Yoshimi Benno

Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR.

ABSTRACT A set of PCR primers was designed and validated for specific detection and quantification of Prevotella ruminicola,Prevotella albensis, Prevotella bryantii,Fibrobacter succinogenes, Selenomonas ruminantium-Mitsuokella multiacida, Streptococcus bovis, Ruminococcus flavefaciens,Ruminobacter amylophilus, Eubacterium ruminantium, Treponema bryantii,Succinivibrio dextrinosolvens, and Anaerovibrio lipolytica. By using these primers and the real-time PCR technique, the corresponding species in the rumens of cows for which the diet was switched from hay to grain were quantitatively monitored. The dynamics of two fibrolytic bacteria, F. succinogenesand R. flavefaciens, were in agreement with those of earlier, culture-based experiments. The quantity of F. succinogenes DNA, predominant in animals on the hay diet, fell 20-fold on the third day of the switch to a grain diet and further declined on day 28, with a 57-fold reduction in DNA. TheR. flavefaciens DNA concentration on day 3 declined to approximately 10% of its initial value in animals on the hay diet and remained at this level on day 28. During the transition period (day 3), the quantities of two ruminal prevotella DNAs increased considerably: that of P. ruminicola increased 7-fold and that ofP. bryantii increased 263-fold. On day 28, the quantity of P. ruminicola DNA decreased 3-fold, while P. bryantii DNA was still elevated 10-fold in comparison with the level found in animals on the initial hay diet. The DNA specific for another xylanolytic bacterium, E. ruminantium, dropped 14-fold during the diet switch and was maintained at this level on day 28. The concentration of a rumen spirochete, T. bryantii, decreased less profoundly and stabilized with a sevenfold decline by day 28. The variations in A. lipolytica DNA were not statistically significant. After an initial slight increase in S. dextrinosolvens DNA on day 3, this DNA was not detected at the end of the experiment. S. bovis DNA displayed a 67-fold increase during the transition period on day 3. However, on day 28, it actually declined in comparison with the level in animals on the hay ration. The amount of S. ruminantium-M. multiacida DNA also increased eightfold following the diet switch, but stabilized with only a twofold increase on day 28. The real-time PCR technique also uncovered differential amplification of rumen bacterial templates with the set of universal bacterial primers. This observation may explain why some predominant rumen bacteria have not been detected in PCR-generated 16S ribosomal DNA libraries.

Phylogenetic Analysis of the Human Gut Microbiota Using 16S rDNA Clone Libraries and Strictly Anaerobic Culture-Based Methods

The human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16S rDNA libraries and a culture‐based method. Direct counts ranged from 1.9 × 1011 to 4.0 × 1011 cells/g (wet weight), and plate counts totaled 6.6 × 1010 to 1.2 × 1011 CFU/g (wet weight). Sixty to seventy percent of the bacteria in the human intestinal tract cannot be cultured with currently available methods. The 16S rDNA libraries from three subjects were generated from total community DNA in the intestinal tract with universal primer sets. Randomly selected clones were partially sequenced. All purified colonies detected from the surface of the agar plate were used for a partial sequencing of 16S rDNA. On the basis of sequence similarities, the clones and colonies were classified into several clusters corresponding to the major phylum of the domain Bacteria. Among a total of 744 clones obtained, approximately 25% of them belonged to 31 known species. About 75% of the remaining clones were novel “phylotypes” (at least 98% similarity of clone sequence). The predominant intestinal microbial community consisted of 130 species or phylotypes according to the sequence data in this study. The 16S rDNA libraries and colonies included the Bacteroides group, Streptococcus group, Bifidobacterium group, and Clostridium rRNA clusters IV, IX, XIVa, and XVIII. Moreover, several previously uncharacterized and uncultured microorganisms were recognized in clone libraries and colonies. Our results also showed marked individual differences in the composition of intestinal microbiota.

The intestinal microflora of infants: composition of fecal flora in breast-fed and bottle-fed infants.

