pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures - PubMed (original) (raw)

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures

Zehra Esra Ilhan et al. mSphere. 2017.

Abstract

pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut. IMPORTANCE The human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are unknown. Here, we show that, for in vitro conditions, pH was the strongest driver of microbial community structure and function and microbial and metabolic interactions among pH-sensitive fermentative species. The balance between bicarbonate alkalinity and formation of fatty acids by fermentation determined the pH, which controlled microbial community structure. Our results underscore the influence of pH balance on microbial function in diverse microbial ecosystems such as the human gut.

Keywords: alkalinity; bacterial diversity; lactate utilizers; microbial communities; microbial fermentation; propionate producers; substrate type.

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Figures

FIG 1

FIG 1

(A) Weighted UniFrac (32) analysis visualized on principal coordinates shows that mainly the initial pH along with buffering determined the main phylotypes that drove the community structures in the system. Each circle represents microbial communities from pooled DNA samples from triplicate reactors. (B and C) Abundance-based coverage estimator (ACE) (33) (B) and PD whole-tree (34) (C) indices calculated from 16S rRNA gene sequences for inoculum and pH 6.0, 6.5, and 6.9 cultures.

FIG 2

FIG 2

Major fermentation end products—lactate, acetate, and propionate—in mixed cultures fed glucose, fructose, or cellobiose at initial pH values of 6.0, 6.5, or 6.9. The millimoles of each acid produced was normalized per millimole of hexose consumed. Error bars represent the standard deviations of triplicates for each condition. *, Mann-Whitney U-test P value of <0.05.

FIG 3

FIG 3

Relative abundance of phylotypes at the genus level in inoculum and fermentation cultures with initial pH values of 6.0, 6.5, or 6.9 and with glucose, fructose, or cellobiose as the initial substrate.

FIG 4

FIG 4

Nonparametric correlation coefficients (Spearman’s rank) between combinations of taxa, initial pH, and fermentation end products.

References

    1. Walker AW, Duncan SH, Leitch ECM, Child MW, Flint HJ. 2005. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol 71:3692–3700. doi: 10.1128/AEM.71.7.3692-3700.2005. - DOI - PMC - PubMed
    1. Chung WSF, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ. 2016. Modulation of the human gut microbiota by dietary fibres occurs at the species level. BMC Biol 14:3. doi: 10.1186/s12915-015-0224-3. - DOI - PMC - PubMed
    1. Evans DF, Pye G, Bramley R, Clark AG, Dyson TJ, Hardcastle JD. 1988. Measurement of gastrointestinal pH profiles in normal ambulant human subjects. Gut 29:1035–1041. doi: 10.1136/gut.29.8.1035. - DOI - PMC - PubMed
    1. Nugent SG, Kumar D, Rampton DS, Evans DF. 2001. Intestinal luminal pH in inflammatory bowel disease: possible determinants and implications for therapy with aminosalicylates and other drugs. Gut 48:571–577. doi: 10.1136/gut.48.4.571. - DOI - PMC - PubMed
    1. Fallingborg J. 1999. Intraluminal pH of the human gastrointestinal tract. Dan Med Bull 46:183–196. - PubMed

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