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Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease

BACKGROUND: This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn’s disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison. METHODS: A case–control study with age, sex and ethnicity matched healthy controls was conducted....

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Autores principales: Hu, Shijia, Png, Eileen, Gowans, Michelle, Ong, David E. H., de Sessions, Paola Florez, Song, Jie, Nagarajan, Niranjan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7905567/
https://www.ncbi.nlm.nih.gov/pubmed/33632307
http://dx.doi.org/10.1186/s13099-021-00409-5
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author Hu, Shijia
Png, Eileen
Gowans, Michelle
Ong, David E. H.
de Sessions, Paola Florez
Song, Jie
Nagarajan, Niranjan
author_facet Hu, Shijia
Png, Eileen
Gowans, Michelle
Ong, David E. H.
de Sessions, Paola Florez
Song, Jie
Nagarajan, Niranjan
author_sort Hu, Shijia
collection PubMed
description BACKGROUND: This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn’s disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison. METHODS: A case–control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted. RESULTS: The study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn’s disease subjects. This was more likely in CD subjects with higher Crohn’s Disease Activity Index (184.3 ± 2.9 vs 67.1 ± 82.5, p = 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p = 0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00–4.56] vs 13.69[5.32–18.71], p = 0.010), Roseburia inulinivorans (0.00[0.00–0.03] vs 0.21[0.01–0.53], p = 0.010) and Alistipes senegalensis (0.00[0.00–0.00] vs 0.00[0.00–0.02], p = 0.029). While Clostridium nexile (0.00[0.00–0.12] vs 0.00[0.00–0.00], p = 0.038) and Ruminococcus gnavus (0.43[0.02–0.33] vs 0.00[0.00–0.13], p = 0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p = 0.001) and isoprene (Linear-discriminant-analysis: 3.058, p < 0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn’s disease. CONCLUSIONS: There was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification.
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spelling pubmed-79055672021-02-25 Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease Hu, Shijia Png, Eileen Gowans, Michelle Ong, David E. H. de Sessions, Paola Florez Song, Jie Nagarajan, Niranjan Gut Pathog Research BACKGROUND: This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn’s disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison. METHODS: A case–control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted. RESULTS: The study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn’s disease subjects. This was more likely in CD subjects with higher Crohn’s Disease Activity Index (184.3 ± 2.9 vs 67.1 ± 82.5, p = 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p = 0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00–4.56] vs 13.69[5.32–18.71], p = 0.010), Roseburia inulinivorans (0.00[0.00–0.03] vs 0.21[0.01–0.53], p = 0.010) and Alistipes senegalensis (0.00[0.00–0.00] vs 0.00[0.00–0.02], p = 0.029). While Clostridium nexile (0.00[0.00–0.12] vs 0.00[0.00–0.00], p = 0.038) and Ruminococcus gnavus (0.43[0.02–0.33] vs 0.00[0.00–0.13], p = 0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p = 0.001) and isoprene (Linear-discriminant-analysis: 3.058, p < 0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn’s disease. CONCLUSIONS: There was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification. BioMed Central 2021-02-25 /pmc/articles/PMC7905567/ /pubmed/33632307 http://dx.doi.org/10.1186/s13099-021-00409-5 Text en © The Author(s) 2021 Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Hu, Shijia
Png, Eileen
Gowans, Michelle
Ong, David E. H.
de Sessions, Paola Florez
Song, Jie
Nagarajan, Niranjan
Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title_full Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title_fullStr Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title_full_unstemmed Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title_short Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease
title_sort ectopic gut colonization: a metagenomic study of the oral and gut microbiome in crohn’s disease
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7905567/
https://www.ncbi.nlm.nih.gov/pubmed/33632307
http://dx.doi.org/10.1186/s13099-021-00409-5
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