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

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...

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Autores principales: Jangid, Aditi, Fukuda, Shinji, Suzuki, Yutaka, Taylor, Todd D., Ohno, Hiroshi, Prakash, Tulika
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9038746/
https://www.ncbi.nlm.nih.gov/pubmed/35468931
http://dx.doi.org/10.1038/s41598-022-10762-3
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author Jangid, Aditi
Fukuda, Shinji
Suzuki, Yutaka
Taylor, Todd D.
Ohno, Hiroshi
Prakash, Tulika
author_facet Jangid, Aditi
Fukuda, Shinji
Suzuki, Yutaka
Taylor, Todd D.
Ohno, Hiroshi
Prakash, Tulika
author_sort Jangid, Aditi
collection PubMed
description 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.
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spelling pubmed-90387462022-04-27 Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice Jangid, Aditi Fukuda, Shinji Suzuki, Yutaka Taylor, Todd D. Ohno, Hiroshi Prakash, Tulika Sci Rep Article 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. Nature Publishing Group UK 2022-04-25 /pmc/articles/PMC9038746/ /pubmed/35468931 http://dx.doi.org/10.1038/s41598-022-10762-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Jangid, Aditi
Fukuda, Shinji
Suzuki, Yutaka
Taylor, Todd D.
Ohno, Hiroshi
Prakash, Tulika
Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title_full Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title_fullStr Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title_full_unstemmed Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title_short Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
title_sort shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9038746/
https://www.ncbi.nlm.nih.gov/pubmed/35468931
http://dx.doi.org/10.1038/s41598-022-10762-3
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