiments, the probiotic composition of the présent invention includes a prebiotic compound in an amount of from about 1 to about 30% by weight, respect to the total weight composition, (e.g. from 5 to 20% by weight). Carbohydrates may be selected from the group consisting of: fructo- oligosaccharides (or FOS), short-chain fructo-oligosaccharides, inulin, isomalt-oligosaccharides, pectins, xylo-oligosaccharides (or XOS), chitosan-oligosaccharides (or COS), beta-glucans, arable gum modified and résistant starches, polydextrose, D-tagatose, acacia fibers, carob, oats, and citrus fibers. In one aspect, the prebiotics are the short-chain fructooligosaccharides (for simplicity shown herein below as FOSs-c.c); said FOSs-c.c. are not digestible carbohydrates, generally obtained by the conversion of the beet sugar and including a saccharose molécule to which three glucose molécules are bonded.

The compositions of the invention may comprise pharmaceutically acceptable excipients or carriers. Ex amples of such suitable excipients may be found in the référencé [34], Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art and are described, for example, in référencé [35]. Examples of suitable carriers include lactose, starch, glucose, methyl cellulose, magnésium stéarate, mannitol, sorbitol and the like. Examples of suitable diluents include éthanol, glycerol and water. The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may comprise as, or in addition to, the carrier, excipient or diluent any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s). Examples of suitable btnders include starch, gelatin, natural sugars such as glucose, anhydrous lactose, free-flow lactose, beta-lactose, corn sweeteners, natural and synthetic gums, such as acacia, tragacanth or sodium alginate, carboxymethyl cellulose and polyethylene glycol. Examples of suitable lubricants include sodium oleate, sodium stéarate, magnésium stéarate, sodium benzoate, sodium acetate, sodium chloride and the like. Preservatïves, stabilizers, dyes and even flavouring agents may be provided in the pharmaceutical composition. Ex amples of preservatïves include sodium benzoate, sorbic acid, cysteine and esters of p-hydroxybenzoic acid. Antioxidants and suspending agents may be also used. A further example of a suitable carrier is saccharose. A further example of a préservait ve is cysteine.

The compositions of the invention may be formulated as a food product. For example, a food product may provide nutritional benefit in addition to the therapeutic effect of the invention, such as in a nutritional supplément. Similarly, a food product may be formulated to enhance the taste of the composition of the invention or to make the composition more attractive to consume by being more simîlar to a common food item, rather than to a pharmaceutical composition. In certain embodiments, the composition of the invention is formulated as a milk-based product. The term milk-based product means any liquid or semi-solid milk- or whey- based product having a varying fat content. The milk-based product can be, e.g., cow's milk, goat's milk, sheep's milk, skimmed milk, whole milk, milk recombined from powdered milk and whey without any processing, or a processed product, such as yoghurt, curdled milk, curd, sour milk, sour whole milk, butter milk and other sour milk products. Another important group includes milk beverages, such as whey beverages, fermented milks, condensed milks, infant or baby milks; flavoured milks, ice cream; milk-contaîning food such as sweets.

In certain embodiments, the compositions of the invention contain a single bacterîal straîn or species and do not contain any other bacterîal strains or species. Such compositions may comprise only de minimis or biologically irrelevant amounts of other bacterîal strains or species. Such compositions may be a culture or lyophilisate that is substantially free from other species of organism.

In certain embodiments, the compositions of the invention comprise one or more bacterîal strains of the genus Bacteroides and do not contain any other bacterîal généra, or which comprise only de minimis or biologically irrelevant amounts of bacteria from another genus. In certain embodiments, the compositions of the invention comprise a single species of Bacteroides, preferably Bacteroides thetaiotaomicron, and do not contain any other bacterîal species, or which comprise only de minimis or biologically irrelevant amounts of bacteria from another species. In certain embodiments, the compositions of the invention comprise a single strain of Bacteroides, for example, of Bacteroides thetaiotaomicron NCIMB 42341 and do not contain any other bacterîal strains or species, or which comprise only de minimis or biologically inelevant amounts of bacteria from another strain or species.

In some embodiments, the compositions of the invention comprise more than one bacterîal straîn or species. For example, in some embodiments, the compositions of the invention comprise more than one strain from within the same species (e.g. more than 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40 or 45 strains), and, optionally, do not contain bacteria from any other species. In some embodiments, the compositions of the invention comprise less than 50 strains from within the same species (e.g. less than 45, 40, 35, 30, 25, 20, 15, 12, 10, 9, 8, 7, 6, 5, 4 or 3 strains), and, optionally, do not contain bacteria from any other species. In some embodiments, the compositions of the invention comprise 1-40, 1-30, 1-20, 1-19, 1-18, 1-15, 1 -10, 1-9, 1-8, 17, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-4Ü, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 strains from within the same species and, optionally, do not contain bacteria from any other species. In some embodiments, the compositions of the invention comprise more than one species from within the same genus (e.g. more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, 23, 25, 30, 35 or 40 species), and, optionally, do not contain bacteria from any other genus. In some embodiments, the compositions of the invention comprise less than 50 species from within the same genus (e.g. less than 50, 45, 40, 35, 30, 25, 20, 15, 12, 10, 8, 7, 6, 5, 4 or 3 species), and, optionally, do not contain bacteria from any other genus. In some embodiments, the compositions of the invention comprise 1-50, 1-40, 1-30, 1-20, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 120538

5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 species from within the same genus and, optionally, do not contain bacteria from any other genus, The invention comprises any combination of the foregoing.

In some embodiments, the composition comprises a microbial consortium. For example, în some embodiments, the composition comprises the Bacteroides bacterial strain, for example, a Bacteroides thetaiotaomicron bacterial strain as part of a microbial consortium. For example, in some embodiments, the Bacteroides bacterial strain is présent in combination with one or more (e.g. at least 2, 3, 4, 5, 10, 15 or 20) other bacterial strains from other généra with which it can live symbiotically in vivo in the intestine. For ex ample, in some embodiments, the composition comprises a bacterial strain of Bacteroides thetaiotaomicron in combination with a bacterial strain from a different genus. In some embodiments, the microbial consortium comprises two or more bacterial strains obtained from a faeces sample of a single organism, e.g, a human. In some embodiments, the microbial consortium is not found together in nature. For example, in some embodiments, the microbial consortium comprises bacterial strains obtained from faeces samples of at least two different organisms. In some embodiments, the two different organisms are from the same species, e.g. two different humans. In some embodiments, the two different organisms are an infant human and an adult human. In some embodiments, the two different organisms are a human and a non-human mammal.

In some embodiments, the composition of the invention additionally comprises a bacterial strain that has the same safety and therapeutic efficacy characteristics as the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341, but which is not the Bacteroides thetaiotaomicron strain deposited under accession number NCIMB 42341, or which is not a Bacteroides thetaiotaomicron strain.

In some embodiments in which the composition of the invention comprises more than one bacterial strain, species or genus, the individual bacterial strains, species or généra may be for separate, simultaneous or sequentîal administration. For example, the composition may comprise ail of the more than one bacterial strains, species or généra, or the bacterial strains, species or généra may be stored separateîy and be administered separately, simultaneously or sequentially. In some embodiments, the more than one bacterial strains, species or généra are stored separately but are mixed together prier to use.

In some embodiments, the bacterial strain for use in the invention is obtained from human adult faeces. In some embodiments in which the composition of the invention comprises more than one bacterial strain, ail of the bacterial strains are obtained from human adult faeces or if other bacterial strains are présent they are présent only in de minimis amounts. In some embodiments, the bacteria may hâve been cultured subséquent to being obtained from the human adult faeces and being used in a composition of the invention.

