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The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides
Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being the third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focuse...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8971754/ https://www.ncbi.nlm.nih.gov/pubmed/35372092 http://dx.doi.org/10.3389/fcimb.2022.854122 |
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author | Kijner, Sivan Cher, Avital Yassour, Moran |
author_facet | Kijner, Sivan Cher, Avital Yassour, Moran |
author_sort | Kijner, Sivan |
collection | PubMed |
description | Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being the third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2’-FL, DFL, 3’-SL, 6’-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization. |
format | Online Article Text |
id | pubmed-8971754 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-89717542022-04-02 The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides Kijner, Sivan Cher, Avital Yassour, Moran Front Cell Infect Microbiol Cellular and Infection Microbiology Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being the third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2’-FL, DFL, 3’-SL, 6’-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization. Frontiers Media S.A. 2022-03-18 /pmc/articles/PMC8971754/ /pubmed/35372092 http://dx.doi.org/10.3389/fcimb.2022.854122 Text en Copyright © 2022 Kijner, Cher and Yassour https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cellular and Infection Microbiology Kijner, Sivan Cher, Avital Yassour, Moran The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title | The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title_full | The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title_fullStr | The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title_full_unstemmed | The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title_short | The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides |
title_sort | infant gut commensal bacteroides dorei presents a generalized transcriptional response to various human milk oligosaccharides |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8971754/ https://www.ncbi.nlm.nih.gov/pubmed/35372092 http://dx.doi.org/10.3389/fcimb.2022.854122 |
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