-
Journal of Bacteriology Oct 1997We report the construction and analysis of a Bacteroides thetaiotaomicron recA disruption mutant and an investigation of whether RecA is required for excision and...
We report the construction and analysis of a Bacteroides thetaiotaomicron recA disruption mutant and an investigation of whether RecA is required for excision and integration of Bacteroides mobile DNA elements. The recA mutant was deficient in homologous recombination and was more sensitive than the wild-type strain to DNA-damaging agents. The recA mutant was also more sensitive to oxygen than the wild type, indicating that repair of DNA contributes to the aerotolerance of B. thetaiotaomicron. Many Bacteroides clinical isolates carry self-transmissible chromosomal elements known as conjugative transposons. These conjugative transposons can also excise and mobilize in trans a family of unlinked integrated elements called nonreplicating Bacteroides units (NBUs). The results of a previous study had raised the possibility that RecA plays a role in excision of Bacteroides conjugative transposons, but this hypothesis could not be tested in Bacteroides spp. because no RecA-deficient Bacteroides strain was available. We report here that the excision and integration of the Bacteroides conjugative transposons, as well as NBU1 and Tn4351, were unaffected by the absence of RecA activity.
Topics: Aerobiosis; Bacteroides; Conjugation, Genetic; DNA Damage; DNA Repair; DNA Transposable Elements; DNA, Bacterial; Escherichia coli; Methyl Methanesulfonate; Metronidazole; Molecular Sequence Data; Mutagenesis, Insertional; Mutagens; Rec A Recombinases; Recombination, Genetic; Superoxide Dismutase
PubMed: 9335266
DOI: 10.1128/jb.179.20.6221-6227.1997 -
Nature May 2016Cooperative phenotypes are considered central to the functioning of microbial communities in many contexts, including communication via quorum sensing, biofilm...
Cooperative phenotypes are considered central to the functioning of microbial communities in many contexts, including communication via quorum sensing, biofilm formation, antibiotic resistance, and pathogenesis. The human intestine houses a dense and diverse microbial community critical to health, yet we know little about cooperation within this important ecosystem. Here we test experimentally for evolved cooperation within the Bacteroidales, the dominant Gram-negative bacteria of the human intestine. We show that during growth on certain dietary polysaccharides, the model member Bacteroides thetaiotaomicron exhibits only limited cooperation. Although this organism digests these polysaccharides extracellularly, mutants lacking this ability are outcompeted. In contrast, we discovered a dedicated cross-feeding enzyme system in the prominent gut symbiont Bacteroides ovatus, which digests polysaccharide at a cost to itself but at a benefit to another species. Using in vitro systems and gnotobiotic mouse colonization models, we find that extracellular digestion of inulin increases the fitness of B. ovatus owing to reciprocal benefits when it feeds other gut species such as Bacteroides vulgatus. This is a rare example of naturally-evolved cooperation between microbial species. Our study reveals both the complexity and importance of cooperative phenotypes within the mammalian intestinal microbiota.
Topics: Animals; Bacteroides; Biological Evolution; Dietary Carbohydrates; Gastrointestinal Microbiome; Germ-Free Life; Glycoside Hydrolases; Humans; In Vitro Techniques; Intestines; Inulin; Male; Mice; Symbiosis
PubMed: 27111508
DOI: 10.1038/nature17626 -
Infection and Immunity Apr 1984Organisms of the Bacteroides melaninogenicus and Bacteroides fragilis groups are often found mixed with facultatively anaerobic organisms in infections. The relative... (Comparative Study)
Comparative Study
Organisms of the Bacteroides melaninogenicus and Bacteroides fragilis groups are often found mixed with facultatively anaerobic organisms in infections. The relative importance of these Bacteroides groups and facultative anaerobic pathogens in mixed infections was investigated in a subcutaneous abscess model in mice. This was determined by observing the effect of antimicrobial therapy directed against one or both organisms present in the abscess. Clindamycin or metronidazole was used for treatment of infections caused by Bacteroides species, and either gentamicin, penicillin, ampicillin, or oxacillin was used for treatment of infections caused by facultative flora. In almost all instances the aerobic counterparts in the infection were more important than the unencapsulated Bacteroides species. On the other hand, encapsulated B. melaninogenicus group organisms were found to be more important in abscess formation than were group A streptococci, Streptococcus pneumoniae, Klebsiella pneumoniae, Haemophilus influenzae, and Staphylococcus aureus. Encapsulated B. fragilis group organisms were found to be more important than or as important as Escherichia coli and group D streptococci and less important than S. aureus, group A streptococci, and K. pneumoniae in induction of subcutaneous abscesses. This study demonstrates that encapsulated Bacteroides species are a factor that should be considered in the treatment of mixed infections with antibiotics.