ïn some embodiments, the one or more Bacteroides bacterial strains (for example the Bacteroides thetaiotaomicron strain) is/are the only therapeutically active agent(s) in a composition of the invention. In some embodiments, the bacterial strain(s) in the composition is/are the only therapeutically active agent(s) in a composition of the invention.

The compositions for use in accordance with the invention may or may not require marketing approval.

In certain embodiments, the invention provides the above pharmaceutical composition, wherein said bacterial strain is lyophilised. In certain embodiments, the invention provides the above phannaceutical composition, wherein said bacterial strain is spray dried. In certain embodiments, the invention provides the above pharmaceutical composition, wherein the bacterial strain is lyophilised or spray dried and wherein it is live. In certain embodiments, the invention provides the above phannaceutical composition, wherein the bacterial strain is lyophilised or spray dried and wherein it is viable. In certain embodiments, the invention provides the above pharmaceutical composition, wherein the bacterial strain is lyophilised or spray dried and wherein it is capable of partially or totally colonising the intestine. In certain embodiments, the invention provides the above phannaceutical composition, wherein the bacterial strain is lyophilised or spray dried and wherein it is viable and capable of partially or totally colonising the intestine.

In some cases, the lyophilised or spray dried bacterial strain is reconstituted prior to administration. In some cases, the reconstitution is by use of a diluent described herein.

The compositions of the invention can comprise pharmaceutically acceptable excipients, diluents or carriers.

In certain embodiments, the invention provides a phannaceutical composition comprising: a bacterial strain as used in the invention; and a pharmaceutically acceptable excipient, carrier or diluent; wherein the bacterial strain is in an amount sufficient to increase the microbiota diversity in a subject and/or induce stability of the microbiota and/or treat a disorder associated with reduced microbiota diversity and/or reduced stability of the microbiota when administered to a subject in need thereof, the disorder associated with microbiota diversity being selected from, for example, IBS, IBD, cancer, obesity, type 2 diabètes, one or more infections diseases, one or more allergie diseases, one or more autoimmune diseases or one or more metabolic di seases/disorders.

In certain embodiments, the invention provides the above pharmaceutical composition, wherein the amount of the bacterial strain is from about 1 * 10³ to about 1 x lü¹¹ colony forming units per gram with respect to a weîght of the composition.

In certain embodiments, the invention provides the above pharmaceutical composition, wherein the composition is administered at a dose of 1 g, 3 g, 5 g or 10 g.

In certain embodiments, the invention provides the above pharmaceutical composition, wherein the composition is administered by a method selected from the group consisting of oral, rectal, subeutaneous, nasal, buccal, and sublingual.

In certain embodiments, the invention provides the above pharmaceutical composition, comprising a carrier selected from the group consisting of lactose, starch, glucose, methyl cellulose, magnésium stéarate, mannitol and sorbîtol.

In certain embodiments, the invention provides the above pharmaceutical composition, comprising a diluent selected from the group consisting of éthanol, glycerol and water.

In certain embodiments, the invention provides the above pharmaceutical composition, comprising an excipient selected from the group consisting of starch, gelatin, glucose, anhydrous lactose, free-flow lactose, beta-lactose, corn sweetener, acacia, tragacanth, sodium algînate, carboxymethyl cellulose, polyethylene glycol, sodium oleate, sodium stéarate, magnésium stéarate, sodium benzoate, sodium acetate and sodium chloride.

In certain embodiments, the invention provides the above pharmaceutical composition, further comprising at least one of a preservative, an antioxidant and a stabilizer.

In certain embodiments, the invention provides the above pharmaceutical composition, comprising a preservative selected from the group consisting of sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid.

In certain embodiments, the invention provides the above pharmaceutical composition, wherein said bacterial strain is lyophilised.

In certain embodiments, the invention provides the above phannaceutical composition, wherein when the composition is stored in a sealed container at about 4°C or about 25°C and the container is placed in an atmosphère having 50% relative humidîty, at least 80% of the bacterial strain as measured in colony forming units, remains after a period of at least about: 1 month, 3 months, 6 months, 1 year, 1.5 years, 2 years, 2.5 years or 3 years.

In some embodiments, the composition of the invention is provided in a sealed container comprising a composition as described herein. In some embodiments, the sealed container is a sachet or bottle. In some embodiments, the composition of the invention is provided in a syringe comprising a composition as described herein.

The composition of the présent invention may, in some embodiments, be provided as a phannaceutical formulation. For example, the composition may be provided as a tablet or capsule. In some embodiments, the capsule is a gélatine capsule (“gel-cap”).

In some embodiments, the compositions of the invention are administered orally. Oral administration may involve swallowing, so that the compound enters the gastro intestinal tract, and/or buccal, lingual, or sublingual administration by which the compound enters the blood stream directly from the mouth.

Pharmaceutical formulations suitable for oral administration include solid plugs, solid microparticulates, semi-solid and liquid (including multiple phases or dispersed Systems) such as tablets; soft or hard capsules containing muiti- or nano-particulates, liquids (e.g. aqueous solutions), émulsions or powders; lozenges (including liquid-filled); chews; gels; fast dispersing dosage fonns; films; ovules; sprays; and buccal/mucoadhesive patches.

In some embodiments the phannaceutical fonnulation is an enteric formulation, i.e. a gastrorésistant formulation (for ex ample, résistant to gastric pH) that is suitable for delivery of the composition of the invention to the intestine by oral administration. Enteric formulations may be parti cul arly useful when the bacteria or another component of the composition is acidsensitive, e.g. prone to dégradation under gastric conditions.

In some embodiments, the enteric fonnulation comprises an enteric coating. In some embodiments, the formulation is an enteric-coated dosage form. For example, the formulation may be an enteric-coated tablet or an enteric-coated capsule, or the lîke. The enteric coatîng may be a conventional enteric coating, for example, a conventional coating for a tablet, capsule, or the like for oral delivery. The formulation may comprise a film coating, for example, a thin film layer of an enteric polymer, e.g. an acid-insoluble polymer.

In some embodiments, the enteric formulation is intrinsically enteric, for example, gastrorésistant without the need for an enteric coating. Thus, in some embodiments, the formulation is an enteric formulation that does not comprise an enteric coating. In some embodiments, the formulation is a capsule made from a thermogelling material. In some embodiments, the thermogelling material is a cellulosic material, such as methylceliulose, hydroxymethylcellulose or hydroxypropyhn ethyl cellulose (HPMC). In some embodiments, the capsule comprises a shell that does not contain any film fonning polymer. In some embodiments, the capsule comprises a shell and the shell comprises hydroxypropylmethyl cellulose and does not comprise any film forming polymer (e.g. see [36 ]). In some embodiments, the formulation is an intrinsically enteric capsule (for example, Vcaps® from Capsugel).

In some embodiments, the formulation is a soft capsule. Soft capsules are capsules which may, owing to additions of softeners, such as, for example, glycerol, sorbitol, maltitol and polyethylene glycols, présent in the capsule shell, hâve a certain elasticity and softness. Soft capsules can be produced, for example, on the basis of gélatine or starch. Gelatîne-based soft capsules are commercially available from various suppliers. Depending on the method of administration, such as, for example, orally or rectally, soft capsules can hâve various shapes, they can be, for example, round, oval, oblong or torpedo-shaped. Soft capsules can be produced by conventional processes, such as, for example, by the Scherer process, the Accogel process or the droplet or blowing process.

Culturing methods

The bacterial strains for use in the présent invention can be cultured using standard microbiology techniques as detailed in, for example, references [37-39].

