Short-Chain Fatty Acids Modulate Microbiota Composition and Functional Potential

Many studies have focused on the metabolic capacity of human gut microbiota to produce short chain fatty acids and subsequent effects on host physiology. Given scarce data on how SCFAs produced by gut bacteria participate in cross-feeding to influence community structure and function, we evaluated the potential of SCFAs to modulate human gut microbiota in vitro. We employed anaerobic fecal cultivation in chemically-defined medium supplemented with one of nine SCFAs to determine effects on both gut microbial community structure via 16S rRNA sequencing and function via genome reconstruction analysis. Each SCFA displayed significant modulatory potential with respect to the relative abundance of bacterial taxa. Analysis of SCFA-supplemented communities revealed that alterations of individual closely related phylotypes, approximating a species displayed coherent changes, although exceptions were also observed suggesting strain-dependent differences in SCFA-induced changes. We used genome reconstruction to evaluate the functional implications of SCFA-mediated restructuring of fecal communities. We note that some SCFA-supplemented cultures displayed a reduction in the predicted abundance of other SCFA producers, suggesting a possible undefined negative feedback mechanism. We conclude that SCFAs are not simply end-products of metabolism but serve to modulate the gut microbiota through cross-feeding that alters the fitness of specified taxa. These results are important in the identification of prebiotics that elevate specific SCFAs for therapeutic benefit and highlight SCFA-consumers as a salient part of the overall metabolic flux pertaining to bacterial fermentative processes.