The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production

Abstract

Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated in vitro, and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness. This corresponded with an increased abundance of Ruminococcaceae Ruminococcus, and Erysipelotrichaceae Erysipelatoclostridium, and a decreased abundance of Coriobacteriaceae Collinsella, and Enterobacteriaceae Shigella for both the luminal and mucosal communities. Total SCFA levels were significantly higher, primarily due to an increase in acetic and 2-methylbutanoic acids. Lowering pH decreased luminal community evenness and decreased mucosal community evenness and richness. This corresponded with an increased abundance of Lachnospiraceae Enterocloster, Veillonellaceae Megasphaera, Veillonellaceae Sporomusa, Erysipelotrichaceae Eubacterium, and Alcaligenaceae Sutterella, and decreased abundance of Odoribacteraceae Butyricimonas, Fusobacteriaceae Fusobacterium, Veillonellaceae Phascolarctobacterium, and multiple Enterobacteriaceae species for both the luminal and mucosal communities. Total SCFA levels were significantly lower, with an observed drop in acetic and propionic acids, and increased butyric and valeric acids. Taken together, these results indicate that alterations to environmental pH can modulate the gut microbiota community structure and function, and some changes may occur in a donor-independent manner.

Modulation of the Gut Microbiota Structure and Function by Two Structurally Different Lemon Pectins

“…Alpha diversity was calculated during the control, lemon pectin treatment, and post-treatment periods based on richness, which indicated the number of taxonomic units detected, diversity based on Shannon’s diversity index, and biodiversity based on Faith’s phylogenetic diversity (Faith’s P.D.) ( Figure 1 ) [ 22 , 23 ]. For LMW-HDE lemon pectin, both donor communities responded with enhanced richness, although this did not reach significance during the treatment period; However, when treatment with LMW-HDE pectin was halted, there was a significant reduction in richness, even below that of the control period ( Figure 1 A).…”

“…DNA was extracted from samples of communities during the control, lemon pectin treatment, and post-treatment period using the DNEasy Powersoil Kit as described previously (Qiagen, Hilden, Germany) [ 23 , 28 ]. The amount of DNA from each sample was quantified using Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA) and 16S rRNA gene sequencing was performed on the V1-V2 region using the Miseq platform (Illumina, San Diego, CA, USA) and a 2 × 250 bp chemistry as described previously [ 23 , 28 ]. Controls run included extraction blanks, DNA-free water, and a positive control of 8 artificial 16S gene fragments purchased from Integrated DNA Technologies (IDT, Coralville, IA, USA) [ 30 ].…”

“…Short-chain fatty acids (SCFAs) were quantified using a GC/MS Shimadzu QP2010 Ultra (Shimadzu, Kyoto, Japan) equipped with Stabilwax-DA column, 30 m, 0.25 mm ID, 0.25 μm, (Restek Corporation, Belfonte, PA, USA) following a previously published protocol [ 23 , 28 ]. All reagents were obtained from Sigma Aldrich.…”

“…Briefly, samples were centrifuged at 5000× g at 4 °C for 10 min then the supernatant was filtered with a 0.2 μM PES filter (Corning, Corning, NY, USA). Samples were prepared and loaded to GC autosampler and analyzed using a Gas Chromatography Mass Spectrophotometer (GC-MS) [ 23 , 28 ]. Sample at a volume of 1 µL was input as a 1:20 split mode at 260 °C, the interface temperature was 250 °C and ion source temperatures was 220 °C.…”

“…To isolate the interactions between pectin and the microbes, an in vitro experimental design was utilized to remove the multifarious interactions that occur between the gut microbiota and mammalian cells in an in vivo model [ 22 ]. Changes to the gut microbiota community structure and function were determined using 16S rRNA gene sequencing and SCFA analysis [ 22 , 23 ]. The results of this study provided detailed information on how pectins with different chemical structures modulate the gut microbiota in divergent manners, which advances our understanding of how pectin MW and DE may impact this interaction, which is critical to its application as a prebiotic.…”