-
Microbiome Oct 2016Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated...
BACKGROUND
Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort.
RESULTS
A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components.
CONCLUSIONS
We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits.
Topics: Bacteroides; Diet; Diet, High-Fat; Diet, Vegetarian; Dietary Fiber; Dietary Proteins; Feces; Feeding Behavior; Gastrointestinal Microbiome; Gastrointestinal Tract; Prevotella; RNA, Ribosomal, 16S
PubMed: 27769291
DOI: 10.1186/s40168-016-0202-1 -
Microbiology (Reading, England) Dec 2011Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA,...
Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.
Topics: Bacterial Proteins; Bacterial Typing Techniques; Bacteroides; Cluster Analysis; Genotype; Multilocus Sequence Typing; Phylogeny; Polymerase Chain Reaction; RNA, Ribosomal, 16S
PubMed: 21948050
DOI: 10.1099/mic.0.052332-0 -
Journal of Clinical Microbiology Apr 1981Bacteroides fragilis group and Bacteroides melaninogenicus group fluorescent-antibody kits were evaluated with 188 clinical specimens and 116 fresh aerobic and anaerobic... (Comparative Study)
Comparative Study
Bacteroides fragilis group and Bacteroides melaninogenicus group fluorescent-antibody kits were evaluated with 188 clinical specimens and 116 fresh aerobic and anaerobic bacterial isolates. Fluorescent-antibody and culture results corresponded in 88% of clinical specimens of the B. fragilis group and 94% of clinical specimens of the B. melaninogenicus group. There was greater than or equal to 90% correlation for both kits with colony smears. Antigen sharing by Bacteroides bivius, Bacteroides disiens, and B. melaninogenicus was demonstrated.
Topics: Bacteriological Techniques; Bacteroides; Bacteroides Infections; Bacteroides fragilis; Body Fluids; Humans; Prevotella melaninogenica
PubMed: 6112238
DOI: 10.1128/jcm.13.4.798-800.1981 -
Gut Microbes 2019: Bacteriotherapy aimed at addressing dysbiosis may be therapeutic for Inflammatory Bowel Diseases (IBDs). We sought to determine if defined -based bacteriotherapy could... (Comparative Study)
Comparative Study
: Bacteriotherapy aimed at addressing dysbiosis may be therapeutic for Inflammatory Bowel Diseases (IBDs). We sought to determine if defined -based bacteriotherapy could be an effective and consistent alternative to fecal microbiota transplantation (FMT) in a murine model of IBD. : We induced experimental colitis in 8- 12-week-old C57BL/6 mice using 2-3% dextran sodium sulfate. Mice were simultaneously treated by oral gavage with a triple- cocktail, individual strains, FMT using stool from healthy donor mice, or their own stool as a control. Survival, weight loss and markers of inflammation (histology, serum amyloid A, cytokine production) were correlated to gene profiling of fecal and mucosal microbiomes. : Triple- combination therapy was more protective against weight loss and mortality than traditional FMT therapy. ATCC8483 was more effective than any individual strain, or a combination of strains, in preventing weight loss, decreasing histological damage, dampening inflammatory response, and stimulating epithelial recovery. Irrespective of the treatment group, overall abundance associated with treatment success and decreased cytokine production while the presence of correlated with treatment failure. However, the therapeutic benefit associated with high abundance was negated in the presence of . : monotherapy was more consistent and effective than traditional FMT at ameliorating colitis and stimulating epithelial recovery in a murine model of IBD. Given the tolerability of ATCC 8483 in an active, on-going human study, this therapy may be repurposed for the management of IBD in a clinically expedient timeline.