The solid or liquid medium used for culture may be YCFA agar or YCFA medium. YCFA medium may include (per 100ml, approximate values): Casitone (1.0 g), yeast extract (0.25 g), NaHCO₃ (0.4 g), cysteine (0.1 g), K₂HPO₄ (0.045 g), KH₂PO₄ (0.045 g), NaCl (0.09 g), (NH₄)₂SO₄ (0.09 g), MgSO₄ · 7H₂O (0.009 g), CaCl₂ (0.009 g), resazurin (0.1 mg), hemin (1 mg), biotin (1 pg), cobalamin (1 pg), p-aminobenzoîc acid (3 pg), folie acid (5 pg), and pyridoxamine (15 pg).

Bacterial strains for use in vaccine compositions

The inventors hâve identified that the bacterial strains of the invention are useful for treating or 5 preventing diseases or disorders assocîated with a level of microbiota diversity that is reduced relative to the microbiota diversity of a hcalthy subject (or relative to the microbiota diversity of a population of healthy subjects) and/or diseases or disorders that are associated with reduced stability of the microbiota compared to a healthy subject (or compared to a population of healthy subjects). This is likely to be a resuit of the effect that the bacterial strains of the invention hâve 10 on the host immune System. Therefore, the compositions of the invention may also be useful for preventing such diseases or disorders when administered as vaccine compositions. These vaccines comprise a B. thetaiotaomicron antigen. In certain such embodiments, the bacterial strains of the invention are viable. In certain such embodiments, the bacterial strains of the invention are capable of partially or totally colonising the intestine. In certain such 15 embodiments, the bacterial strains of the invention are viable and capable of partially or totally colonising the intestine. In other certain such embodiments, the bacterial strains of the invention may be killed, inactivated or attenuated. In certain such embodiments, the compositions may comprise a vaccine adjuvant. In certain embodiments, the compositions are for administration via injection, such as via subeutaneous injection.

General

The practice of the présent invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, molecular biology, immunology and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., référencés [40] and [41-47], etc.

The tenu “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X + Y.

The tenu “about” in relation to a numerical value x is optional and means, for example, x+10%.

The word “substantially” does not exclude “completely” e.g. a composition which is “substantially free” from Y may be completely free from Y. Where necessary, the word 30 “substantially” may be omitted from the définition of the invention.

References to a percentage sequence identity between two nucléotide sequences means that, when alîgned, that percentage of nucléotides are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be detennined using software programs known in the art, for example those described in section 7.7.18 of ref. [48], A preferred alignment is determined by the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology search algorithm is disclosed in ref. [49].

Unless specifically stated, a process or method comprising numerous steps may comprise additional steps at the beginning or end of the method, or may comprise additional intervening steps. Also, steps may be combined, omitted or performed in an alternative order, if appropriate.

Various embodiments of the invention are described herein. It will be appreciated that the features specified in each embodiment may be combined with other specified features, to provide further embodiments. In parti cular, embodiments highlighted herein as being suitable, typical or preferred may be combined with each other (except when they are mutually exclusive).

MODES FOR CARRYING OUT THE INVENTION

Example 1 - Effect of Thetanix on Microbiota Diversity

Thetanix is a live biotherapeutic contaîning the bacterium Bacteroides thetaiotaomicron (B. Thêta) as the active ingrédient. It is lyophilised and formulated as gastro-résistant capsules for oral administration. Each capsule contains jq^{7 73±l 43} colony forming units (CFUs).

Overall study design

The study was a randomised, double-blind, placebo-controlled, multiple dose study in subjects aged 16 to 18 years with Crohn’s disease. Subjects suitable for the study were identifîed from patient lists at appropriate gastroenterology clinics.

The patients receîved daily dosing over 7.5 days where the first dose was taken on Day 0 (D0) in clinic, the next 13 doses were taken at home and the 15th dose was taken in the clinic. Subject received a dose of B. Thêta or placebo an hour before fbod every 12 hours during the 7.5 day dosing period.

Stool samples were collected at D0, Dl, D7 and D56. These were analysed by quantitative polymerase Chain reaction (PCR) for B. thêta and other common constituents of the microbiome.

Results

The effect of treatment on microbiota diversity was assessed using the number of Observed species per sample (richness) and the Shannon Diversity Index which represents the number of taxa (richness) and their relative abundances (evenness) wîthin each sample. The effects of Thetanîx treatment on microbiota diversity are shown in Figure 1 which shows a significant différence in Shannon Diversity between the study timepoints (DO, D7 and D56). Similarly, microbiota evenness was found to be significant across the study timepoints, as shown in Figure 2.

Conclusions

B. Thêta was well tolerated in the study. There were no serious adverse events, deaths or subjects who discontinued from the study after treatment. There were no trends in haematology, clinical chemistry, vital signs, or physical examinations to suggest an adverse effect of B. Thêta on these parameters.

Although the study was conducted in a small population, Thetanîx shows promise as an agent capable of încreasing diversity and evenness in the microbiota. Given the association between disease and a loss of microbiota diversity, Thetanîx can be expected to treat conditions like Crohn’s disease which are associated with reduced microbiome diversity.

Furthermore, a signifant change in the faecal calprotectin levels was observed in several of the patients administered Thetanîx over the course of the study indicating the efficacy of Thetanîx treatment in Crohn’s disease.

The invention has been described above by way of example only and it will be understood that further modifications may be made which fall wîthin the scope of the daims.

Sequences

SEQ ID NO:1 (Bacteroides thetaiotaomicron straîn NCIMB 42341 16S ribosomal RNA gene) cttttacaat gaagagtttg atcctggctc aggatgaacg ctagctacag gcttaacaca 60 tgcaagtcga ggggcagcat ttcagtttgc ttgcaaactg gagatggcga ccggcgcacg 120 ggtgagtaac acgtatccaa cctgccgata actcggggat agcctttcga aagaaagatt 180

	aatacccgat ggttatcgat ggggatgcgt cgatggatag	ggtataatca 240 tccattaggc 300	gaccgcatgg agttggtgag	tttgattatt gtaacggctc	aaagaatttc accaaacctt
5	gggttctgag tcctacggga	aggaaggtcc 360	cccacattgg	aactgagaca	cggtccaaac
	ggcagcagtg tagcgtgaag	aggaatattg 420	gtcaatgggc	gcaggcctga	accagccaag
10	gatgactgcc ccacgtgtgg	ctatgggttg 480	taaacttctt	ttatatggga	ataaagtttt
	aattttgtat ccgcggtaat	gtaccatatg 540	aataaggatc	ggctaactcc	gtgccagcag
	acggaggatc gtggacagtt	cgagcgttat 600	ccggatttat	tgggtttaaa	gggagcgtag
15	aagtcagttg ggctgtcttg	tgaaagtttg 660	cggctcaacc	gtaaaattgc	agttgatact
	agtacagtag tatcacgaag	aggtgggcgg 720	aattcgtggt	gtagcggtga	aatgcttaga
20	aactccgatt gaaagtgtgg	gcgaaggcag 780	ctcactggac	tgcaactgac	actgatgctc
	gtatcaaaca actcgctgtt	ggattagata 840	ccctggtagt	ccacacagta	aacgatgaat
	tgcgatatac gagtacgccg	agtaagcggc 900	caagcgaaag	cattaagtat	tccacctggg
25	gcaacggtga catgtggttt	aactcaaagg 960	aattgacggg	ggcccgcaca	agcggaggaa
	aattcgatga atattggaaa	tacgcgagga 1020	accttacccg	ggcttaaatt	gcatttgaat
30	cagtatagcc cgtgccgtga	gtaaggcaaa 1080	tgtgaaggtg	ctgcatggtt	gtcgtcagct
	ggtgtcggct acaggtcatg	taagtgccat 1140	aacgagcgca	acccttatct	ttagttacta

	ctgaggactc gacgtcaaat cagcacggcc agaaggcagc	tagagagact 1200 cttacgtccg 1260	gccgtcgtaa gggctacaca	gatgtgagga cgtgttacaa	aggtggggat tggggggtac
5	tacctggtga agtctgcaac	caggatgcta 1320	atcccaaaag	cctctctcag	ttcggatcga
	ccgacttcgt ggtgaatacg	gaagctggat 1380	tcgctagtaa	tcgcgcatca	gccatggcgc
10	ttcccgggcc ctgaagtacg	ttgtacacac 1440	cgcccgtcaa	gccatgaaag	ccgggggtac
	taaccgcaag 1482	gagcgtccta	gggtaaaact	ggtaattggg	gc

