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Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system

ABSTRACT: Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbial communities is a major challenge, which can be addressed using in vitro fermenters hosting complex microbial communities. Here, by employing 16S rRNA gene amplicon sequencing, we investigated the adaptation and succession of human fecal microbial communities in an automated in vitro fermenter. We performed two independent experiments each using a different human donor fecal sample – the first experiment was configured with two units of three colon compartments each studied for 22 days, and the second experiment with one unit of two colon compartments studied for 31 days. In both experiments, the fermenter maintained a trend of increasing microbial alpha-diversity along colon compartments, mimicking that of the human gastrointestinal tract. Within each experiment, microbial compositions followed compartment-specific trajectories over time and reached compartment-specific stable configurations. Microbial compositions were highly similar between the replicate units in the first experiment, thus showing reproducibility. Yet, microbial compositions and their trajectories were clearly separated between the two experiments, showing that these in vitro communities maintained the individuality of fecal inocula rather than converging on a fermenter-specific composition. Using longitudinal relative abundance profiles, we identified different dynamics exhibited by individual amplicon sequence variants (ASVs). While we could not detect some fecal ASVs in the in vitro communities, we observed that many ASVs undetected in the fecal sample flourished under in vitro conditions, which we named bloomers. In both experiments, bloomer ASVs accounted for significant proportions of ASV relative abundance after stabilization – 69% and 43% in the descending compartments in the two experiments. Bloomer ASVs included clinically relevant microbes associated with human health such as Bacteroides fragilis and Akkermansia muciniphila. This turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be modulated. We characterized the exometabolites in the first experiment, derived a microbe-exometabolite bipartite network for its descending colon compartment, and identified 6 coherent groups based on the exometabolites. Our results suggest that in vitro fermenters are promising tools to study complex microbial communities harboring important members of human gut microbiota.

INSTRUMENT(S): Liquid Chromatography MS - positive - reverse phase

SUBMITTER: Manimozhiyan Arumugam

PROVIDER: MTBLS2531 | MetaboLights | 2021-07-15

REPOSITORIES: MetaboLights

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Project description:We developed a laboratory-scale model to improve our understanding and capacity to assess the biological risks of genetically engineered bacteria and their genetic elements in the natural environment. Our hypothetical scenario concerns an industrial bioreactor failure resulting in the introduction of genetically engineered bacteria to a downstream municipal wastewater treatment plant (MWWTP). As the first step towards developing a model for this scenario, we sampled microbial communities from the aeration basin of a MWWTP at three seasonal time points. Having established a baseline for community composition, we investigated how the community changed when propagated in the laboratory, including cell culture media conditions that could provide selective pressure in future studies. Specifically, using PhyloChip 16S rRNA gene-targeting microarrays, we compared the compositions of sampled communities to those of inoculates propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources (glucose, chloroacetate, D-threonine) or the ionic liquid 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl). Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in aeration basin and laboratory-cultured populations. Laboratory-cultured populations were enriched in Gammaproteobacteria. Enterobacteriaceae and Aeromonadaceae were enriched by glucose, Pseudomonadaceae by chloroacetate and D-threonine, and Burkholderiaceae by high (50 mM) concentrations of chloroacetate. Microbial populations cultured with chloroacetate and D-threonine were more similar to sampled populations than thoes cultured with glucose or [C2mim]Cl. Although observed relative richness in operational taxonomic units was lower for laboratory cultures than for sampled populations, both flask and reactor systems cultured phylogenetically diverse communities. These results importantly provide a foundation for laboratory models of industrial bioreactor failure scenarios. 46 samples, flask and reactor experiments were conducted in triplicate with two exceptions: [C2mim]Cl_flask and No-Carbon_flask treatments had only one sample (no replicates).

			Action	DRS
	MTBLS2531	Other
	FILES	Other
	MTBLS-fixed-isa.json	Other
	a_MTBLS2531_LC-MS_positive_reverse-phase_metabolite_profiling.txt	Txt
	files-all.json	Other

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Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system

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