Duncan SH, Louis P, Thomson JM, Flint HJ. Environmental Microbiology. 2009;11(8):2112-2122. doi:10.1111/j.1462-2920.2009.01931.x
Background & Rationale
Colonic pH varies by site, being more acidic proximally due to short-chain fatty acid (SCFA) production during carbohydrate fermentation, and more neutral distally. While low pH is known to restrict pathogens such as Escherichia coli, its effect on competition among dominant commensal anaerobes was unclear. This study examined how mildly acidic pH, typical of the proximal colon, affects growth of individual bacterial species and community structure, and whether phylogeny predicts pH tolerance.
Study Design
Thirty-three human colonic isolates from Bacteroidetes, Proteobacteria, Firmicutes and Actinobacteria were grown anaerobically in YCFA medium with SCFAs and glucose at initial pH 5.5, 6.2 and 6.7, with growth rates calculated from exponential-phase optical density. Four starch-utilising strains were further tested across eleven pH values using starch alone. SCFA contribution to inhibition was assessed by comparing Bacteroides thetaiotaomicron growth with and without the SCFA mixture. Community effects were studied in a continuous-flow fermentor inoculated with human faecal bacteria at pH 5.5 or 6.5, with composition assessed via 16S rRNA clone library sequencing. ANOVA was used for growth comparisons, with significance testing for phylum-level differences.
Patient Population
No human subjects were enrolled. Isolates came from existing culture collections derived from human faeces, representing dominant phylogenetic groups. The fermentor experiment used a single faecal inoculum from one healthy, methanogenic adult who had avoided antibiotics for at least six months. As no participant groups were compared, demographic factors are not applicable.
Key Findings
All eight Bacteroides species and both E. coli strains showed markedly reduced growth at pH 5.5 versus 6.7, several nearly failing to grow at the lowest pH. Conversely, 19 of 23 Gram-positive anaerobes retained at least half their pH 6.7 growth rate at pH 5.5. Butyrate producers related to Eubacterium rectale and Roseburia were especially tolerant, with E. rectale A1-86 the most resilient overall. Adding SCFAs increased inhibition of B. thetaiotaomicron at pH 5.5, cutting growth to under 10% of the pH 6.7 rate, versus about 40% inhibition without SCFAs.
In the fermentor, Bacteroidetes made up 86% of sequences at pH 6.7 but only 27% at pH 5.5, while E. rectale/Roseburia-related sequences rose from undetectable at pH 6.5 to 50% at pH 5.5, a highly significant shift.
Discussion
These results indicate that mildly acidic, proximal-colon-like pH suppresses Bacteroidetes while favouring Gram-positive butyrate producers such as Roseburia and E. rectale. The authors suggest SCFAs, present at physiological concentrations, add to this inhibition beyond the direct effect of pH itself. This pH-driven competition may explain earlier links between dietary carbohydrate intake and shifts in faecal butyrate-producing bacteria. As an in vitro/ex vivo study, no safety or tolerability data apply.
Authors’ Conclusions
The authors conclude colonic pH strongly influences competitive outcomes between phylogenetically distinct bacterial groups, with dietary-driven pH fluctuations likely causing ongoing shifts in major bacterial populations. They note the sequence-based community analysis used only one fermentor run, so species-level results may vary between individuals, though broader taxonomic shifts had been reproduced in earlier replicate experiments with different inocula.
Reference
Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol. 2009;11(8):2112-2122. doi:10.1111/j.1462-2920.2009.01931.x
This Scientific Publication Summary is an objective summary of the published trial for personal and educational use. It does not constitute clinical advice, endorsement of the intervention, or a recommendation to alter clinical practice.