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The ISME Journal Nov 2023Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin...
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.
Topics: Humans; Bacteroides thetaiotaomicron; Bacteroides; Mucins; Glucose
PubMed: 37670028
DOI: 10.1038/s41396-023-01501-1 -
Nutrients Mar 2020Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced...
Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced proinflammatory capacity is characterized by depletion of anaerobic commensals, increased proportion of facultatively anaerobic bacteria, as well as reduced diversity and stability. In this study, we developed a high-throughput in vitro screening assay to isolate intestinal commensal bacteria with anti-inflammatory capacity from a healthy fecal microbiota transplantation donor. Freshly isolated gut bacteria were screened for their capacity to attenuate lipopolysaccharide (LPS)-induced interleukin 8 (IL-8) release from HT-29 cells. The screen yielded a number of and isolates, which were identified as , , , , , and using whole genome sequencing. We observed that a cell-cell contact with the epithelium was not necessary to alleviate in vitro inflammation as spent culture media from the isolates were also effective and the anti-inflammatory action did not correlate with the enterocyte adherence capacity of the isolates. The anti-inflammatory isolates also exerted enterocyte monolayer reinforcing action and lacked essential genes to synthetize hexa-acylated, proinflammatory lipid A, part of LPS. Yet, the anti-inflammatory effector molecules remain to be identified. The strains isolated and characterized in this study have potential to be used as so-called next-generation probiotics.
Topics: Adult; Anti-Inflammatory Agents; Bacteroides; Bacteroidetes; Caco-2 Cells; Feces; Female; Gastrointestinal Microbiome; High-Throughput Screening Assays; Homeostasis; Humans; Interleukin-8; Lipopolysaccharides; Probiotics
PubMed: 32230951
DOI: 10.3390/nu12040935 -
Microbiology (Reading, England) Jul 2011Many bacterial pathogens interfere with the contact system (kallikrein-kinin system) in human plasma. Activation of this system has two consequences: cleavage of...
Many bacterial pathogens interfere with the contact system (kallikrein-kinin system) in human plasma. Activation of this system has two consequences: cleavage of high-molecular-mass kininogen (HK) resulting in release of the potent proinflammatory peptide bradykinin, and initiation of the intrinsic pathway of coagulation. In this study, two species of the Gram-negative anaerobic commensal organism Bacteroides, namely Bacteroides fragilis and Bacteroides thetaiotaomicron, were found to bind HK and fibrinogen, the major clotting protein, from human plasma as shown by immunoelectron microscopy and Western blot analysis. In addition, these Bacteroides species were capable of activating the contact system at its surface leading to a significant prolongation of the intrinsic coagulation time and also to the release of bradykinin. Members of the genus Bacteroides have been known to act as opportunistic pathogens outside the gut, with B. fragilis being the most common isolate from clinical infections, such as intra-abdominal abscesses and bacteraemia. The present results thus provide more insight into how Bacteroides species cause infection.
Topics: Bacterial Outer Membrane Proteins; Bacteroides; Bacteroides fragilis; Blood Coagulation; Bradykinin; Fibrinogen; Humans; Kallikrein-Kinin System; Kallikreins; Kininogens; Kinins
PubMed: 21527472
DOI: 10.1099/mic.0.046862-0 -
Gut Microbes 2021Dysbiosis of gut microbiota has been retrospectively linked to autism spectrum disorders but the temporal association between gut microbiota and early neurodevelopment...