Topics: Animals; Bacteria; Bacteroides; Colitis; Dextran Sulfate; Disease Models, Animal; Fecal Microbiota Transplantation; Feces; Gastrointestinal Tract; Inflammation; Male; Mice, Inbred C57BL; RNA, Ribosomal, 16S; Survival Analysis; Treatment Outcome
PubMed: 30663928
DOI: 10.1080/19490976.2018.1560753 -
Periodontology 2000 Oct 2010
Review
Topics: Animals; Bacterial Proteins; Bacteroides; Biofilms; Cysteine Endopeptidases; Disease Models, Animal; Glycoside Hydrolases; Humans; Membrane Proteins; Microbial Interactions; Periodontitis; Virulence Factors
PubMed: 20712636
DOI: 10.1111/j.1600-0757.2009.00332.x -
MBio Oct 2013CTnDOT is a 65-kb conjugative transposon that is found in Bacteroides spp., which are one of the more abundant members within the lower human gastrointestinal tract.... (Review)
Review
UNLABELLED
CTnDOT is a 65-kb conjugative transposon that is found in Bacteroides spp., which are one of the more abundant members within the lower human gastrointestinal tract. CTnDOT encodes resistance to the antibiotics erythromycin and tetracycline (Tc). An interesting feature of CTnDOT is that exposure to low levels of Tc induces a cascade of events that ultimately results in CTnDOT conjugative transfer. However, Tc is apparently not a switch that activates transfer but rather a signal that appears to override a series of negative regulators that inhibit premature excision and transfer of CTnDOT. In this minireview, we summarize over 20 years of research that focused on elucidating the highly coordinated regulation of excision, mobilization, and transfer of CTnDOT.
IMPORTANCE
Bacteroides spp. are abundant commensals in the human colon, but they are also considered opportunistic pathogens, as they can cause life-threatening infections if they should escape the colon. Bacteroides spp. are the most common cause of anaerobic infections and are rather difficult to treat due to the prevalence of antibiotic resistance within this genus. Today over 80% of Bacteroides are resistant to tetracycline (Tc), and a study looking at both clinical and community isolates demonstrated that this resistance was specifically due to the conjugative transposon CTnDOT.
Topics: Bacteroides; Conjugation, Genetic; DNA Transposable Elements; Drug Resistance, Bacterial; Gastrointestinal Tract; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Humans; Tetracycline
PubMed: 24169574
DOI: 10.1128/mBio.00569-13 -
MBio Feb 2024Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, species have been...
Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, species have been identified as major producers of sphingolipids, and -produced sphingolipids have been shown to be modulators of host immune and metabolic functions. While species are a prominent feature of the gut microbiomes of populations living in industrialized countries, , a member of the same phyla, albeit a different family, is the dominant feature across the remainder of the global population, although their sphingolipid-producing capabilities have not been as thoroughly investigated. To fill this gap, we examined the genomes of over 60 diverse isolates of and identified several key enzymes involved in sphingolipid synthesis in . Combining bioorthogonal labeling and liquid chromatography-mass spectrometry (LC-MS) based lipidomics, we functionally characterized the first step in sphingolipid synthesis in addition to profiling the sphingolipidomes of strains, identifying key enzymes that may play roles in producing a diverse set of sphingolipids. Given the limited genetic engineering tools amenable for use in , our approach takes advantage of comparative genomics and phenotypic profiling to explore sphingolipid production in these understudied, yet highly prevalent, organisms.IMPORTANCESphingolipids are important signaling molecules for maintaining metabolic and immune homeostasis in the host. These lipids are also produced by gut commensals, most notably by species. Despite the global prevalence of in gut microbiomes of individuals, little is known about the types of sphingolipids they produce and whether they are similar in composition and structure to those produced by . Given the varied associations of with diverse sphingolipid-related health outcomes, such as rheumatoid arthritis and glucose intolerance, it is important to first characterize the specific sphingolipids produced by individual strains of and to identify the genes involved in their pathways of production. This characterization of -derived sphingolipids provides further insight into how bacterial sphingolipid production can serve as a mechanism for microbial modulation of host phenotypes.