Topics: Abscess; Aerobiosis; Animals; Anti-Bacterial Agents; Bacterial Infections; Bacteroides; Bacteroides Infections; Bacteroides fragilis; Haemophilus influenzae; Klebsiella pneumoniae; Male; Mice; Prevotella melaninogenica; Staphylococcus aureus; Streptococcus
PubMed: 6142862
DOI: 10.1128/iai.44.1.12-15.1984 -
Journal of Bacteriology Oct 2021The last two decades have seen numerous studies connecting physiological behaviors in -including polysaccharide degradation and capsule production-with elements of...
The last two decades have seen numerous studies connecting physiological behaviors in -including polysaccharide degradation and capsule production-with elements of global regulation, but a complete model is still elusive. A new study by Adams et al. in this issue of the reveals another layer of regulation by describing a novel family of RNA-binding proteins in Bacteroides thetaiotaomicron that modify expression of genes involved in carbohydrate utilization and capsule expression, among others (A. N. D. Adams, M. S. Azam, Z. A. Costliow, X. Ma, et al., J Bacteriol 203:e00217-21, 2021, https://doi.org/10.1128/JB.00217-21).
Topics: Bacteroides; Bacteroides thetaiotaomicron; Gene Expression Regulation, Bacterial; Humans; Polysaccharides; RNA
PubMed: 34370557
DOI: 10.1128/JB.00383-21 -
Scientific Reports Oct 2020Yeast mannan (YM) is an indigestible water-soluble polysaccharide of the yeast cell wall, with a notable prebiotic effect on the intestinal microbiota. We previously...
Yeast mannan (YM) is an indigestible water-soluble polysaccharide of the yeast cell wall, with a notable prebiotic effect on the intestinal microbiota. We previously reported that YM increased Bacteroides thetaiotaomicron abundance in in vitro rat faeces fermentation, concluding that its effects on human colonic microbiota should be investigated. In this study, we show the effects of YM on human colonic microbiota and its metabolites using an in vitro human faeces fermentation system. Bacterial 16S rRNA gene sequence analysis showed that YM administration did not change the microbial diversity or composition. Quantitative real-time PCR analysis revealed that YM administration significantly increased the relative abundance of Bacteroides ovatus and B. thetaiotaomicron. Moreover, a positive correlation was observed between the relative ratio (with or without YM administration) of B. thetaiotaomicron and B. ovatus (r = 0.92), suggesting that these bacteria utilise YM in a coordinated manner. In addition, YM administration increased the production of acetate, propionate, and total short-chain fatty acids. These results demonstrate the potential of YM as a novel prebiotic that selectively increases B. thetaiotaomicron and B. ovatus and improves the intestinal environment. The findings also provide insights that might be useful for the development of novel functional foods.
Topics: Bacteroides; Colon; Functional Food; Gastrointestinal Microbiome; Humans; Mannans; Prebiotics; Species Specificity; Yeasts
PubMed: 33060635
DOI: 10.1038/s41598-020-74379-0 -
Glycobiology Jun 2021The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these...