Dysbiosis of gut microbiota has been retrospectively linked to autism spectrum disorders but the temporal association between gut microbiota and early neurodevelopment in healthy infants is largely unknown. We undertook this study to determine associations between gut microbiota at two critical periods during infancy and neurodevelopment in a general population birth cohort.Here, we analyzed data from 405 infants (199 females) from the CHILD (Canadian Healthy Infant Longitudinal Development) Cohort Study. Neurodevelopmental outcomes were objectively assessed using the Bayley Scale of Infant Development (BSID-III) at 1 and 2 years of age. Microbiota profiling with 16S rRNA gene sequencing was conducted on fecal samples obtained at a mean age of 4 and 12 months.Using clustering methods, we identified three groups of infants based on relative abundance of gut microbiota at 12 months: -dominant cluster (22.4% higher abundance at 12 months), -dominant cluster (46.0% higher abundance at 12 months) and Bacteroidetes-dominant cluster (31.6% higher abundance at 12 months). Relative to the -dominant cluster, the -dominant cluster was associated with higher scores for cognitive (4.8 points; FDRp = .02), language (4.2 points; FDRp≤0.001), and motor (3.1 points; FDRp = .03) development at age 2 in models adjusted for covariates. When stratified by sex, only male infants with a -dominant microbiota had more favorable cognitive (5.9 points, FDRp = .06) and language (7.9 points; FDRp≤0.001) development. Genus abundance in gut microbiota was positively correlated with cognitive and language scores at age 2. Fully adjusted linear mixed model analysis revealed a positive association between -dominant cluster and change in cognitive and language performance from 1 to 2 years, predominantly among males. No associations were evident between 4-month microbiota clusters and BSID-II scores. Noteworthy is that enhanced sphingolipid synthesis and metabolism, and antagonism or competition between and were characteristic of a -dominant gut microbiota.This study found strong evidence of positive associations between Bacteroidetes gut microbiota in late infancy and subsequent neurodevelopment, most prominently among males but not females.
Topics: Bacteria; Bacteroides; Canada; Child Development; Female; Follow-Up Studies; Gastrointestinal Microbiome; Humans; Infant; Male; Nervous System; RNA, Ribosomal, 16S; Retrospective Studies
PubMed: 34132157
DOI: 10.1080/19490976.2021.1930875 -
Anaerobe Jun 2021Eleven metronidazole resistant Bacteroides and one newly classified Phocaeicola dorei strain from Kuwait were investigated for their resistance mechanisms and the... (Comparative Study)
Comparative Study
Eleven metronidazole resistant Bacteroides and one newly classified Phocaeicola dorei strain from Kuwait were investigated for their resistance mechanisms and the emergence of their resistant plasmids. All but one strain harbored nimE genes on differently sized plasmids. Of the 11 nimE genes, 9 were preceded by full copies of the prototype ISBf6 insertion sequence element, one carried a truncated ISBf6 and one was activated by an additional copy of IS612B. Nucleotide sequencing results showed that the nimE ISBf6 distances were constant and all five different plasmids shared a common region, suggesting that (i) the nimE-ISBf6 configuration was inserted into an undisclosed common genetic element, (ii) over time, this common element was mutated by insertions and deletions, spreading the resultant plasmids. Of the 10 B. fragilis strains in this collection, 6 were also cfiA-positive, one with full imipenem resistance, indicating a tendency for multidrug resistance (MDR) among such isolates. The significant number of metronidazole resistant Bacteroides spp. and P. dorei strains with the MDR phenotype warns of difficulties in treatment and suggests promoting adherence to antibiotic stewardship recommendations in Kuwait.
Topics: Anti-Bacterial Agents; Bacteroides; Bacteroides Infections; Drug Resistance, Bacterial; Genetic Variation; Genotype; Humans; Kuwait; Metronidazole; Microbial Sensitivity Tests
PubMed: 33713801
DOI: 10.1016/j.anaerobe.2021.102357 -
Proceedings of the National Academy of... Sep 2023Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial...
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of or by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in , a knockdown-responsive taxon. In vitro and in vivo tests of the resulting mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
Topics: Humans; Animals; Mice; Bacteroides; Polysaccharides; Bacteroides thetaiotaomicron; Biological Assay; Diet, Western
PubMed: 37733741
DOI: 10.1073/pnas.2311422120 -
MBio Nov 2016A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations...
UNLABELLED
A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.
IMPORTANCE
This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.
Topics: Bacteroides; Bacteroides fragilis; Colitis, Ulcerative; Colonic Pouches; Cross-Sectional Studies; Genetic Variation; Genome, Bacterial; Host-Pathogen Interactions; Humans; Ileum; Inflammation; Longitudinal Studies; Metagenomics; Microbiota; Mucous Membrane; Pouchitis; Prospective Studies
PubMed: 27935837
DOI: 10.1128/mBio.01713-16 -
Applied and Environmental Microbiology Mar 2019The identification of sewage contamination in water has primarily relied on the detection of human-associated using markers within the V2 region of the 16S rRNA gene....
