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Research Article | Host-Microbe Biology

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village

Kelly V. Ruggles, Jincheng Wang, Angelina Volkova, Monica Contreras, Oscar Noya-Alarcon, Orlana Lander, Hortensia Caballero, Maria G. Dominguez-Bello
Katherine McMahon, Editor
Kelly V. Ruggles
aDepartment of Medicine, New York University Langone Medical Center, New York, New York, USA
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Jincheng Wang
aDepartment of Medicine, New York University Langone Medical Center, New York, New York, USA
bDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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Angelina Volkova
aDepartment of Medicine, New York University Langone Medical Center, New York, New York, USA
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Monica Contreras
cCenter for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
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Oscar Noya-Alarcon
dInstituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
eAmazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, Venezuela
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Orlana Lander
dInstituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
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Hortensia Caballero
fDepartment of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
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Maria G. Dominguez-Bello
aDepartment of Medicine, New York University Langone Medical Center, New York, New York, USA
bDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
gDepartment of Anthropology, New York University, New York, New York, USA
hDepartment of Anthropology, Rutgers University, New Brunswick, New Jersey, USA
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Katherine McMahon
University of Wisconsin-Madison
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DOI: 10.1128/mSphere.00193-18
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ABSTRACT

People living traditional lifestyles have higher gut microbiota diversity than urban subjects. We hypothesized that shifting lifestyles from an urban environment to a traditional rainforest village would lead to changes in the microbiota of visitors, which would become more similar to the microbiota of villagers. Here, we characterized at different time points the microbiota of 7 urban visitors (5 adults and 2 children) staying in a rainforest Amerindian village for 16 days and compared them with a reference collection of samples from age-matched local villagers. We performed a 16S rRNA gene survey of samples from multiple body sites (including fecal, oral, nasal, and skin samples) using Illumina MiSeq sequencing. The main factor segregating the microbiotas of each body site was the human group (i.e., visitors versus villagers), with the visitor microbiota tending to have lower alpha diversity; the lowered alpha diversity was statistically significant in the microbiota of skin and in the children’s fecal and oral microbiota. During the rainforest period, all visitors experienced microbiota changes within their personal cloud of variation. For all body sites, the microbiota conformations in the visitor children better matched the microbiota conformations in villagers of the same age than did those of the visitor adults, which showed a lower “microbiota age” than the microbiota of the villagers. The results suggest higher stability in the adult microbiota, with the less resilient children’s microbiota responding more to dietary changes.

IMPORTANCE Despite the limitations of a small study, our results evidence higher resilience of the gut microbiota with respect to dietary manipulation in adults than in children and urge further studies to understand the extent of microbiota plasticity in response to dietary changes and the mechanisms underlying microbiota resilience. These studies are relevant to the potential of future human pre- and probiotics in preventing or curing microbiota-associated diseases.

  • Copyright © 2018 Ruggles et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village
Kelly V. Ruggles, Jincheng Wang, Angelina Volkova, Monica Contreras, Oscar Noya-Alarcon, Orlana Lander, Hortensia Caballero, Maria G. Dominguez-Bello
mSphere Aug 2018, 3 (4) e00193-18; DOI: 10.1128/mSphere.00193-18

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Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village
Kelly V. Ruggles, Jincheng Wang, Angelina Volkova, Monica Contreras, Oscar Noya-Alarcon, Orlana Lander, Hortensia Caballero, Maria G. Dominguez-Bello
mSphere Aug 2018, 3 (4) e00193-18; DOI: 10.1128/mSphere.00193-18
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KEYWORDS

Amerindian
diet
microbiome

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