Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice

Abstract

In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.

Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans

“…Actinobacteria in the treatment order placebo-start (BA) group did not increase during the prebiotic phase. A bloom in Desulfobacteria from prebiotic fibres has been reported previously [92] (see Supplemental Figure S8 for stack bar charts of phylum level changes).…”

“…In addition, we observed an increase in Desulfobacteria ( p = < 0.05, unadjusted) in one of our treatment order groups during the prebiotic intervention. Lignin and RS2 are both insoluble fibres, and Jangid and colleagues [ 92 ] recently demonstrated an increase in Desulfovibrio from an insoluble fibre intervention in mice, the bloom, hypothesised to be the result of increased hydrogen (H 2 ) formation from an influx of insoluble fibres available for fermentation. Key bacterial fibre fermentation products include both SCFAs and gases such as hydrogen (H 2 ) and methane [ 202 ], and members of the genus Desulfovibrio help in the removal of excessive H 2 by converting it into hydrogen sulphide (H 2 S) frequently reported to have an odour like ‘eggy sulphur’, as reported by one of our subjects during the prebiotic phase in our study [ 203 ].…”

Impact of a Whole-Food, High-Soluble Fiber Diet on the Gut–Muscle Axis in Aged Mice

“…Although Lactobacillus and Bifidobacteria species have been shown to reduce body weight and fat mass in mice [56,57], body weight and fat mass were reduced in HSFD-fed mice despite reductions for Lactobacillus and Bifidobacteria, which suggests that other bacteria contributed to these alterations. Lactobacillus was higher in mice fed a grain-based diet when compared to a purified, soluble-fiber-devoid diet [58]. Similarly, Bifidobacteria were increased in response to dietary supplementation with the wheat-bran-derived fiber, arabinoxylan, in conjunction with reduced fat mass [41].…”

SEQUENCING OF THE 16S rRNA GENE V3-V4 REGION TO DETERMINE THE COMPOSITION AND RELATIONSHIPS OF THE MICROBIOTA DURING INFLAMMATION OF THE UDDER AND REPRODUCTIVE TRACT IN COWS (Bos taurus)

“…По данным британских ученых, виды Psychrobacter редко вызывают заболевания у животных (47). Mailhella massiliensis обладает сульфатредуцирующими свойствами, которые ингибируют процесс образования метана в рубце у крупного рогатого скота (48,49), а Oligella ureolytica редко обнаруживается в микробиологических исследованиях как с использованием культуральных методов, так и с помощью секвенирования последовательности гена 16S rRNA (50). Следует отметить, что в известных нам исследованиях развитие репродуктивных заболеваний у коров связывали с высокой относительной численностью бактерий филума Fusobacteria (16,51), однако подобные данные о Proteobacteria получены нами впервые.…”