The fecal flora of 35 breast‐fed and 35 bottle‐fed babies was determined. Bifidobacteria were the predominant fecal bacteria in both groups. Conversely, the counts of most of the other bacteria, such as bacteroides, eubacteria, peptococci, veillonella, clostridia, enterobacteria, streptococci, and bacilli in the bottle‐fed group were significantly higher than those in the breast‐fed group. The frequencies of occurrence of lecithinase positive Clostridia, clostridia‐others, pseudomonas and bacilli in the bottle‐fed group were significantly higher than those in the breast‐fed group. Twenty‐one genera and 103 species or biovars of microorganisms were isolated from the feces of the breast‐fed group and 20 genera and 97 species or biovars from the bottle‐fed group. The organism that showed the highest number and the highest frequency of occurrence in both groups was Bifidobacterium breve. Bifidobacterium infantis, which was formerly the most prevalent Bifidobacterium species in baby feces, was never isolated in this study. Further, the counts and incidences of Clostridium paraputrificum, C. perfringens, and Bacillus subtilis, the counts of C. clostridiiforme, Bacteroides vulgatus, Veillonella parvula, Lactobacillus acidophilus, Escherichia coli, Streptococcus bovis, S. faecalis, and S. faecium and the incidences of C. difficile, C. tertium, and Pseudomonas aeruginosa in the bottle‐fed infants were significantly higher than those in the breast‐fed infants.

Innate lymphoid cells regulate intestinal epithelial cell glycosylation

INTRODUCTION The combination of food intake and the resident gut microbiota exposes the gastrointestinal (GI) tract to numerous antigens. Intestinal epithelial cells (ECs) compose a physical barrier separating the internal organs from the gut microbiota and other pathogenic microorganisms entering the GI tract. Although anatomically contained, the gut microbiota is essential for developing appropriate host immunity. Thus, the mucosal immune system must simultaneously maintain homeostasis with the gut microbiota and protect against infection by pathogens. Maintenance of the gut microbiota requires epithelial cell-surface glycosylation, with fucose residues in particular. Epithelial fucosylation is mediated by the enzyme fucosyltransferase 2 (Fut2). Polymorphisms in the FUT2 gene are associated with the onset of multiple infectious and inflammatory diseases and metabolic syndrome in humans. ILC3s regulate epithelial glycosylation. Commensal bacteria, including segmented filamentous bactiera (SFB), induce IL-22 production by ILC3. LT is produced by ILC3 in a commensal bacteria–independent manner. ILC3-derived IL-22 and LT cooperatively induce the production of Fut2 and subsequent epithelial fucosylation, which protects the host against Salmonella typhimurium infection. RATIONALE Despite its importance, the mechanisms underlying epithelial fucosylation in the GI tract is not well understood. In particular, although commensals such as Bacteroides thetaiotaomicron induce epithelial fucosylation, how mucosal immune cells participate in this process is unknown. We used a combination of bacteriological, gnotobiological, and immunological techniques to elucidate the cellular and molecular basis of epithelial fucosylation by mucosal immune cells in mice, especially innate lymphoid cells (ILCs). To explore the role of ILCs in the induction and maintenance of epithelial fucosylation, we used genetically engineered mice lacking genes associated with the development and function of ILCs. To investigate the physiological functions of ILC-induced epithelial fucosylation, we used a Fut2-deficient mouse model of S. typhimurium infection. RESULTS The induction and maintenance of Fut2 expression and subsequent epithelial fucosylation in the GI tract required type 3 ILCs (ILC3s) that express the transcription factor RORγt and the cytokines interleukin-22 (IL-22) and lymphotoxin (LT). Commensal bacteria, including segmented filamentous bacteria (SFB), induced fucosylation of intestinal columnar ECs and goblet cells. Expression of IL-22 by ILC3 required commensal bacteria, whereas LT was expressed in a commensal-independent manner. Ablation of IL-22 or LT in ILC3 resulted in a marked reduction in epithelial fucosylation, demonstrating that both cytokines are critical for the induction and regulation of epithelial fucosylation. Fucosylation of ECs in response to the intestinal pathogen S. typhimurium was also mediated by ILC3. Compared with control mice, Fut2-deficient mice were more susceptible to pathogenic inflammation as a result of S. typhimurium infection, suggesting that epithelial fucosylation contributes to host defense against S. typhimurium infection. CONCLUSION We demonstrate the critical role of the cytokines IL-22– and/or LT-producing ILC3 in the induction and regulation of intestinal epithelial fucosylation. We also show that ILC3-mediated epithelial fucosylation protects the host from invasion of S. typhimurium into the intestine. Our results provide important details of the glycosylation system and homeostatic responses created by the trilateral ILC3–EC–commensal axis in the intestine. Modulation of mucosal immune cell–mediated epithelial glycosylation may provide novel targets for the treatment or prevention of infectious diseases in humans. Immune cells and bugs make a sugary coat Epithelial cells line the intestinal tract and help to keep the peace between our immune system and our trillions of gut microbes. Such peacekeeping requires glycosylated proteins (proteins with attached carbohydrate chains) present on the epithelial cell surface, but how glycosylation occurs is unclear. Goto et al. find that fucosylation (a type of glycosylation) of gut epithelial cells in mice requires gut microbes (see the Perspective by Hooper). This process also requires innate lymphoid cells there, which produce the cytokines interleukin-22 and lymphotoxin, presumably in response to microbial signals. These cytokines signal epithelial cells to add fucose to membrane proteins, which allows the détente between microbes and immune cells to continue. Science, this issue 10.1126/science.1254009; see also p. 1248 Glycosylation of gut epithelial cells requires gut microbes, innate lymphoid cells, and cytokines. [Also see Perspective by Hooper] Fucosylation of intestinal epithelial cells, catalyzed by fucosyltransferase 2 (Fut2), is a major glycosylation mechanism of host–microbiota symbiosis. Commensal bacteria induce epithelial fucosylation, and epithelial fucose is used as a dietary carbohydrate by many of these bacteria. However, the molecular and cellular mechanisms that regulate the induction of epithelial fucosylation are unknown. Here, we show that type 3 innate lymphoid cells (ILC3) induced intestinal epithelial Fut2 expression and fucosylation in mice. This induction required the cytokines interleukin-22 and lymphotoxin in a commensal bacteria–dependent and –independent manner, respectively. Disruption of intestinal fucosylation led to increased susceptibility to infection by Salmonella typhimurium. Our data reveal a role for ILC3 in shaping the gut microenvironment through the regulation of epithelial glycosylation.