Topics: Humans; Sphingolipids; Prevotella; Eukaryota; Gastrointestinal Microbiome; Bacteroides
PubMed: 38236049
DOI: 10.1128/mbio.02409-23 -
Glycobiology May 2013While it is now evident that the two Bacteroidales species Bacteroides fragilis and Tannerella forsythia both have general O-glycosylation systems and share a common...
While it is now evident that the two Bacteroidales species Bacteroides fragilis and Tannerella forsythia both have general O-glycosylation systems and share a common glycosylation sequon, the ability of these organisms to glycosylate a protein native to the other organism has not yet been demonstrated. Here, we report on the glycosylation of heterologous proteins between these two organisms. Using genetic tools previously developed for Bacteroides species, two B. fragilis model glycoproteins were expressed in the fastidious anaerobe T. forsythia and the attachment of the known T. forsythia O-glycan to these proteins was demonstrated by liquid chromatography electrospray ionization tandem mass spectrometry. Likewise, two predominant T. forsythia glycoproteins were expressed in B. fragilis and glycosylation with the B. fragilis O-glycan was confirmed. Purification of these proteins from B. fragilis allowed the preliminary characterization of the previously uncharacterized B. fragilis protein O-glycan. Based on mass spectrometric data, we show that the B. fragilis protein O-glycan is an oligosaccharide composed of nine sugar units. Compositional and structural similarities with the T. forsythia O-glycan suggest commonalities in their biosynthesis. These data demonstrate the feasibility of exploiting these organisms for the design of novel glycoproteins.
Topics: Bacterial Proteins; Bacteroides; Carbohydrate Sequence; Glycoproteins; Glycosylation; Molecular Sequence Data; Oligosaccharides; Polysaccharides
PubMed: 23258847
DOI: 10.1093/glycob/cws172 -
Microbiological Reviews Mar 1988
Review
Topics: Antigens, Bacterial; Bacterial Toxins; Bacteroides; Microbial Sensitivity Tests; Virulence
PubMed: 3280965
DOI: 10.1128/mr.52.1.134-152.1988 -
Gut Microbes Nov 2020glucans are the dietary nutrients present in oats, barley, algae, and mushrooms. The macromolecules are well known for their immune-modulatory activity; however, how the...
glucans are the dietary nutrients present in oats, barley, algae, and mushrooms. The macromolecules are well known for their immune-modulatory activity; however, how the human gut bacteria digest them is vaguely understood. In this study, JCM 13288 was found to grow on laminarin, pustulan, and porphyran. We sequenced the genome of the strain, which was about 5.05 megabase pairs and contained 4868 protein-coding genes. On the basis of growth patterns of the bacterium, two putative polysaccharide utilization loci for glucans were identified from the genome, and associated four putative genes were cloned, expressed, purified, and characterized. Three glycoside hydrolases (GHs) that were endo-acting enzymes (GH16, GH30, and GH158), and one which was an exo-acting (GH3) enzyme. The GH3, GH16, and GH158 can cleave linear exo/endo- 1-3 linkages while GH30 can digest endo- 1-6 linkages. GH30 and GH158 were further explored for their roles in digesting glucans and generation of oligosaccharides, respectively. The GH30 predominately found to cleave long chain 1-6 linked glucans, and obtained final product was gentiobiose. The GH158 used for producing oligosaccharides varying from degree of polymerization 2 to 7 from soluble curdlan. We demonstrated that these oligosaccharides can be utilized by gut bacteria, which either did not grow or poorly grew on laminarin. Thus, JCM 13288 is not only capable of utilizing glucans but also shares these glycans with human gut bacteria for potentially maintaining the gut microbial homeostasis.
Topics: Bacteroides; Carbohydrate Conformation; Gastrointestinal Microbiome; Genetic Loci; Genome, Bacterial; Glycoside Hydrolases; Gram-Positive Bacteria; Microbial Interactions; Oligosaccharides; Polysaccharides; beta-Glucans
PubMed: 33043794
DOI: 10.1080/19490976.2020.1826761