SEQ ID NO: 2 (Bacteroides thetaiotaomicron (ATCC 29148) 16S rRNA)

	cantgaagag cacatgcaag tcgaggggca cacgggtgag	tttgatcctg 60 gcatttcnnt 120	gctcaggatn ttgcttgcaa	aacgctagct actnnagatg	acaggcttaa gcgaccggcg
20	taacacgtat gattaatacc	ccaacctgcc 180	gataactcgg	ggatagcctt	tcgaaagaaa
	cgatggcata cgatggggat	atcanaccgc 240	atggtcttat	tattaaagaa	tttcggttat
25	gcgttccatt ataggggttc	aggcagttgg 300	tgaggtaacg	gctcacnaaa	ccttcgatgg
	tgagaggaag gggaggcagc	gtcccccaca 360	ttggaactga	gacacggtcc	naactcctac
	agtgaggaat gaaggatgac	attggtcaat 420	gggcgcaggc	ctnaaccagc	caagtagcgt
30	tgccctatgg gtggaatttt	gttgtaaact 480	nctnttatat	gggaataaag	tnttccacgt
	gtatgtacca tnatacggag	tatgaataag 540	gatcggctaa	ctccgtgcca	gcagccgcgg

	gatccgagcg agttaagtca gttgtgaaag cttgagtaca	ttatccggat 600 tttgcggctc 660	ttattgggtt aaccgtaaaa	taaagggagc ttgcagttga	gtaggtggac tactggctgt
5	gtagaggtgg gaagaactcc	gcggaattcg 720	tggtgtagcg	gtgaaatgct	tagatatcac
	gattgcgaag gtgggtatca	gcagctcact 780	ggactgcaac	tgacactgat	gctcgaaagt
10	aacaggatta tgtttgcgat	gataccctgg 840	tagtccacac	agtaaacgat	gaatactcgc
	atacagtaag gccggcaacg	cggccaagcg 900	aaagcattaa	gtattccacc	tggggagtac
	gtgaaactca gtttaattcg	aaggaattga 960	cgggggcccg	cacaagcgga	ggaacatgtg
15	atgatacgcg gaaacaggtt	aggaacctta 1020	cccgggctta	aattgcattt	gaataatctg
	agccgcaagg gtgaggtgtc	caaatgtgaa 1080	ggtgctgcat	ggttgtcgtc	agctcgtgcc
20	ggcttaagtg catgctgagg	ccataacgag 1140	cgcaaccctt	atctttagtt	actaacaggt
	actctagaga aaatcagcac	gactgccgtc 1200	gtaagatgtg	aggaaggtgg	ggatgacgtc
	ggcccttacg cagctacctg	tccggggcta 1260	cacacgtgtt	acaatggggg	gtacagaagg
25	gtgacaggat caacccgact	gctnatccca 1320	aaagcctctc	tcagttcgga	tcgaagtctg
	tcgtgaagct tacgttcccg	ggattcgcta 1380	gtaatcgcgc	atcagccatg	gcgcggtgaa
30	ggccttgtac tacgtaaccg caaggagcgt 1475	acaccgcccg 1440 cctagggtaa	tcaanccatg aactggtaat	anagccgggg tgggg	gtacctgaag

	SEQ ID NO: 3 cttntacaat gcttaacaca tgcaagtcna	(Bacteroides thetaiotaomicron strain WAL 2926 (M58763) I6S rRNA)
gaagagtttg atcctggctc	aggatnaacg ttgcaaactg	ctagctacag gagatggcga
60 ggggcagcat	ttcagtttgc
5	ccggcgcacg	120
	ggtgagtaac aagaaagatt	acgtatccaa 180	cctgccgata	actcggggat	agcctttcga
	aatacccnat ggttatcgat	ggtataatca 240	gaccgcatng	tcttrttatt	aaagaatttc
10	ggggatgcgt cgatggatag	tccattaggc 300	agttggtgag	gtaacggctc	acnnaacctt
	gggttctgag tcctacggga	aggaaggtcc 360	cccacattgg	aactgagaca	cggtccaaac
15	ggcagcagtg tagcgtgaag	aggaatattg 420	gtcaatgggc	gcaggcctga	accagccaag
	gatgactgcc ccacgtgtgg	ctatgggttg 480	taaacttctt	ttatatggga	ataaagtttt
	aattttgtat ccncgntnat	gtaccatatg 540	aataaggatc	ggctaactcc	gtgccagcag
20	acggagnatc gtggacagtt	cgagcgttat 600	ccggatttat	tgggtttaaa	gggagcgtag
	aagtcagttg ggctgtcttg	tgaaagtttg 660	cggctcaacc	gtaaaattgc	agttgatact
25	agtacagtag tatcacgaag	aggtgggcgg 720	aattcgtggt	gtagcggtga	aatgcttaga
	aactccgatt gaaagtgtgg	gcgaaggcag 780	ctcactggac	tgcaactgac	actgatgctc
	gtatcaaaca actcgctgtt	ggattagata 840	ccctggtagt	ccacacagta	aacgatgaat
30	tgcgatatac gagtacgccg	agtaagcggc 900	caagcgaaag	cattaagtat	tccacctggg
	gcaacggtga catgtggttt	aactcaaagg 960	aattgacggg	ggccngcaca	agcggaggaa

	aattcgatga atattggaaa cagtatagcc cgtgccgtga	tacgcgagga 1020 gyaaggcaaa 1080	accttacccg tgtgaaggtg	ggcttaaatt ctgcatggtt	gcatttgaat gtcgtcagct
5	ggtgtcggct acaggtcatg	taagtgccat 1140	aacgagcgca	acccttatct	ttagttacta
	ctgaggactc gacgtcaaat	tagagagact 1200	gccgtcgtaa	gatgtgagga	aggtggggat
10	cagcacngcc agaaggcagc	cntacgtccg 1260	gggctacaca	cgtgttacaa	tggggggtac
	tacctggtga agtctgcaac	caggatgcta 1320	atcccaaaag	cctctctcag	ttcggatcga
	ccgacttcgt ggtgaatacg	gaagctggat 1380	tcgctagtaa	tcgcgcatca	gccatggcgc
15	ttcccgggcn ctgaagtacg	ttgtacacac 1440	cgcccgtcaa	gccatgaaag	ccgggggtac
	taaccgcaag 1482	gagcgtccta	gggtaaaact	ggtaattggg	gc
20	SEQ ID NO:4 (Bacteroides thetaiotaomicron gene for 16S rRNA	- BT-A)
	gttttcccta ttcatggctt	ggacgctcct 60	tgcggttacg	tacttcaggt	acccccggct
	gacgggcggt atgcgcgatt	gtgtacaagg 120	cccgggaacg	tattcaccgc	gccatggctg
25	actagcgaat gagagaggct	ccagcttcac 180	gaagtcgggt	tgcagacttc	gatccgaact
	tttgggatta gtaacacgtg	gcatcctgtc 240	accaggtagc	tgccttctgt	accccccatt
30	tgtagccccg ctcacatctt	gacgtaaggg 300	ccgtgctgat	ttgacgtcat	ccccaccttc
	acgacggcag ataagggttg	tctctctaga 360	gtcctcagca	tgacctgtta	gtaactaaag