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
Topics: Bacteroides; Bacteroides thetaiotaomicron; Bacteroidetes; Glycosaminoglycans; Heparitin Sulfate; Humans; Polysaccharides
PubMed: 32518945
DOI: 10.1093/glycob/cwaa054 -
Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts.Proceedings of the National Academy of... Sep 2020Mechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular...
Mechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular processes in actively growing bacteria. Although underappreciated, many gut "anaerobes" are able to respire using oxygen as the terminal electron acceptor. The oxygen continually released from gut epithelial cells creates an oxygen gradient from the mucus layer to the anaerobic lumen [L. Albenberg et al., Gastroenterology 147, 1055-1063.e8 (2014)], with oxygen available to bacteria growing at the mucus layer. Here, we show that species are metabolically and energetically robust and do not mount stress responses in the presence of 0.10 to 0.14% oxygen, defined as nanaerobic conditions [A. D. Baughn, M. H. Malamy, Nature 427, 441-444 (2004)]. Taking advantage of this metabolic capability, we show that nanaerobic growth provides sufficient oxygen for the maturation of oxygen-requiring fluorescent proteins in species. Type strains of four different species show bright GFP fluorescence when grown nanaerobically versus anaerobically. We compared four different red fluorescent proteins and found that mKate2 yields the highest red fluorescence intensity in our assay. We show that GFP-tagged proteins can be localized in nanaerobically growing bacteria. In addition, we used time-lapse fluorescence microscopy to image dynamic type VI secretion system processes in metabolically active The ability to visualize fluorescently labeled and fluorescently linked proteins in actively growing nanaerobic gut symbionts ushers in an age of imaging analyses not previously possible in these bacteria.
Topics: Aerobiosis; Bacterial Proteins; Bacteroides; Gastrointestinal Microbiome; Humans; Oxygen; Type VI Secretion Systems
PubMed: 32938803
DOI: 10.1073/pnas.2009556117 -
MBio Nov 2015Many symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted...
UNLABELLED
Many symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted to other complex nutrient environments, gut symbionts give different metabolic priorities to substrates present in mixtures. We investigated the responses of Bacteroides thetaiotaomicron, a common human intestinal bacterium that metabolizes more than a dozen different polysaccharides, including the O-linked glycans that are abundant in secreted mucin. Experiments in which mucin glycans were presented simultaneously with other carbohydrates show that degradation of these host carbohydrates is consistently repressed in the presence of alternative substrates, even by B. thetaiotaomicron previously acclimated to growth in pure mucin glycans. Experiments with media containing systematically varied carbohydrate cues and genetic mutants reveal that transcriptional repression of genes involved in mucin glycan metabolism is imposed by simple sugars and, in one example that was tested, is mediated through a small intergenic region in a transcript-autonomous fashion. Repression of mucin glycan-responsive gene clusters in two other human gut bacteria, Bacteroides massiliensis and Bacteroides fragilis, exhibited variable and sometimes reciprocal responses compared to those of B. thetaiotaomicron, revealing that these symbionts vary in their preference for mucin glycans and that these differences occur at the level of controlling individual gene clusters. Our results reveal that sensing and metabolic triaging of glycans are complex processes that vary among species, underscoring the idea that these phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which microorganisms preferentially commit to various niches in a constantly changing nutritional environment.
IMPORTANCE
Human intestinal microorganisms impact many aspects of health and disease, including digestion and the propensity to develop disorders such as inflammation and colon cancer. Complex carbohydrates are a major component of the intestinal habitat, and numerous species have evolved and refined strategies to compete for these coveted nutrients. Our findings reveal that individual bacteria exhibit different preferences for carbohydrates emanating from host diet and mucosal secretions and that some of these prioritization strategies are opposite to one another. Thus, we reveal new aspects of how individual bacteria, some with otherwise similar metabolic potential, partition to "preferred niches" in the complex gut ecosystem, which has important and immediate implications for understanding and predicting the behavioral dynamics of this community.
