Abstract
SummaryInterspecies cross‐feeding is a fundamental factor in anaerobic microbial communities. In the human colon, formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM‐RS medium with 0.2% Novelose resistant starch (RS3) as energy source. Batch co‐culturing on starch with the acetogen Blautia hydrogenotrophica however led to the disappearance of formate and increased levels of acetate, which is proposed to occur through the routing of formate via the Wood Ljungdahl pathway of B. hydrogenotrophica. We investigated these inter‐species interactions further using RNAseq to examine gene expression in continuous co‐cultures of R. bromii and B. hydrogenotrophica. Transcriptome analysis revealed upregulation of B. hydrogenotrophica genes involved in the Wood‐Ljungdahl pathway and of a 10 gene cluster responsible for increased branched chain amino acid fermentation in the co‐cultures. Cross‐feeding between formate‐producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production. Transcriptome analysis also indicated competition for the vitamin thiamine and downregulation of dissimilatory sulfate reduction and key redox proteins in R. bromii in the co‐cultures, thus demonstrating the wide‐ranging consequences of inter‐species interactions in this model system.
Highlights
The anaerobic microbial communities found in the mammalian large intestine and rumen represent the most densely-colonized microbial ecosystems in nature (Whitman et al, 1998)
Many gut bacteria produce formate as a major product in pure culture but little or no formate is normally detected in faecal samples
The observations reported here indicate that formate utilization by acetogenic bacteria may be a significant factor explaining the high acetate production and low formate levels that are seen in vivo
Summary
The anaerobic microbial communities found in the mammalian large intestine and rumen represent the most densely-colonized microbial ecosystems in nature (Whitman et al, 1998). R. bromii is reported to produce ethanol, acetate and formate in pure culture with fructose as the carbon source (Herbeck and Bryant, 1974), suggesting that excess reducing equivalents are disposed largely through the production of formate and ethanol in this species. Methanogenic archaea are reported to utilize either formate or H2 and CO2 and have been shown to influence metabolism in hydrogen-producing Firmicutes (Chassard and BernalierDonadille, 2005) but are present in very low numbers in around 50% of the human population (Florin et al, 2000). Coculture is shown to have wide-ranging consequences for metabolic outputs and for gene expression in both species through interactions that involve vitamins, redox pathways, alternative energy sources and carbon flow
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