Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status

ABSTRACT Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in micro...

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Autores principales:	Tao Ding, Timothy Song, Bin Zhou, Adam Geber, Yixuan Ma, Lingdi Zhang, Michelle Volk, Shashi N. Kapadia, Stephen G. Jenkins, Mirella Salvatore, Elodie Ghedin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	16S RNA sequencing influenza virus microbiome vaccination Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/8bb91d0b7c8f4deabc7506051b05b117
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spelling	oai:doaj.org-article:8bb91d0b7c8f4deabc7506051b05b1172021-11-15T16:22:09ZMicrobial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status10.1128/mBio.01296-192150-7511https://doaj.org/article/8bb91d0b7c8f4deabc7506051b05b1172019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01296-19https://doaj.org/toc/2150-7511ABSTRACT Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia. IMPORTANCE Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications.Tao DingTimothy SongBin ZhouAdam GeberYixuan MaLingdi ZhangMichelle VolkShashi N. KapadiaStephen G. JenkinsMirella SalvatoreElodie GhedinAmerican Society for Microbiologyarticle16S RNA sequencinginfluenza virusmicrobiomevaccinationMicrobiologyQR1-502ENmBio, Vol 10, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S RNA sequencing influenza virus microbiome vaccination Microbiology QR1-502
spellingShingle	16S RNA sequencing influenza virus microbiome vaccination Microbiology QR1-502 Tao Ding Timothy Song Bin Zhou Adam Geber Yixuan Ma Lingdi Zhang Michelle Volk Shashi N. Kapadia Stephen G. Jenkins Mirella Salvatore Elodie Ghedin Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
description	ABSTRACT Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia. IMPORTANCE Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications.
format	article
author	Tao Ding Timothy Song Bin Zhou Adam Geber Yixuan Ma Lingdi Zhang Michelle Volk Shashi N. Kapadia Stephen G. Jenkins Mirella Salvatore Elodie Ghedin
author_facet	Tao Ding Timothy Song Bin Zhou Adam Geber Yixuan Ma Lingdi Zhang Michelle Volk Shashi N. Kapadia Stephen G. Jenkins Mirella Salvatore Elodie Ghedin
author_sort	Tao Ding
title	Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
title_short	Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
title_full	Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
title_fullStr	Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
title_full_unstemmed	Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status
title_sort	microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/8bb91d0b7c8f4deabc7506051b05b117
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Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status

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