Topics: Bacteroides; Dietary Carbohydrates; Gastrointestinal Microbiome; Gene Expression Regulation, Bacterial; Humans; Intestinal Mucosa; Intestines; Mucins; Multigene Family; Polysaccharides; Symbiosis
PubMed: 26556271
DOI: 10.1128/mBio.01282-15 -
Applied and Environmental Microbiology Dec 2013Cocultures of strains from two Bifidobacterium and two Bacteroides species were performed with exopolysaccharides (EPS) previously purified from bifidobacteria, with...
Cocultures of strains from two Bifidobacterium and two Bacteroides species were performed with exopolysaccharides (EPS) previously purified from bifidobacteria, with inulin, or with glucose as the carbon source. Bifidobacterium longum NB667 and Bifidobacterium breve IPLA20004 grew in glucose but showed poor or no growth in complex carbohydrates (inulin, EPS E44, and EPS R1), whereas Bacteroides grew well in the four carbon sources tested. In the presence of glucose, the growth of Bacteroides thetaiotaomicron DSM-2079 was inhibited by B. breve, whereas it remained unaffected in the presence of B. longum. Ba. fragilis DSM-2151 contributed to a greater survival of B. longum, promoting changes in the synthesis of short-chain fatty acids (SCFA) and organic acids in coculture with respect to monocultures. In complex carbohydrates, cocultures of bifidobacterium strains with Ba. thetaiotaomicron did not modify the behavior of Bacteroides nor improve the poor growth of bifidobacteria. The metabolic activity of Ba. fragilis in coculture with bifidobacteria was not affected by EPS, but greater survival of bifidobacteria at late stages of incubation occurred in cocultures than in monocultures, leading to a higher production of acetic acid than in monocultures. Therefore, cocultures of Bifidobacterium and Bacteroides can behave differently against fermentable carbohydrates as a function of the specific characteristics of the strains from each species. These results stress the importance of considering specific species and strain interactions and not simply higher taxonomic divisions in the relationship among intestinal microbial populations and their different responses to probiotics and prebiotics.
Topics: Bacteroides; Bifidobacterium; Bioreactors; Carbohydrate Metabolism; Carbon; Carboxylic Acids; Fatty Acids, Volatile; Fermentation; Microbial Interactions; Microbial Viability
PubMed: 24077708
DOI: 10.1128/AEM.02545-13 -
Journal of Clinical Microbiology Mar 2002Chronic periodontitis is a common infectious disease in the adult population. The etiology is clearly bacterial, and a small number of bacterial species have been...
Chronic periodontitis is a common infectious disease in the adult population. The etiology is clearly bacterial, and a small number of bacterial species have been consistently associated with periodontitis, including Bacteroides forsythus and Porphyromonas gingivalis. Comparatively little attention has been paid to the identification of health-associated and potentially beneficial bacterial species that may reside in the gingival sulcus. The purpose of the present study was to examine the relationship of the presence of B. forsythus and a newly identified Bacteroides phylotype, oral clone BU063, to periodontal health status. The study was accomplished with a set of samples that were collected from subjects with periodontitis and healthy controls. These samples had previously been analyzed for the presence of P. gingivalis. An oral sampling strategy that included every tooth and a PCR-based detection method were used to maximize detection sensitivity. The presence of B. forsythus in the oral cavity was strongly associated with periodontitis, and its nearest genetic neighbor, oral clone BU063, was associated with oral health (P < 0.0001 for both). Colonization with P. gingivalis was independent of the presence of either Bacteroides species, but the two Bacteroides species were found together less often than would be expected by chance (P < 0.0001). This suggests the presence of a specific exclusionary mechanism between the two Bacteroides species. Comparisons between these two organisms may prove useful for studies that determine how B. forsythus functions in the disease process. In addition, oral clone BU063 deserves further study as a possible preventive or therapeutic intervention for periodontitis.
Topics: Bacteroides; DNA, Ribosomal; Humans; Periodontitis; Polymerase Chain Reaction; RNA, Ribosomal, 16S
PubMed: 11880400
DOI: 10.1128/JCM.40.3.821-825.2002