Molecular Analysis of Fecal Microbiota in Elderly Individuals Using 16S rDNA Library and T‐RFLP

Fecal microbiota in six elderly individuals were characterized by the 16S rDNA libraries and terminal restriction fragment length polymorphism (T‐RFLP) analysis. Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets from total genomic DNA extracted from feces of three elderly individuals. These clones were partially sequenced (about 500 bp). T‐RFLP analysis was performed using 16S rDNA amplified from six subjects. The lengths of the terminal restriction fragment (T‐RF) were analyzed after digestion by HhaI and MspI. Among 240 clones obtained, approximately 46% belonged to 27 known species. About 54% of the other clones were 56 novel “phylotypes” (at least 98% homology of clone sequence). These libraries included 83 species or phylotypes. In addition, about 13% (30 phylotypes) of these phylotypes were newly discovered in these libraries. A large number of species that are not yet known exist in the feces of elderly individuals. 16S rDNA libraries and T‐RFLP analysis revealed that the majority of bacteria were Bacteroides and relatives, Clostridium rRNA cluster IV, IX, Clostridium rRNA subcluster XIVa, and “Gammaproteobacteria”. The proportion of Clostridium rRNA subcluster XIVa was lower than in healthy adults. In addition, although Ruminococcus obeum and its closely related phylotypes were detected in high frequency in healthy young subjects, hardly any were detected in our elderly individuals. “Gammaproteobacteria” were detected at high frequency.

Taxonomic Study of the Lactobacillus acidophilus Group, with Recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and Synonymy of Lactobacillus acidophilus Group A3 (Johnson et al. 1980) with the Type Strain of Lactobacillus amylovorus (Nakamura 1981)

Biochemical properties and DNA-DNA reassociation studies of Lactobacillus acidophilus strains isolated from humans and animals indicate that these include six genomospecies. Two new species can be differentiated from the established species of the genus Lactobacillus: L. gallinarum sp. nov. (type strain, ATCC 33199) and L. johnsonii sp. nov. (type strain, ATCC 33200). Furthermore, it was clarified that L. acidophilus group A3 (Johnson et al. 1980) is synonymous with L. amylovorus.

Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation

Fecal microbial diversity in a strictly vegetarian woman was determined by the 16S rDNA library method, terminal restriction fragment length polymorphism (T‐RFLP) analysis and a culture‐based method. The 16S rDNA library was generated from extracted fecal DNA, using bacteria‐specific primers. Randomly selected clones were partially sequenced. T‐RFLP analysis was performed using amplified 16S rDNA. The lengths of T‐RF were analyzed after digestion by HhaI and MspI. The cultivated bacterial isolates were used for partial sequencing of 16S rDNA. Among 183 clones obtained, approximately 29% of the clones belonged to 13 known species. About 71% of the remaining clones were novel “phylotypes” (at least 98% similarity of clone sequence). A total of 55 species or phylotypes were identified among the 16S rDNA library, while the cultivated isolates included 22 species or phylotypes. In addition, many new phylotypes were detected from the 16S rDNA library. The 16S rDNA library and isolates commonly included the Bacteroides group, Bifidobacterium group, and Clostridium rRNA clusters IV, XIVa, XVI and XVIII. T‐RFLP analysis revealed the major composition of the vegetarian gut microbiota were Clostridium rRNA subcluster XIVa and Clostridium rRNA cluster XVIII. The dominant feature of this strictly vegetarian gut microbiota was the detection of many Clostridium rRNA subcluster XIVa and C. ramosum (Clostridium rRNA cluster XVIII).

Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov.

The characteristics of the fusiform species Bacteroides forsythus, isolated from human periodontal pockets, were examined. 165 rDNA sequence analysis confirmed that B. forsythus was not a species within the genus Bacteroides sensu stricto. Although B. forsythus was phylogenetically related to Bacteroides distasonis and Bacteroides merdae in the phylogenetic tree, the ratio of anteiso-15:0 to iso-15:0 in whole-cell methanolysates of B. forsythus was different from those of B. distasonis, B. merdae and other Bacteroides species. B. forsythus did not grow on medium containing 20% bile, but members of the Bacteroides fragilis group did. B. forsythus was the only species tested that was trypsin-positive in API ZYM tests. The dehydrogenase enzyme pattern was of no use for the differentiation of B. forsythus and the B. fragilis group. On the basis of these data, a new genus, Tannerella, is proposed for Bacteroides forsythus, with one species, Tannerella forsythensis corrig., gen. nov., comb. nov. The type strain of Tannerella forsythensis is JCM 10827T (= ATCC 43037T).

Indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis

The indigenous bacteria create natural cohabitation niches together with mucosal Abs in the gastrointestinal (GI) tract. Here we report that opportunistic bacteria, largely Alcaligenes species, specifically inhabit host Peyers patches (PPs) and isolated lymphoid follicles, with the associated preferential induction of antigen-specific mucosal IgA Abs in the GI tract. Alcaligenes were identified as the dominant bacteria on the interior of PPs from naïve, specific-pathogen-free but not from germ-free mice. Oral transfer of intratissue uncultured Alcaligenes into germ-free mice resulted in the presence of Alcaligenes inside the PPs of recipients. This result was further supported by the induction of antigen-specific Ab-producing cells in the mucosal (e.g., PPs) but not systemic compartment (e.g., spleen). The preferential presence of Alcaligenes inside PPs and the associated induction of intestinal secretory IgA Abs were also observed in both monkeys and humans. Localized mucosal Ab-mediated symbiotic immune responses were supported by Alcaligenes-stimulated CD11c+ dendritic cells (DCs) producing the Ab-enhancing cytokines TGF-β, B-cell-activating factor belonging to the TNF family, and IL-6 in PPs. These CD11c+ DCs did not migrate beyond the draining mesenteric lymph nodes. In the absence of antigen-specific mucosal Abs, the presence of Alcaligenes in PPs was greatly diminished. Thus, indigenous opportunistic bacteria uniquely inhabit PPs, leading to PP-DCs-initiated, local antigen-specific Ab production; this may involve the creation of an optimal symbiotic environment on the interior of the PPs.

Rapid Detection and Quantification of Five Periodontopathic Bacteria by Real‐Time PCR

The quantity of periodontopathic bacteria in plaque samples is an important determinant for understanding the etiologic role of bacteria. The real‐time PCR method was used to detect and quantify periodontopathic bacteria, such as Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, Treponema denticola, and Treponema socranskii, in saliva and subgingival plaque samples. There was good agreement between the results of conventional PCR and real‐time PCR methods. Using the LightCycler™ system we were able to determine the amount of periodontopathic bacteria within an hour. The real‐time PCR method was linear for samples containing from 103 to more than 108 cells (r2=0.999). The application of the real‐time PCR method should be useful in the rapid detection and quantification of periodontopathic bacteria in clinical samples.