	cgctcgttat ccatgcagca ccttcacatt tttaagcccg	ggcacttaag 420 tgccttacgg 480	ccgacacctc ctatactgtt	acggcacgag tccaatatat	ctgacgacaa tcaaatgcaa
5	ggtaaggttc tgcgggcccc	ctcgcgtatc 540	atcgaattaa	accacatgtt	cctccgcttg
	cgtcaattcc acttaatgct	tttgagtttc 600	accgttgccg	gcgtactccc	caggtggaat
10	ttcgcttggc ctgtgtggac	cgcttactgt 660	atatcgcaaa	cagcgagtat	tcatcgttta
	taccagggta cagttgcagt	tctaatcctg 720	tttgataccc	acactttcga	gcatcagtgt
	ccagtgagct accgctacac	gccttcgcaa 780	tcggagttct	tcgtgatatc	taagcatttc
15	cacgaattcc aattttacgg	gcccacctct 840	actgtactca	agacagccag	tatcaactgc
	ttgagccgca taaacccaat	aactttcaca 900	actgacttaa	ctgtccacct	acgctccctt
20	aaatccggat agttagccga	aacgctcgga 960	tcctccgtat	taccgcggct	gctggcacgg
	tccttattca ccatataaaa	tatggtacat 1020	acaaaattcc	acacgtggaa	aactttattc
	gaagtttaca aggcctgcgc	acccataggg 1080	cagtcatcct	tcacgctact	tggctggttc
25	ccattgacca tctcagttcc	atattcctca 1140	ctgctgcctc	ccgtaggagt	ttggaccgtg
	antgtggggg gccgttacct	accttcctct 1200	cagaacccct	atccatcgaa	ggtttggtga
30	caccaactgc taacaagacc	ctaatggaac 1260	gcatccccat	cgataaccga	aattctttaa
	atgcggtcta ccccgagtta	attataccat 1320	cggatattaa	tctttctttc	gaaaggctat

tcggcaggtt ggatacgtgt tactcacccg tgcgccggtc gccatcttca gttgcaagca 1380 aactgaaatg ctgcccctcg acttgcatgg taagcc 1416

SEQ ID NO:5 (Bacteroides thetaiotaomicron gene for 16S rRNA -BT-B) gctccttgcg gttacgtact tcaggtaccc ccggctttca tggcttgacg ggcggtgtgt 60 acaaggcccg ggaacgtatt caccgcgcca tggctgatgc gcgattacta gcgaatccag 120 cttcacgaag tcgggttgca gacttcgatc cgaactgaga gaggcttttg ggattagcat 180 cctgtcacca ggtagctgcc ttctgtaccc cccattgtaa cacgtgtgta gccccggacg 240 taagggccgt gctgatttga cgtcatcccc accttcctca catcttacga cggcagtctc 300 tctagagtcc tcagcataac ctgttagtaa ctaaagataa gggttgcgct cgttatggca 360 cttaagccga cacctcacgg cacgagctga cgacaaccat gcagcacctt cacatttgcc 420 ttgcgactaa cctgtttcca gattattcaa atgcaattta agcccgggta aggttcctcg 480 cgtatcatcg aattaaacca catgttcctc cgcttgtgcg ggcccccgtc aattcctttg 540 agtttcaccg ttgccggcgt actccccagg tggaatactt aatgctttcg cttggccgct 600 tactgtatat cgcaaacagc gagtattcat cgtttactgt gtggactacc agggtatcta 660 atcctgtttg atacccacac tttcgagcat cagtgtcagt tgcagtccag tgagctgcct 720 tcgcaatcgg agttcttcgt gatatctaag catttcaccg ctacaccacg aattccgccc 780 acctctactg tactcaagac agccagtatc aactgcaatt ttacggttga gccgcaaact 840 ttcacaactg acttaactgt ccacctacgc tccctttaaa cccaataaat ccggataacg 900 ctcggatcct ccgtattacc gcggctgctg gcacggagtt agccgatcct tattcatatg 960 gtacatacaa aattccacac gtggaaaact ttattcccat ataaaagaag tttacaaccc 1020 atagggcagt catccttcac gctacttggc tggttcaggc ctgcgcccat tgaccaatat 1080 tcctcactgc tgcctcccgt aggagtttgg accgtgtctc agttccaatg tgggggacct ii40 tcctctcaga acccctatcc atcgaaggtt tggtgagccg ttacctcacc aactgcctaa 1200 tggaacgcat ccccatcgat aaccgaaatt ctttaataac aagaccatgc ggtctaatta 1260 taccatcggg tattaatctt tctttcgaaa ggctatcccc gagttatcgg caggttggat 1320 acgtgttact cacccgtgcg ccggtcgcca tctccagttt gcaagcaaac tgaaatgctg 1380 cccctcgact gca 1393

SEQ ID NO:6 (Bacteroides thetaiotaomicron gene for 16S rRNA - BT-C) gctccttgcg gttacgtact tcaggtaccc ccggctttca tggcttgacg ggcggtgtgt 60 acaaggcccg ggaacgtatt caccgcgcca tggctgatgc gcgattacta gcgaatccag 120 cttcacgaag tcgggttgca gacttcgatc cgaactgaga gaggcttttg ggattagcat 180 cctgtcacca ggtagctgcc ttctgtaccc cccattgtaa cacgtgtgta gccccggacg 240

	taagggccgt cggcagtctc tctagagtcc cgttatggca	gctgatttga 300 teageatgae 360	cgtcatcccc ctgttagtaa	accttcctca ctaaagataa	catcttacga gggttgcgct
5	cttaagccga cacatttgcc	cacctcacgg 420	cacgagctga	cgacaaccat	gcagcacctt
	ttacggctat aggttcctcg	actgtttcca 480	gtatattcaa	atgcaattta	agcccgggta
10	cgtatcatcg aattcctttg	aattaaacca 540	catgttcctc	cgcttgtgcg	ggcccccgtc
	agtttcaccg ettggccgct	ttgccggcgt 600	actccccagg	tggaataett	aatgetttcg
	taetgtatat agggtatcta	cgcaaacagc 660	gagtatteat	cgtttactgt	gtggactacc
15	atcctgtttg tgagctgcct	atacccacac 720	tttegageat	cagtgtcagt	tgcagtccag
	tcgcaatcgg aattccgccc	agttcttcgt 780	gatatctaag	catttcaccg	ctacaccacg
20	acctctactg gccgcaaact	tactcaagac 840	agccagtatc	aaetgeaatt	ttaeggttga
	ttcacaactg ccggataacg	acttaactgt 900	ccacctacgc	teeetttaaa	cccaataaat
	ctcggatcct tatteatatg	ccgtattacc 960	gcggctgctg	geaeggagtt	agccgatcct
25	gtacatacaa tttacaaccc	aattccacac 1020	gtggaaaact	ttattcccat	ataaaagaag
	atagggcagt tgaccaatat	catccttcac 1080	gctacttggc	tggttcaggc	ctgcgcccat
30	tcctcactgc tgggggacct	tgcctcccgt 1140	aggagtttgg	accgtgtctc	agttccaatg
	tcctctcaga aactgcctaa	acccctatcc 1200	ategaaggtt	tggtgagccg	ttacctcacc

tggaacgcat	ccccatcgat	aaccgaaatt	etttaataac	aagaccatgc
ggtctgatta	1260
taccatcggg	tattaatctt	tctttcgaaa	ggctatcccc	gagttategg
caggttggat	1320
acgtgttact	cacccgtgcg	ccggtcgcca	tctccagttt	gcaagcaaac
tgaaatgctg	1380
cccctcgact	gca
1393

