Abstract
The same prebiotics have produced inconsistent effects on microbiota when evaluated in different batch fermentation studies. To understand the reasons behind these discrepancies, we compared impact of one prebiotic formula on the same inoculated fecal microbiota in two frequently used batch systems: phosphate-buffered saline (PBS, oligotrophic) and basal culture medium (BCM, eutrophic). The microbiota was monitored using 454 pyrosequencing. Negative controls (no prebiotic) of both systems showed significant shifts in the microbiota during fermentation, although their pH remained relatively stable, especially in BCM, with increases in Bilophila and Escherichia/Shigella but a decrease in Faecalibacterium. We identified prebiotic responders via redundancy analysis by including both baseline and negative controls. The key positive and negative responders in the two systems were very different, with only 8 consistently modulated OTUs (7 of the 28 positive responders and 1 of the 35 negative responders). Moreover, some OTUs within the same genus responded to the prebiotic in opposite ways. Therefore, to obtain a complete in vitro evaluation of the modulatory effects of a prebiotic on microbiota, it is necessary to use both oligotrophic and eutrophic systems, compare treatment groups with both baseline and negative controls, and analyze the microbiota changes down to the OTU level.
Highlights
By selectively stimulating the growth and/or activity of one or a limited number of bacterial species already resident in the colon,”[12] are promising and widely used approaches for modulating gut microbiota
After discarding sequences that had no near neighbors in the entire Greengenes database, we used a total of 50,056 reads for downstream analysis (Supplementary Fig. S1a)
Rarefaction analysis and the Shannon Diversity Index (H’) based on the abundance of the representative Operational taxonomic units (OTUs) sequences revealed that, new rare phylotypes would be expected with additional sequencing, most of the diversity had already been captured (Supplementary Fig. S1d,e)
Summary
By selectively stimulating the growth and/or activity of one or a limited number of bacterial species already resident in the colon,”[12] are promising and widely used approaches for modulating gut microbiota. Potential prebiotics are typically tested using in vitro batch fermentation models inoculated with human fecal matter to mimic the human digestive tract environment[15,18] Such studies allow in vitro modeling of how the composition of the human gut microbiota changes in response to prebiotic nutrients. The phosphate-buffered saline (PBS) system[19,22,25] and the basal culture medium (BCM) system[20,21,26,27] are the two most widely used oligotrophic and eutrophic systems, respectively These two systems mirror the differences in intestinal trophic status induced by a calorie-restricted diet, in which available nutrients are absorbed primarily while passing through the upper parts of the GI tract (oligotrophic), and a high-fat/ high-protein diet, in which excess nutrients reach the colon (eutrophic)[29,30]. Merging all the species in the same genus together may overlook real patterns or generate spurious patterns of prebiotic-induced microbial change
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