Bacteroides Plebeius Research Articles

Structure of a glycoside hydrolase family 50 enzyme from a subfamily that is enriched in human gut microbiome bacteroidetes.

The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution X-ray crystal structure of BpGH50 confirmed its possession of the core (α/β)8 barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues. Examination of the structure supports assignment of this protein as a β-galactosidase but suggests that it may utilize a different, possibly hybrid, algal galactan substrate. Proteins 2016; 85:182-187. © 2016 Wiley Periodicals, Inc.

Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery

ObjectivesPreventing postoperative recurrence after ileocolonic resection (ICR) for Crohn's disease (CD) is challenging. Defining the disturbances of the microbial composition and community structure after ICR and their link with early...

Su2093 Glucagon Like Peptide-2 Production and Sensitivity in Infants Post-Resection or Gastroschisis

G A A b st ra ct s enhanced microbial fermentation of dietary fiber and dysregulation of choline metabolism. The OPLS-DA model constructed based on samples collected post DI (R2X=30.7%, Q2Y= 0.37) showed higher concentrations of glutamate and 6-aminosalicylic acid in AA compared with AF. Microbial data acquired using HITChip was integrated with fecal profiles using OPLS. At the phylum level, 2 out of 22 identified phyla were significantly correlated with fecal profiles, which are Cyanobacteria and uncultured Mollicutes significantly correlating with fecal glutamate and valerate. By statistically integrating the fecal metabonome and the 130 microbial genus, Bacteroides vulgates et rel. and Bacteroides plebeius et rel. were observed to be correlated with choline, whereas Uncultured Clostridiales II was correlated with pyroglutamate. Uncultured Mollicutes, Eubacterium siraeum et rel and Aneurinibacillus demonstrated similar metabolic activity. Conclusions: These findings indicate that after only two-weeks of a dietary exchange diet, the fecal metabolic profile is significantly altered and that these metabolic changes are closely associated with alterations in the structure and function of the gut microbial network.

Su2095 Survival and Cause-Specific Mortality in an Intestinal Failure Cohort Depending on Home Parenteral Nutrition (HPN) in a Referral Centre From 1970 to 2010

G A A b st ra ct s enhanced microbial fermentation of dietary fiber and dysregulation of choline metabolism. The OPLS-DA model constructed based on samples collected post DI (R2X=30.7%, Q2Y= 0.37) showed higher concentrations of glutamate and 6-aminosalicylic acid in AA compared with AF. Microbial data acquired using HITChip was integrated with fecal profiles using OPLS. At the phylum level, 2 out of 22 identified phyla were significantly correlated with fecal profiles, which are Cyanobacteria and uncultured Mollicutes significantly correlating with fecal glutamate and valerate. By statistically integrating the fecal metabonome and the 130 microbial genus, Bacteroides vulgates et rel. and Bacteroides plebeius et rel. were observed to be correlated with choline, whereas Uncultured Clostridiales II was correlated with pyroglutamate. Uncultured Mollicutes, Eubacterium siraeum et rel and Aneurinibacillus demonstrated similar metabolic activity. Conclusions: These findings indicate that after only two-weeks of a dietary exchange diet, the fecal metabolic profile is significantly altered and that these metabolic changes are closely associated with alterations in the structure and function of the gut microbial network.

Thermophilic anaerobic biodegradation test and analysis of eubacteria involved in anaerobic biodegradation of four specified biodegradable polyesters

The anaerobic biodegradability of 4 bioplastics powders (125–250 μm), polycaprolactone (PCL), poly(lactic acid) (PLA), polyhydroxybutyrate (PHB) and poly(butylene succinate) (PBS), were compared at 55 °C under aquatic conditions using our evaluation system reported previously, (the modified ISO 13975 method). In order of increasing anaerobic biodegradation rate, the bioplastics were ranked PHB > PCL > PLA. The biodegradability of PHB, PCL, and PLA was 90% in 14 days, 80% in 50 days, and 75% in 75 days, respectively. PBS could not be anaerobically biodegraded by the sludge used in this study. The eubacteria participating in anaerobic bioplastic biodegradation were detected using modern polymerase chain reaction techniques that distinguish metabolically active cells from resting, dormant, or starved cells. Some of the eubacteria participating in anaerobic biodegradation of PHB, PCL, and PLA were of unique character. Organisms involved in anaerobic biodegradation of PHB were 97, 100, and 98% identical to Peptococcaceae bacterium Ri50, Bacteroides plebeius, and Catenibacterium mitsuokai, respectively. The organism involved in the anaerobic biodegradation of PCL, however, was poorly related (<95% similarity) to any of the cultured-bacterium database sequences. Anaerobic biodegradation of PLA was undertaken by an organism with 100% identity to Ureibacillus sp., and by three organisms with poor similarity (≤95%) to any database sequence. Bacillus infernus, Propionibacterium sp., and two unidentified species were implicated in the anaerobic biodegradation of all three biodegradable plastics.

Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight into the Degradation (of a Polysaccharide from) Red Seaweeds

Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating D-galactose and 3,6-anhydro-L-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds.

High temporal and inter‐individual variation detected in the human ileal microbiota

The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 10⁷ -10⁸ bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9-28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.

Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum

Eight bacterial strains isolated from the caecum of chicken, BL2(T), BL66, EG3, EG6, M27, BL78(T), C35(T) and C43, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus Bacteroides. One group of five strains (BL2(T), BL66, EG3, EG6 and M27) was related most closely to Bacteroides coprocola JCM 12979(T), with approximately 93 % 16S rRNA gene sequence similarity, and to Bacteroides plebeius JCM 12973(T), with about 92 % similarity, and shared >or=99.6 % similarity with each other. Strain BL78(T) exhibited 90.5 % similarity to B. plebeius JCM 12973(T) and 89.8 % similarity to B. coprocola JCM 12979(T) and differed from the above group of five strains at >or=10 % sequence divergence. Strains C35(T) and C43 were related most closely to Bacteroides eggerthii JCM 12986(T), with 95.1 % sequence similarity, to Bacteroides stercoris JCM 9496(T), with 94.6 % similarity, and to Bacteroides uniformis JCM 5828(T), with 94.4 % similarity, and shared 100 % similarity with each other. From results of phenotypic examination, cellular fatty acid composition analysis, menaquinone composition analysis and DNA G+C contents, the group of five strains as well as strain BL78(T) were shown to differ from the type strains of B. coprocola and B. plebeius. Strain BL78(T) differed from the others based on its menaquinone composition, which included MK-11 and MK-12. Strains C35(T) and C43 could also be differentiated from the type strains of B. eggerthii, B. stercoris and B. uniformis. The group of five strains, strain BL78(T), B. coprocola JCM 12979(T) and B. plebeius JCM 12973(T) showed low levels of DNA-DNA relatedness (<35 %) with each other. High levels of DNA-DNA relatedness were obtained within the group of five strains (>75 %). Strains C35(T) and C43 exhibited a high level of DNA-DNA relatedness (>88 %) with each other, but low levels with B. eggerthii JCM 12986(T) (<40 %), B. stercoris JCM 9496(T) (<37 %) and B. uniformis JCM 5828(T) (<16 %). On the basis of these data, three novel Bacteroides species are proposed: Bacteroides barnesiae sp. nov. (type strain BL2(T)=JCM 13652(T)=DSM 18169(T)), Bacteroides salanitronis sp. nov. (type strain BL78(T)=JCM 13657(T)=DSM 18170(T)) and Bacteroides gallinarum sp. nov. (type strain C35(T)=JCM 13658(T)=DSM 18171(T)).

Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces

Nine strains of Gram-negative, anaerobic rod were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included within the Bacteroides cluster and were divided into two clusters. Strains from the two clusters showed 16S rRNA gene sequence similarities of 90.4 and 92.7% to the nearest recognized species, Bacteroides vulgatus. The strains also formed two clusters exhibiting a 16S rRNA gene sequence divergence of approximately 6%. DNA-DNA hybridization studies confirmed that the two novel strain clusters were distinct from each other. Based on the phenotypic and phylogenetic findings, two novel species, Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., are proposed, each representing one of the two strain clusters. The DNA G+C content of the type strains were 43.9 mol% for B. plebeius (M12(T)=JCM 12973(T)=DSM 17135(T)) and 42.4 mol% for B. coprocola (M16(T)=JCM 12979(T)=DSM 17136(T)).