10	SEQ 1D NO:7 (Bacteroides thetaiotaomicron gene for 16S rRNA — BT-D)
gctccttgcg ggcggtgtgt acaaggcccg gcgaatccag	gttacgtact tcaggtaccc	ccggctttca tggctgatgc	tggettgaeg gcgattacta
60 ggaacgtatt 120	caccgcgcca
15	etteaegaag ggattageat	tcgggttgea 180	gaettegate	egaaetgaga	gaggcttttg
	cctgtcacca gccccggacg	ggtagetgee 240	ttctgtaccc	cccattgtaa	cacgtgtgta
20	taagggccgt cggcagtctc	getgatttga 300	cgtcatcccc	accttcctca	catcttacga
	tctagagtcc cgttatggca	teageatgae 360	ctgttagtaa	ctaaagataa	gggttgcgct
	cttaagccga cacatttgcc	cacctcacgg 420	cacgagctga	cgacaaccat	gcagcacctt
25	ttaeggetat aggttcctcg	actgtttcca 480	gtatattcaa	atgcaattta	agcccgggta
	cgtatcatcg aatteetttg	aattaaacca 540	catgttcctc	cgcttgtgcg	ggcccccgtc
30	agtttcaccg cttggccgct	ttgccggcgt 600	actccccagg	tggaataett	aatgctttcg
	taetgtatat agggtateta	cgcaaacagc 660	gagtatteat	cgtttactgt	gtggactacc

	atcctgtttg tgagctgcct tcgcaatcgg aattccgccc	atacccacac 720 agttcttcgt 780	tttcgagcat gatatctaag	cagtgtcagt catttcaccg	tgcagtccag ctacaccacg
5	acctctactg	tactcaagac	agccagtatc	aactgcaatt	ttacggttga
	gccgcaaact ttcacaactg	840 acttaactgt	ccacctacgc	tccctttaaa	cccaataaat
	ccggataacg ctcggatcct	900 ccgtattacc	gcggctgctg	gcacggagtt	agccgatcct
10	tattcatatg gtacatacaa	960 aattccacac	gtggaaaact	ttattcccat	ataaaagaag
	tttacaaccc atagggcagt	1020 catccttcac	gctacttggc	tggttcaggc	ctgcgcccat
15	tgaccaatat tcctcactgc	1080 tgcctcccgt	aggagtttgg	accgtgtctc	agttccaatg
	tgggggacct tcctctcaga	1140 acccctatcc	atcgaaggtt	tggtgagccg	ttacctcacc
	aactgcctaa tggaacgcat	1200 ccccatcgat	aaccgaaatt	ctttaataac	aagaccatgc
20	ggtctgatta taccatcggg	1260 tattaatctt	tctttcgaaa	ggctatcccc	gagttatcgg
	caggtggata cgtgttactc	1320 acccgtgcgc	cggtcgccat	etccagtttg	caagcaaact
25	gaaatgctgc 1380 ccctcgactg catg 1394 SEQ ID NO:8 {Bacteroides thetaiotaomicron gene for 16S rRNA	- BT-E)
	gctccttgcg	gttacgtact	tcaggtaccc	ccggctttca	tggettgaeg
30	ggcggtgtgt acaaggcccg	60 ggaacgtatt	caccgcgcca	tggctgatgc	gcgattacta

gcgaatccag 120

	cttcacgaag ggattagcat cctgtcacca gccccggacg	tcgggttgca 180 ggtagetgee 240	gaettegate ttctgtaccc	egaaetgaga cccattgtaa	gaggettttg cacgtgtgta
5	taagggccgt cggcagtetc	gctgatttga 300	cgtcatcccc	accttcctca	catcttacga
	tctagagtcc cgttatggea	teageatgae 360	ctgttagtaa	ctaaagataa	gggttgcgct
10	et taagccga cacatttgcc	cacctcacgg 420	cacgagctga	cgacaaccat	gcagcacctt
	ttaeggetat aggttcctcg	actgtttcca 480	gtatattcaa	atgcaattta	agcccgggta
	cgtatcatcg aattcctttg	aattaaacca 540	catgttcctc	cgcttgtgcg	ggcccccgtc
15	agtttcaccg ettggccgct	ttgccggcgt 600	actccccagg	tggaatactt	aatgetttcg
	taetgtatat agggtatcta	cgcaaacagc 660	gagtatteat	cgtttaetgt	gtggactacc
20	atcctgtttg tgagctgcct	atacccacac 720	tttegageat	cagtgtcagt	tgcagtccag
	tcgcaatcgg aattccgccc	agttcttcgt 780	gatatctaag	catttcaccg	ctacaccacg
	acctetaetg gccgcaaact	tactcaagac 840	agccagtatc	aaetgeaatt	ttacggttga
25	ttcacaactg ccggataacg	acttaactgt 900	ccacctacgc	tccctttaaa	cccaataaat
	etcggatcct tatteatatg	ccgtattacc 960	gcggctgctg	gcacggagtt	agccgatcct
30	gtacatacaa tttacaaccc	aattccacac 1020	gtggaaaact	ttattcccat	ataaaagaag
	atagggcagt tgaccaatat	catccttcac 1080	gctacttggc	tggttcaggc	ctgcgcccat

	tcctcactgc tgggggacct tcctctcaga aactgcctaa	tgcctcccgt 1140 acccctatcc 1200	aggagtttgg atcgaaggtt	accgtgtctc tggtgagccg	agttccaatg ttacctcacc
5	tggaacgcat	ccccatcgat	aaccgaaatt	ctttaataac	aagaccatgc
	ggtctgatta taccatcggg	1260 tattaatctt	tctttcgaaa	ggctatcccc	gagttatcgg
	caggttggat acgtgttact	1320 cacccgtgcg	ccggtcgcca	tctccagttt	gcaagcaaac
10	tgaaatgctg 1380 cccctcgact gcatg 1395 SEQ ID NO:9 (Bacteroides thetaiotaomicron gene for 16S rRNA	- BT-F)
15	gctccttgcg	gttacgtact	tcaggtaccc	ccggctttca	tggcttgacg
	ggcggtgtgt acaaggcccg	60 ggaacgtatt	caccgcgcca	tggctgatgc	gcgattacta
	gcgaatccag cttcacgaag	120 tcgggttgca	gacttcgatc	cgaactgaga	gaggcttttg
20	ggattagcat cctgtcacca	180 ggtagctgcc	ttctgtaccc	cccattgtaa	cacgtgtgta
	gccccggacg taagggccgt	240 gctgatttga	cgtcatcccc	accttcctca	catcttacga
25	cggcagtctc tctagagtcc	300 tcagcatgac	ctgttagtaa	ctaaagataa	gggttgcgct
	cgttatggca cttaagccga	360 cacctcacgg	cacgagctga	cgacaaccat	gcagcacctt
	cacatttgcc ttacggctat	420 actgtttcca	gtatattcaa	atgcaattta	agcccgggta
30	aggttcctcg cgtatcatcg	480 aattaaacca	catgttcctc	cgcttgtgcg	ggcccccgtc