The identification of sewage contamination in water has primarily relied on the detection of human-associated using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., ) and other organisms (e.g., ), the potential for more human-associated markers in this genus has not been explored in depth. We examined the population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts ( = 76) and uncontaminated water samples ( = 30) demonstrated the high specificity of the assays for sewage. Freshwater were also identified in uncontaminated water samples, demonstrating that measures of total do not reflect fecal pollution. A comparison of two previously described human assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived provided an independent measure of sewage-impacted waters. are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of within sewage to contextualize the well-studied HF183 marker for a human-associated The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.
Topics: Animals; Bacteroides; DNA, Bacterial; Feces; Fresh Water; Humans; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Sewage; Water Pollution
PubMed: 30635376
DOI: 10.1128/AEM.02696-18 -
Clinical Microbiology and Infection :... Sep 2019The prevalence of resistance genes in two important anaerobic genera, Bacteroides and Prevotella, was assessed by applying PCR specifically directed to genes of interest.
OBJECTIVES
The prevalence of resistance genes in two important anaerobic genera, Bacteroides and Prevotella, was assessed by applying PCR specifically directed to genes of interest.
METHODS
A total of 101 Bacteroides spp. and 99 Prevotella spp. human clinical isolates were identified using MALDI-TOF MS. The presence of the resistance genes cfxA, cepA, cfiA, tetQ, ermF and nim, was assessed. Prevalence of resistance genes was compared with the phenotypic resistance against amoxicillin, clindamycin, meropenem and metronidazole.
RESULTS
Even though the majority of the Bacteroides isolates (95.0%) showed resistance towards amoxicillin, only 52/101 of the isolates harboured one of the resistance genes, accounting for this resistance. Within the genus Prevotella the presence of cfxA (50/99) almost perfectly matched the amoxicillin resistance (48/99). No difference in prevalence of the ermF gene (16/101 and 9/99) and clindamycin resistance (16/101 and 10/99) was observed within Bacteroides and Prevotella, respectively. Two isolates of Prevotella were resistant to metronidazole. One harboured the nim gene. One metronidazole-susceptible isolate of Bacteroides harboured a nim gene. Within the Bacteroides and Prevotella genera, 6/101 strains and 5/99 isolates harboured three different resistance genes, respectively, among them tetQ. TetQ is often located on a conjugative transposon, increasing the chance of horizontal gene transfer between isolates.
CONCLUSIONS
An unknown mechanism in Bacteroides non-fragilis isolates causes resistance to β-lactam antibiotics. The fact that the prevalence of the tetQ gene among Prevotella is increasing and the existence of isolates harbouring three resistance genes are worrisome developments.
Topics: Anti-Bacterial Agents; Bacteroidaceae Infections; Bacteroides; Drug Resistance, Bacterial; Genes, Bacterial; Humans; Microbial Sensitivity Tests; Netherlands; Prevalence; Prevotella
PubMed: 30802650
DOI: 10.1016/j.cmi.2019.02.017 -
Cell Host & Microbe Jun 2009Much of the mutualistic relationship between humans and their resident intestinal Bacteroides species is founded on glycans. The host provides plant polysaccharides and... (Review)
Review
Much of the mutualistic relationship between humans and their resident intestinal Bacteroides species is founded on glycans. The host provides plant polysaccharides and host-derived glycans and, in return, receives beneficial end products of bacterial fermentation. Glycans from the bacteria themselves are required for the establishment and survival of these organisms in the colonic ecosystem and provide immunomodulatory properties to the host. Coordinated synthesis and catabolism of bacterial glycans is likely to contribute to the host-bacterial mutualism.
Topics: Bacteroides; Humans; Intestines; Models, Biological; Polysaccharides; Symbiosis
PubMed: 19527880
DOI: 10.1016/j.chom.2009.05.010