Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

Abstract

Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

“…3); most models fermented sugars into short-chain fatty acids and organic acids, with acetate, succinate, formate, lactate, propionate, and ethanol being the most commonly produced metabolites. As expected, butyrate was secreted by the Fusobacteria models 26 and by many Firmicutes models 27 , and methane secretion was specific to the Euryarchaeota. Carbon source utilization capabilities were found to be in agreement with the literature 28 .…”

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

“…We found that the alpha diversity of the gut microbiota was negatively correlated with BMI z ‐score and we recovered the same broad trends as we observed with obesity classification such as a positive correlation with the Firmicutes / Bacteroidetes ratio, but with additional insights such as positive correlation of Faecalibacterium OTU 3 ( F. prausnitzii ) with BMI z ‐score and a negative correlation of Bacteroides OTU 7 and 49 ( B. vulgatus and B. stercoris respectively) with BMI z ‐score. Faecalibacterium , a group of major butyrate producers in the colon (Louis et al ., 2009), was also positively correlated with acetate and butyrate, reinforcing the tight link between SCFAs and obesity. Literature data are conflicting about the level of F. prausnitzii in obesity, with studies showing positive (Balamarugan et al ., 2010), negative (Borgo et al ., 2016) or no association (Feng et al ., 2014).…”

Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology

“…In our study, the addition of glycerol selectively enhanced survival of members of the Roseburia  spp./ E. rectale group. The diverse Roseburia  spp./ E. rectale group, encompassing species such as Roseburia inulinivorans or Roseburia intestinalis, is estimated to represent between 5% and 10% of the faecal microbiota (Aminov et al ., 2006; Louis and Flint, 2009). In addition to its cryoprotective action, glycerol may also serve as substrate for a broad range of microbes during reactivation (Engels et al ., 2016).…”