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Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota

The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad pa...

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Autores principales: Pennycook, Joseph Hugh, Scanlan, Pauline Deirdre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498795/
https://www.ncbi.nlm.nih.gov/pubmed/33822937
http://dx.doi.org/10.1093/femsre/fuab018
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author Pennycook, Joseph Hugh
Scanlan, Pauline Deirdre
author_facet Pennycook, Joseph Hugh
Scanlan, Pauline Deirdre
author_sort Pennycook, Joseph Hugh
collection PubMed
description The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems.
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spelling pubmed-84987952021-10-08 Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota Pennycook, Joseph Hugh Scanlan, Pauline Deirdre FEMS Microbiol Rev Review Article The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems. Oxford University Press 2021-04-06 /pmc/articles/PMC8498795/ /pubmed/33822937 http://dx.doi.org/10.1093/femsre/fuab018 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review Article
Pennycook, Joseph Hugh
Scanlan, Pauline Deirdre
Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title_full Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title_fullStr Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title_full_unstemmed Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title_short Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota
title_sort ecological and evolutionary responses to antibiotic treatment in the human gut microbiota
topic Review Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498795/
https://www.ncbi.nlm.nih.gov/pubmed/33822937
http://dx.doi.org/10.1093/femsre/fuab018
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