The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status

ABSTRACT Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with chan...

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Autores principales:	Sarah M. Hird, Holly Ganz, Jonathan A. Eisen, Walter M. Boyce
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	avian microbiome ducks evolutionary biology microbial ecology microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/97946574fac14572adf61ea100e7b6aa
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spelling	oai:doaj.org-article:97946574fac14572adf61ea100e7b6aa2021-11-15T15:22:26ZThe Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status10.1128/mSphere.00382-182379-5042https://doaj.org/article/97946574fac14572adf61ea100e7b6aa2018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00382-18https://doaj.org/toc/2379-5042ABSTRACT Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV− cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV− ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV− birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level. IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual’s microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent “flu-like” microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.Sarah M. HirdHolly GanzJonathan A. EisenWalter M. BoyceAmerican Society for Microbiologyarticleavian microbiomeducksevolutionary biologymicrobial ecologymicrobiomeMicrobiologyQR1-502ENmSphere, Vol 3, Iss 5 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	avian microbiome ducks evolutionary biology microbial ecology microbiome Microbiology QR1-502
spellingShingle	avian microbiome ducks evolutionary biology microbial ecology microbiome Microbiology QR1-502 Sarah M. Hird Holly Ganz Jonathan A. Eisen Walter M. Boyce The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
description	ABSTRACT Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV− cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV− ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV− birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level. IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual’s microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent “flu-like” microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.
format	article
author	Sarah M. Hird Holly Ganz Jonathan A. Eisen Walter M. Boyce
author_facet	Sarah M. Hird Holly Ganz Jonathan A. Eisen Walter M. Boyce
author_sort	Sarah M. Hird
title	The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
title_short	The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
title_full	The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
title_fullStr	The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
title_full_unstemmed	The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
title_sort	cloacal microbiome of five wild duck species varies by species and influenza a virus infection status
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/97946574fac14572adf61ea100e7b6aa
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The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status

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