Dataset Information

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

ABSTRACT: Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.

SUBMITTER: Aranda-Diaz A

PROVIDER: S-EPMC9082339 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

Aranda-Díaz Andrés A Ng Katharine Michelle KM Thomsen Tani T Real-Ramírez Imperio I Dahan Dylan D Dittmar Susannah S Gonzalez Carlos Gutierrez CG Chavez Taylor T Vasquez Kimberly S KS Nguyen Taylor H TH Yu Feiqiao Brian FB Higginbottom Steven K SK Neff Norma F NF Elias Joshua E JE Sonnenburg Justin L JL Huang Kerwyn Casey KC

Cell host & microbe 20220119 2

Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different ...[more]

PMID: 35051349

Similar Datasets

Project description:BackgroundContinuous-flow culture models are one tool for studying complex interactions between members of human fecal microbiotas because they allow studies to be completed during an extended period of time under conditions where pH, nutrient availability, and washout of waste products and dead cells can be controlled. Because many of the existing well-validated continuous-flow models are large and complex, we were interested in developing a simpler continuous-flow system that would allow microbial community dynamics to be examined in higher throughput while still maintaining complex microbial communities. To this end, we developed minibioreactor arrays (MBRAs), small volume bioreactors (15 ml) that allow simultaneous cultivation of up to 48 microbial communities in a single anaerobic chamber.ResultsWe used MBRA to characterize the microbial community dynamics of replicate reactors inoculated from three different human fecal donors and reactors seeded with feces pooled from these three donors. We found that MBRA could be used to efficiently cultivate complex microbial communities that were a subset of the initial fecal inoculum (15-25 % of fecal OTUs initially observed). After an initial acclimation period of approximately 1 week, communities in each reactor stabilized and exhibited day-to-day variation similar to that observed in stable mouse fecal communities. Replicate reactors were predominately populated by shared core microbial communities; variation between replicate reactors was primarily driven by shifts in abundance of shared operational taxonomic units (OTUs). Consistent with differences between fecal donors, MBRA communities present in reactors seeded with different fecal samples had distinct composition and structure.ConclusionsFrom these analyses, we conclude that MBRAs can be used to cultivate communities that recapitulate key features of human fecal communities and are a useful tool to facilitate higher-throughput studies of the dynamics of these communities.

Project description:Fecal microbiota transplantation (FMT) documented transplanting a donor fecal sample to a receipt individual for a desired physiologic effect. However, whether the gut microbiota construction, intestinal maturation, and behavioral plasticity are modulated by FMT during the early life of broilers is waiting for verification. To evaluate the role of transfer of fecal microbiota from aged broilers donor (BD) to another individual, 96 birds were equally divided into a check (CK, control) group and a broiler recipient (BR) group. FMT was conducted daily from 5 to 12 days of age to determine the future impact on body weight, behavior, intestinal development, and gut microbiota. Results indicated that fearfulness in the CK group was higher than the BR group in both the behavioral tests (p < 0.05). The muscularis mucosa, thickness of muscle layer, and thickness of serous membrane layer in the BR group were higher compared with those of the CK group in the jejunum (p < 0.05). In the gut microbiota, Shannon diversity showed no difference, while beta diversity presented a difference in principal coordination analysis (PCoA) between the CK and BR groups. At the phylum level, the relative abundance of Lentisphaerae in the CK group was lower than the BR (p = 0.052) and BD (p = 0.054) groups. The relative abundance of Tenericutes in the BD group was higher than that in the CK and BR groups (p < 0.05). At the genus level, Megamonas in the CK group was higher than the BR (p = 0.06) and BD (p < 0.05) groups. In the BR group, the functional capabilities of microbial communities analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were increased in the glutamatergic synapse and N-glycan biosynthesis pathways in comparison with the CK and BD groups (p < 0.05). Some characteristics of gut microbiota in the donor chickens could be transferred to recipient chickens by FMT. In conclusion, exogenous FMT as a probiotic-like administration might be an efficient way to improve the physiology and behavior of chickens. Notably, the role of microbiota for various individuals and periods remains undefined, and the mechanism of microbiota on behaviors still needs further investigation.

