The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon

During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they...

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Main Authors: Eder Soares Pires, Cristiane Cassiolato Pires Hardoim, Karla Rodrigues Miranda, Danielle Angst Secco, Leandro Araújo Lobo, Denise Pires de Carvalho, Jun Han, Christoph H. Borchers, Rosana B. R. Ferreira, Joana Falcão Salles, Regina Maria Cavalcanti Pilotto Domingues, Luis Caetano Martha Antunes
Format: Article
Language:English
Published: Frontiers Media S.A. 2019-09-01
Series:Frontiers in Microbiology
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fmicb.2019.02003/full
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author Eder Soares Pires
Eder Soares Pires
Cristiane Cassiolato Pires Hardoim
Karla Rodrigues Miranda
Danielle Angst Secco
Leandro Araújo Lobo
Denise Pires de Carvalho
Jun Han
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Rosana B. R. Ferreira
Joana Falcão Salles
Regina Maria Cavalcanti Pilotto Domingues
Luis Caetano Martha Antunes
Luis Caetano Martha Antunes
spellingShingle Eder Soares Pires
Eder Soares Pires
Cristiane Cassiolato Pires Hardoim
Karla Rodrigues Miranda
Danielle Angst Secco
Leandro Araújo Lobo
Denise Pires de Carvalho
Jun Han
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Rosana B. R. Ferreira
Joana Falcão Salles
Regina Maria Cavalcanti Pilotto Domingues
Luis Caetano Martha Antunes
Luis Caetano Martha Antunes
The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
Frontiers in Microbiology
gut microbiome
riparian communities
Amazon
high-throughput sequencing
metabolic prediction
metabolomics
author_facet Eder Soares Pires
Eder Soares Pires
Cristiane Cassiolato Pires Hardoim
Karla Rodrigues Miranda
Danielle Angst Secco
Leandro Araújo Lobo
Denise Pires de Carvalho
Jun Han
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Christoph H. Borchers
Rosana B. R. Ferreira
Joana Falcão Salles
Regina Maria Cavalcanti Pilotto Domingues
Luis Caetano Martha Antunes
Luis Caetano Martha Antunes
author_sort Eder Soares Pires
title The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
title_short The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
title_full The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
title_fullStr The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
title_full_unstemmed The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon
title_sort gut microbiome and metabolome of two riparian communities in the amazon
publisher Frontiers Media S.A.
series Frontiers in Microbiology
issn 1664-302X
publishDate 2019-09-01
description During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.
topic gut microbiome
riparian communities
Amazon
high-throughput sequencing
metabolic prediction
metabolomics
url https://www.frontiersin.org/article/10.3389/fmicb.2019.02003/full
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spelling doaj-ffc4859f14fb4f8c8369107002e581442020-11-25T00:51:38ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-09-011010.3389/fmicb.2019.02003462710The Gut Microbiome and Metabolome of Two Riparian Communities in the AmazonEder Soares Pires0Eder Soares Pires1Cristiane Cassiolato Pires Hardoim2Karla Rodrigues Miranda3Danielle Angst Secco4Leandro Araújo Lobo5Denise Pires de Carvalho6Jun Han7Christoph H. Borchers8Christoph H. Borchers9Christoph H. Borchers10Christoph H. Borchers11Rosana B. R. Ferreira12Joana Falcão Salles13Regina Maria Cavalcanti Pilotto Domingues14Luis Caetano Martha Antunes15Luis Caetano Martha Antunes16Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilInstituto Tecnológico Vale – Desenvolvimento Sustentável, Belém, BrazilInstituto de Biociências, Universidade Estadual Paulista, São Vicente, BrazilInstituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, aRio de Janeiro, BrazilUniversity of Victoria – Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, CanadaUniversity of Victoria – Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, CanadaDepartment of Biochemistry and Microbiology, University of Victoria, Victoria, BC, CanadaSegal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, CanadaGerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, CanadaInstituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilMicrobial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, NetherlandsInstituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil0Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil1Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilDuring the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.https://www.frontiersin.org/article/10.3389/fmicb.2019.02003/fullgut microbiomeriparian communitiesAmazonhigh-throughput sequencingmetabolic predictionmetabolomics