aattcctttg 540

	agtttcaccg cttggccgct tactgtatat agggtatcta	ttgccggcgt 600 cgcaaacagc 660	actccccagg gagtattcat	tggaatactt cgtttactgt	aatgctttcg gtggactacc
5	atcctgtttg tgagctgcct	atacccacac 720	tttcgagcat	cagtgtcagt	tgcagtccag
	tcgcaatcgg aattccgccc	agttcttcgt 780	gatatctaag	catttcaecg	ctacaccacg
10	acctctactg gccgcaaact	tactcaagac 840	agccagtatc	aactgcaatt	ttacggttga
	ttcacaactg ccggataacg	acttaactgt 900	ccacctacgc	tccctttaaa	cccaataaat
	ctcggatcct tattcatatg	ccgtattacc 960	gcggctgctg	gcacggagtt	agccgatcct
15	gtacatacaa tttacaaccc	aattccacac 1020	gtggaaaact	ttattcccat	ataaaagaag
	atagggcagt tgaccaatat	catccttcac 1080	gctacttggc	tggttcaggc	ctgcgcccat
20	tcctcactgc tgggggacct	tgcctcccgt 1140	aggagtttgg	accgtgtctc	agttccaatg
	tcctctcaga aactgcctaa	acccctatcc 1200	atcgaaggtt	tggtgagccg	ttacctcacc
	tggaacgcat ggtctgatta	ccccatcgat 1260	aaccgaaatt	etttaataac	aagaccatgc
25	taccatcggg caggtaggat	tattaatctt 1320	tctttcgaaa	ggctatcccc	gagttatcgg
30	acgtgttact tgaaatgctg cccctcgact 1395	cacccgtgcg 1380 gcatg	ccggtcgcca	tctccagttt	gcaagcaaac

SEQ ID NO: 10 (Bacteroides thetaiotaomicron gene for 16S rRNA - BT-G) tttactagga cgctcttgcg gttacgtact tcaggtaccc ccggctttca tggcttgacg 60 ggcggtgtgt acaaggcccg ggaacgtatt caccgcgcca tggctgatgc gcgattacta 120 gcgaatccag cttcacgaag tcgggttgca gacttcgatc cgaactgaga gaggcttttg 180 ggattagcat cctgtcacca ggtagctgcc ttctgtaccc cccattgtaa cacgtgtgta 240 gccccggacg taagggccgt gctgatttga cgtcatcccc accttcctca catcttacga 300 cggcagtctc tctagagtcc tcagcatgac ctgttagtaa ctaaagataa gggttgcgct 360 cgttatggca cttaagccga cacctcacgg cacgagctga cgacaaccat gcagcacctt 420 cacatttgcc ttacggctat actgtttcca gtatattcaa atgcaattta agcccgggta 480 aggttcctcg cgtatcatcg aattaaacca catgttcctc cgcttgtgcg ggcccccgtc 540 aattcctttg agtttcaccg ttgccggcgt actccccagg tggaatactt aatgctttcg 600 cttggccgct tactgtatat cgcaaacagc gagtattcat cgtttactgt gtggactacc 660 agggtatcta atcctgtttg atacccacac tttcgagcat cagtgtcagt tgcagtccag 720 tgagctgcct tcgcaatcgg agttcttcgt gatatctaag catttcaccg ctacaccacg 780 aattccgccc acctctactg tactcaagac agccagtatc aactgcaatt ttacggttga 840 gccgcaaact ttcacaactg acttaactgt ccacctacgc tccctttaaa cccaataaat 900 ccggataacg ctcggatcct ccgtattacc gcggctgctg gcacggagtt agccgatcct 960

tattcatatg	gtacatacaa	aattccacac	gtggaaaact	ttattcccat
ataaaagaag tttacaaccc	1020 atagggcagt	catccttcac	gctacttggc	tggttcaggc
ctgcgcccat tgaccaatat	1080 tcctcactgc	tgcctcccgt	aggagtttgg	accgtgtctc
agttccaatg tgggggacct	1140 tcctctcaga	acccctatcc	atcgaaggtt	tggtgagccg
ttacctcacc aactgcctaa	1200 tggaacgcat	ccccatcgat	aaccgaaatt	ctttaataac
aagaccatgc ggtctgatta	1260 taccatcggg	tattaatctt	tctttcgaaa	ggctatcccc
gagttatcgg caggttggat	1320 acgtgttact	cacccgtgcg	ccggtcgcca	tctccagttg
caagcaaact gaaatgctgc	1380 ccctcgactg	catgtgtagc	cg
1412 SEQ ID NO: 11 (Bacteroides thetaiotaomicron gene for 16S rRNA - BT-H)
ggacgctcct	tgcggttacg	tacttcaggt	acccccggct	ttcatggctt
gacgggcggt gtgtacaagg	60 cccgggaacg	tattcaccgc	gccatggctg	atgcgcgatt
actagcgaat ccagcttcac	120 gaagtcgggt	tgcagacttc	gatccgaact	gagagaggct
tttgggatta gcatcctgtc	180 accaggtagc	tgccttctgt	accccccatt	gtaacacgtg
tgtagccccg gacgtaaggg	240 ccgtgctgat	ttgacgtcat	ccccaccttc	ctcacatctt
acgacggcag tctctctaga	300 gtcctcagca	tgacctgtta	gtaactaaag	ataagggttg
cgctcgttat ggcacttaag	360 ccgacacctc	acggcacgag	ctgacgacaa	ccatgcagca

ccttcacatt 420

4S

	tgccttacgg ggtaaggttc ctcgcgtatc cgtcaattcc	ctatactgtt 480 atcgaattaa 540	tccagtatat accacatgtt	tcaaatgcaa cctccgcttg	tttaagcccg tgcgggcccc
5	tttgagtttc ttcgcttggc	accgttgccg 600	gcgtactccc	caggtggaat	acttaatgct
	cgcttactgt taccagggta	atatcgcaaa 660	cagcgagtat	tcatcgttta	ctgtgtggac
10	tctaatcctg ccagtgagct	tttgataccc 720	acactttcga	gcatcagtgt	cagttgcagt
	gccttcgcaa cacgaattcc	tcggagttct 780	tcgtgatatc	taagcatttc	accgctacac
	gcccacctct ttgagccgca	actgtactca 840	agacagccag	tatcaactgc	aattttacgg
15	aactttcaca aaatccggat	actgacttaa 900	ctgtccacct	acgctccctt	taaacccaat
	aacgctcgga atccttattc	tcctccgtat 960	taccgcggct	gctggncacg	gagttagccg
20	atatggtaca agaagtttac	tacaaaattc 1020	cacacgtgga	aaactttatt	cccatataaa
	aacccatagg cccattgacc	gcagtcatcc 1080	ttcacgctac	ttggctggtt	caggcctgcg
	aatattcctc caatgtgggg	actgctgcct 1140	cccgtaggag	tttggaccgt	gtctcagttc
25	gaccttcctc tcaccaactg	tcagaacccc 1200	tatccatcga	aggtttggtg	agccgttacc
	cctaatggaa catgcggtct	cgcatcccca 1260	tcgataaccg	aaattcttta	ataacaagac
30	gattatacca atcggcaggt	tcgggtatta 1320	atctttcttt	cgaaaggcta	tccccgagtt
	tggatacgtg caaactgaaa	ttactcaccc 1380	gtgcgccggt	cgccatctcc	agtttgcaag