Project description:BackgroundEmerging evidences have indicated that the composition of gut microbiota was significantly influenced by central nervous system diseases. The digestion and metabolism disturbances of patients with amyotrophic lateral sclerosis (ALS) might be strongly associated with ALS; however, this has rarely been evaluated in these populations. This study was to evaluate bacterial and archaeal composition of gut flora and the corresponding metabolism performance of these micro-organisms in fecal samples of patients with ALS.MethodsA comparative study was performed on the intestinal microbiota from eight patients with ALS and eight healthy individuals at Huadong Hospital during November 2017 to April 2018; meanwhile, the metabolite concentrations of human endotoxin, short-chain fatty acids (SCFA), NO2-N/NO3-N, and γ-aminobutyric acid were also evaluated by spectrophotometry methods. The correlations between intestinal microbiota and metabolite concentration were compared between the two groups using one-way analysis of variance; the relative abundance of beneficial and harmful micro-organisms in fecal samples was also analyzed.ResultsIn general, the richness and evenness of bacterial and archaeal communities of healthy individuals were healthier than that of patients with ALS. The phylum Firmicutes/Bacteroidetes ratio, genus Methanobrevibacter showed an enhancive tendency in patients with ALS, whereas the relative abundance of beneficial micro-organisms (genera Faecalibacterium and Bacteroides) presented a significant decrease tendency in patients with ALS. In addition, the average concentrations of human endotoxin, SCFA, NO2-N/NO3-N, and γ-aminobutyric acid in patients with ALS and healthy individuals were 64.2 vs. 65.3 EU/mL, 57.5 vs. 55.3 μg/mL, 5.7 vs. 5.3 ng/mL, and 6.1 vs. 5.4 μmol/L, respectively, indicating that the digestion and metabolism functions of gastrointestinal tract of patients might decline with this disease.ConclusionsThe relative abundance of beneficial and harmful micro-organisms respectively showed decrease and increase tendency in patients with ALS.

Project description:BackgroundThe host-microbiota interaction plays a crucial role in maintaining homeostasis and disease susceptibility, and microbial tryptophan metabolites are potent modulators of host physiology. However, whether and how these metabolites mediate host-microbiota interactions, particularly in terms of inter-microbial communication, remains unclear.ResultsHere, we have demonstrated that indole-3-lactic acid (ILA) is a key molecule produced by Lactobacillus in protecting against intestinal inflammation and correcting microbial dysbiosis. Specifically, Lactobacillus metabolizes tryptophan into ILA, thereby augmenting the expression of key bacterial enzymes implicated in tryptophan metabolism, leading to the synthesis of other indole derivatives including indole-3-propionic acid (IPA) and indole-3-acetic acid (IAA). Notably, ILA, IPA, and IAA possess the ability to mitigate intestinal inflammation and modulate the gut microbiota in both DSS-induced and IL-10-/- spontaneous colitis models. ILA increases the abundance of tryptophan-metabolizing bacteria (e.g., Clostridium), as well as the mRNA expression of acyl-CoA dehydrogenase and indolelactate dehydrogenase in vivo and in vitro, resulting in an augmented production of IPA and IAA. Furthermore, a mutant strain of Lactobacillus fails to protect against inflammation and producing other derivatives. ILA-mediated microbial cross-feeding was microbiota-dependent and specifically enhanced indole derivatives production under conditions of dysbiosis induced by Citrobacter rodentium or DSS, but not of microbiota disruption with antibiotics.ConclusionTaken together, we highlight mechanisms by which microbiome-host crosstalk cooperatively control intestinal homoeostasis through microbiota-derived indoles mediating the inter-microbial communication. These findings may contribute to the development of microbiota-derived metabolites or targeted "postbiotic" as potential interventions for the treatment or prevention of dysbiosis-driven diseases. Video Abstract.

Dataset Information

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

Publications

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets