Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>

ABSTRACT Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonizatio...

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Autores principales:	Andre Mu, Glen P. Carter, Lucy Li, Nicole S. Isles, Alison F. Vrbanac, James T. Morton, Alan K. Jarmusch, David P. De Souza, Vinod K. Narayana, Komal Kanojia, Brunda Nijagal, Malcolm J. McConville, Rob Knight, Benjamin P. Howden, Timothy P. Stinear
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	microbiome multiomics metagenomics metabolomics gut microbiome vancomycin-resistant enterococci Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f5003cdaf3f245779749689be636189d
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spelling	oai:doaj.org-article:f5003cdaf3f245779749689be636189d2021-12-02T18:44:37ZMicrobe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>10.1128/mSystems.00452-202379-5077https://doaj.org/article/f5003cdaf3f245779749689be636189d2020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00452-20https://doaj.org/toc/2379-5077ABSTRACT Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenericutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone and to subsequent VREfm challenge. Using neural networking approaches to find cooccurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition toward a preantibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem and the progression of the microbiome in response to colonization with VREfm. Our results offer insights toward identifying potential nonantibiotic alternatives to eliminate VREfm through metabolic reengineering to preferentially select for Bacteroides. IMPORTANCE This study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.Andre MuGlen P. CarterLucy LiNicole S. IslesAlison F. VrbanacJames T. MortonAlan K. JarmuschDavid P. De SouzaVinod K. NarayanaKomal KanojiaBrunda NijagalMalcolm J. McConvilleRob KnightBenjamin P. HowdenTimothy P. StinearAmerican Society for Microbiologyarticlemicrobiomemultiomicsmetagenomicsmetabolomicsgut microbiomevancomycin-resistant enterococciMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	microbiome multiomics metagenomics metabolomics gut microbiome vancomycin-resistant enterococci Microbiology QR1-502
spellingShingle	microbiome multiomics metagenomics metabolomics gut microbiome vancomycin-resistant enterococci Microbiology QR1-502 Andre Mu Glen P. Carter Lucy Li Nicole S. Isles Alison F. Vrbanac James T. Morton Alan K. Jarmusch David P. De Souza Vinod K. Narayana Komal Kanojia Brunda Nijagal Malcolm J. McConville Rob Knight Benjamin P. Howden Timothy P. Stinear Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
description	ABSTRACT Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenericutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone and to subsequent VREfm challenge. Using neural networking approaches to find cooccurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition toward a preantibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem and the progression of the microbiome in response to colonization with VREfm. Our results offer insights toward identifying potential nonantibiotic alternatives to eliminate VREfm through metabolic reengineering to preferentially select for Bacteroides. IMPORTANCE This study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.
format	article
author	Andre Mu Glen P. Carter Lucy Li Nicole S. Isles Alison F. Vrbanac James T. Morton Alan K. Jarmusch David P. De Souza Vinod K. Narayana Komal Kanojia Brunda Nijagal Malcolm J. McConville Rob Knight Benjamin P. Howden Timothy P. Stinear
author_facet	Andre Mu Glen P. Carter Lucy Li Nicole S. Isles Alison F. Vrbanac James T. Morton Alan K. Jarmusch David P. De Souza Vinod K. Narayana Komal Kanojia Brunda Nijagal Malcolm J. McConville Rob Knight Benjamin P. Howden Timothy P. Stinear
author_sort	Andre Mu
title	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
title_short	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
title_full	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
title_fullStr	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
title_full_unstemmed	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>
title_sort	microbe-metabolite associations linked to the rebounding murine gut microbiome postcolonization with vancomycin-resistant <named-content content-type="genus-species">enterococcus faecium</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/f5003cdaf3f245779749689be636189d
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Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content>

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