tgctgcccct cgactgca

1398

	SEQ ID NO: 12	(Bacteroides thetaiotaomicron gene for 16S rRNA - BT-I)
5	gctccttgcg ggcggtgtgt	gttacgtact tcaggtaccc ccggctttca tggcttgacg 60
	acaaggcccg gcgaatccag	ggaacgtatt caccgcgcca tggctgatgc gcgattacta 120
10	cttcacgaag ggattagcat	tcgggttgca gacttcgatc cgaactgaga gaggcttttg 180
	cctgtcacca gccccggacg	ggtagctgcc ttctgtaccc cccattgtaa cacgtgtgta 240
	taagggccgt cggcagtctc	gctgatttga cgtcatcccc accttcctca catcttacga 300
15	tctagagtcc cgttatggca	tcagcatgac ctgttagtaa ctaaagataa gggttgcgct 360
	cttaagccga cacatttgcc	cacctcacgg cacgagctga cgacaaccat gcagcacctt 420
20	ttgcggctaa aggttcctcg	cctgtttcca gawtattcaa atgcaattta agcccgggta 480
	cgtatcatcg aattcctttg	aattaaacca catgttcctc cgcttgtgcg ggcccccgtc 540
	agtttcaccg cttggccgct	ttgccggcgt actccccagg tggaatactt aatgctttcg 600
25	tactgtatat agggtatcta	cgcaaacagc gagtattcat cgtttactgt gtggactacc 660
	atcctgtttg tgagctgcct	atacccacac tttcgagcat cagtgtcagt tgcagtccag 720
30	tcgcaatcgg aattccgccc	agttcttcgt gatatctaag catttcaccg ctacaccacg 780
	acctctactg gccgcaaact	tactcaagac agccagtatc aactgcaatt ttacggttga 840

ttcacaactg acttaactgt ccacctacgc tccctttaaa cccaataaat ccggataacg 900 ctcggatcct ccgtattacc gcggctgctg gcacggagtt agccgatcct tattcatatg 960 gtacatacaa aattccacac gtggaaaact ttattcccat ataaaagaag tttacaaccc 1020 atagggcagt catccttcac gctacttggc tggttcaggc tttcgtccat tgaccaatat 1080 tcctcactgc tgcctcccgt aggagtttgg accgtgtctc agttccaatg 10 tgggggacct 1140 tcctctcaga acccctatcc atcgaaggtt tggtgagccg ttacctcacc aactgcctaa 1200 tggaacgcat ccccatcgat aaccgaaatt ctttaataac aagaccatgc ggtctaatta 1260 taccatcggg tattaatctt tctttcgaaa ggctatcccc gagttatcgg caggttggat 1320 acgtgttact cacccgtgcg ccggtcgcca tctccagttt gcaagcaaac tgaaatgctg 1380 cccctcgact gca

1393

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Claims

I. A composition comprising a bacterial strain of the species Bacteroides thetaiotaomicron, for use in a method of increasing the microbiota diversity and/or inducing stabilîty of the microbiota of a subject,
2, A composition comprising a bacterial strain having a 16s rRNA sequence that is at least 95%, 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequence of a bacterial strain of Bacteroides thetaiotaomicron deposited under accession number NCIMB 42341, for use in a method of increasing the microbiota diversity and/or inducing stabilîty of the microbiota of a subject.
3. The composition for use according to claim 1 or claim 2, wherein the composition is for use în a method of treating or preventing a disease or disorder in a subject, wherein the disease or disorder is associated with a level of microbiota diversity that is reduced relative to the microbiota diversity of a healthy subject, and wherein the treatment or prévention comprises increasing the microbiota diversity in the subject.
4. The composition for use according to any one of daims l to 3, wherein the subject has:

(a) a reduced microbiota diversity relative to a healthy subject;

(b) fewer than 99 different bacterial species; and/or (c) less than 190 different bacterial strains in its microbiota.
5. The composition for use according to claim 1 or claim 2, wherein the composition is for use in a method of treating or preventing a disease or disorder in a subject, wherein the disease or disorder is associated with reduced stabilîty of the microbiota compared to a healthy subject, and wherein the treatment or prévention comprises inducing stabilîty of the microbiota in the subject.
6. The composition for use according to any one of daims 1 to 5, wherein the subject has reduced stabilîty of its microbiota compared to a healthy subject.
7. The composition for use of any one of daims 1 to 6 wherein the composition is for use in a method of treatment or prévention of IBS, IBD, obesity, type 2 diabètes, one or more infectious diseases, cancer, one or more allergie diseases, one or more autoimmune diseases or one or more metabolic diseases/disorders.
8. The composition for use of daim 7, wherein:

(a) the disease is Crohn’s disease;

(b) the disease is asthma;

(c) the autoimmune disease is rheumatoid arthritis or multiple sclerosis; or (d) the disease is cancer.
9. The composition for use of claim 8(d), wherein the subject is concomitantly treated with chemotherapy.
10. The composition for use of any precedîng claim, wherein the increase in microbiota diversity and/or induction of stability of microbiota is for:

(a) non-acetogenic bacteria; or (b) both acetogenic and non-acetogenic bacteria.
11. The composition for use of any one of the preceding daims, wherein the subject is:

(a) an infant who has been delivered by Caesarean section;

(b) a frail elderly subject; or (c) between 10 and 19 years of âge.
12. The composition for use of any one of the preceding daims, wherein the microbiota diversity is increased and/or stability of the microbiota is induced in:

(a) the intestine of the subject; and/or (b) the distal gut of the subject.
13. The composition for use of daim 1 or daim 2, wherein the composition comprises a bacterial strain of the specîes Bacteroides thetaiotaomicron, for use in a method of increasing the microbiota diversity and/or inducing the stability of the microbiota in a subject diagnosed with IBD.
14. The composition for use of daim 13, wherein the IBD is Crohn’s disease.
15. The composition for use of any preceding daim, wherein the bacterial strain has a 16s rRNA sequence that is at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% identical to the sequence of:

(a) any one of SEQ ID NOs: 1-12; or (b) SEQ ID NO: 1.
16. The composition for use of daim 15(b), wherein the bacterial strain is the Bacteroides thetaiotaomicron bacterîum deposited under accession number NCIMB 42341.
17. The composition for use of any preceding daim, wherein the composition is for oral administration, optionally wherein the composition comprises one or more pharmaceutically acceptable excipients or carriers.
18. The composition for use of any preceding daim, wherein the bacterial strain is:

(a) lyophilised;

(b) viable; and/or (c) capable of partially or totally colonising the intestine.
19. The composition for use of any preceding claim, wherein the composition comprises:

(a) a single strain from the genus Bacteroides-, (b) a bacterial strain from the genus Bacteroides and does not comprise bacteria from any other généra or comprises such other bacteria only in de minimis amounts; and/or (c) Bacteroides thetaiotaomicron and does not comprise bacteria from any other species or comprises such other bacteria only in de minimis amounts.
20. The composition for use of any one of daims 1-19, wherein the composition comprises Bacteroides thetaiotaomicron as part of a microbial consortium.
21. A food product comprising the composition as defined in any preceding claim, for the use of any preceding claim.
22. A vaccine composition comprising the composition as defined in any one of daims 1-20, for the use of any one of daims 1 -20.
23. A composition comprising a bacterial strain having a 16s rRNA sequence that is at least 95%, 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequence of a bacterial strain of Bacteroides thetaiotaomicron deposited under accession number NCIMB 42341, for use in a method of increasing or maîntaining the intestinal microbiota diversity in a subject and/or inducing stability of the intestinal microbiota in a subject.
24. The composition for use according to claim 23, wherein the bacterial strain is of the species Bacteroides thetaiotaomicron.