Dataset Information

The influence of in vitro pectin fermentation on the human fecal microbiome.

ABSTRACT: Pectin is a complex dietary fiber and a prebiotic. To investigate pectin-induced changes in the gut microbiome and their effects on the short chain fatty acids (SCFAs) production, we performed in vitro pectin fermentation using the feces of three Korean donors. The pectin degradations in all three donors were observed. While the donors displayed differences in baseline gut microbiota composition, commonly increased bacteria after pectin fermentation included Lachnospira, Dorea, Clostridium, and Sutterella. Regarding SCFAs, acetate levels rapidly increased with incubation with pectin, and butyrate levels also increased after 6 h of incubation. The results suggest that pectin fermentation increases bacterial species belonging to Clostridium cluster XIV (Lachnospira, Dorea, and Clostridium), with Lachnospira displaying the greatest increase. The results also confirm that pectin fermentation leads to the production of acetate and butyrate.

SUBMITTER: Bang SJ

PROVIDER: S-EPMC6004267 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The influence of in vitro pectin fermentation on the human fecal microbiome.

Bang So-Jung SJ Kim Gayoung G Lim Mi Young MY Song Eun-Ji EJ Jung Dong-Hyun DH Kum Jun-Seok JS Nam Young-Do YD Park Cheon-Seok CS Seo Dong-Ho DH

AMB Express 20180616 1

Pectin is a complex dietary fiber and a prebiotic. To investigate pectin-induced changes in the gut microbiome and their effects on the short chain fatty acids (SCFAs) production, we performed in vitro pectin fermentation using the feces of three Korean donors. The pectin degradations in all three donors were observed. While the donors displayed differences in baseline gut microbiota composition, commonly increased bacteria after pectin fermentation included Lachnospira, Dorea, Clostridium, and ...[more]

PMID: 29909506

Similar Datasets

Project description:Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbiota is a major challenge, which can be addressed using in vitro fermentors 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 multistage fermentor. We performed two independent experiments using different human donor fecal samples, one configured with two units of three colon compartments each studied for 22 days and another with one unit of two colon compartments studied for 31 days. The fermentor maintained a trend of increasing microbial alpha diversity along colon compartments. Within each experiment, microbial compositions followed compartment-specific trajectories and reached independent stable configurations. While compositions were highly similar between replicate units, they were clearly separated between different experiments, showing that they maintained the individuality of fecal inoculum rather than converging on a fermentor-specific composition. While some fecal amplicon sequence variants (ASVs) were undetected in the fermentor, many ASVs undetected in the fecal samples flourished in vitro. These bloomer ASVs accounted for significant proportions of the population and included prominent health-associated microbes such as Bacteroides fragilis and Akkermansia muciniphila. Turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be easily modulated. Our results suggest that in vitro fermentors are promising tools to study complex microbial communities harboring important members of human gut microbiota. IMPORTANCE In vitro fermentors that can host complex gut microbial communities are promising tools to investigate the dynamics of human gut microbiota. In this work, using an automated in vitro gut fermentor consisting of different colon compartments, we investigated the adaptation dynamics of two different human fecal microbial communities over 22 and 31 days. By observing the temporal trends of different community members, we found that many dominant members of the fecal microbiota failed to maintain their dominance in vitro, and some of the low-abundance microbes undetected in the fecal microbiota successfully grew in the in vitro communities. Microbiome compositional changes and blooming could largely be explained by feed composition and pH, suggesting that these communities can be modulated to desired compositions via optimizing culture conditions. Thus, our results open up the possibility of modulating in vitro microbial communities to predefined compositions by optimizing feed composition and culture conditions.

Dataset Information

The influence of in vitro pectin fermentation on the human fecal microbiome.

Publications

The influence of in vitro pectin fermentation on the human fecal microbiome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure