Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

ABSTRACT The purpose of this study was to evaluate the composition and richness of bacterial communities associated with low-birthweight (LBW) infants in relation to host body site, individual, and age. Bacterial 16S rRNA genes from saliva samples, skin swabs, and stool samples collected on postnata...

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Autores principales:	Elizabeth K. Costello, Erica M. Carlisle, Elisabeth M. Bik, Michael J. Morowitz, David A. Relman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/3107c27332464f88b3ea0f5d9b860ebc
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spelling	oai:doaj.org-article:3107c27332464f88b3ea0f5d9b860ebc2021-11-15T15:42:32ZMicrobiome Assembly across Multiple Body Sites in Low-Birthweight Infants10.1128/mBio.00782-132150-7511https://doaj.org/article/3107c27332464f88b3ea0f5d9b860ebc2013-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00782-13https://doaj.org/toc/2150-7511ABSTRACT The purpose of this study was to evaluate the composition and richness of bacterial communities associated with low-birthweight (LBW) infants in relation to host body site, individual, and age. Bacterial 16S rRNA genes from saliva samples, skin swabs, and stool samples collected on postnatal days 8, 10, 12, 15, 18, and 21 from six LBW (five premature) infants were amplified, pyrosequenced, and analyzed within a comparative framework that included analogous data from normal-birthweight (NBW) infants and healthy adults. We found that body site was the primary determinant of bacterial community composition in the LBW infants. However, site specificity depended on postnatal age: saliva and stool compositions diverged over time but were not significantly different until the babies were 15 days old. This divergence was primarily driven by progressive temporal turnover in the distal gut, which proceeded at a rate similar to that of age-matched NBW infants. Neonatal skin was the most adult-like in microbiota composition, while saliva and stool remained the least so. Compositional variation among infants was marked and depended on body site and age. Only the smallest, most premature infant received antibiotics during the study period; this heralded a coexpansion of Pseudomonas aeruginosa and a novel Mycoplasma sp. in the oral cavity of this vaginally delivered, intubated patient. We conclude that concurrent molecular surveillance of multiple body sites in LBW neonates reveals a delayed compositional differentiation of the oral cavity and distal gut microbiota and, in the case of one infant, an abundant, uncultivated oral Mycoplasma sp., recently detected in human vaginal samples. IMPORTANCE Complications of premature birth are the most common cause of neonatal mortality. Colonization by the indigenous microbiota, which begins at delivery, may predispose some high-risk newborns to invasive infection or necrotizing enterocolitis (NEC), and protect others, yet neonatal microbiome dynamics are poorly understood. Here, we present the first cultivation-independent time series tracking microbiota assembly across multiple body sites in a synchronous cohort of hospitalized low-birthweight (LBW) neonates. We take advantage of archived samples and publically available sequence data and compare our LBW infant findings to those from normal-birthweight (NBW) infants and healthy adults. Our results suggest potential windows of opportunity for the dispersal of microbes within and between hosts and support recent findings of substantial baseline spatiotemporal variation in microbiota composition among high-risk newborns.Elizabeth K. CostelloErica M. CarlisleElisabeth M. BikMichael J. MorowitzDavid A. RelmanAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 6 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Elizabeth K. Costello Erica M. Carlisle Elisabeth M. Bik Michael J. Morowitz David A. Relman Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
description	ABSTRACT The purpose of this study was to evaluate the composition and richness of bacterial communities associated with low-birthweight (LBW) infants in relation to host body site, individual, and age. Bacterial 16S rRNA genes from saliva samples, skin swabs, and stool samples collected on postnatal days 8, 10, 12, 15, 18, and 21 from six LBW (five premature) infants were amplified, pyrosequenced, and analyzed within a comparative framework that included analogous data from normal-birthweight (NBW) infants and healthy adults. We found that body site was the primary determinant of bacterial community composition in the LBW infants. However, site specificity depended on postnatal age: saliva and stool compositions diverged over time but were not significantly different until the babies were 15 days old. This divergence was primarily driven by progressive temporal turnover in the distal gut, which proceeded at a rate similar to that of age-matched NBW infants. Neonatal skin was the most adult-like in microbiota composition, while saliva and stool remained the least so. Compositional variation among infants was marked and depended on body site and age. Only the smallest, most premature infant received antibiotics during the study period; this heralded a coexpansion of Pseudomonas aeruginosa and a novel Mycoplasma sp. in the oral cavity of this vaginally delivered, intubated patient. We conclude that concurrent molecular surveillance of multiple body sites in LBW neonates reveals a delayed compositional differentiation of the oral cavity and distal gut microbiota and, in the case of one infant, an abundant, uncultivated oral Mycoplasma sp., recently detected in human vaginal samples. IMPORTANCE Complications of premature birth are the most common cause of neonatal mortality. Colonization by the indigenous microbiota, which begins at delivery, may predispose some high-risk newborns to invasive infection or necrotizing enterocolitis (NEC), and protect others, yet neonatal microbiome dynamics are poorly understood. Here, we present the first cultivation-independent time series tracking microbiota assembly across multiple body sites in a synchronous cohort of hospitalized low-birthweight (LBW) neonates. We take advantage of archived samples and publically available sequence data and compare our LBW infant findings to those from normal-birthweight (NBW) infants and healthy adults. Our results suggest potential windows of opportunity for the dispersal of microbes within and between hosts and support recent findings of substantial baseline spatiotemporal variation in microbiota composition among high-risk newborns.
format	article
author	Elizabeth K. Costello Erica M. Carlisle Elisabeth M. Bik Michael J. Morowitz David A. Relman
author_facet	Elizabeth K. Costello Erica M. Carlisle Elisabeth M. Bik Michael J. Morowitz David A. Relman
author_sort	Elizabeth K. Costello
title	Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
title_short	Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
title_full	Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
title_fullStr	Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
title_full_unstemmed	Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants
title_sort	microbiome assembly across multiple body sites in low-birthweight infants
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/3107c27332464f88b3ea0f5d9b860ebc
work_keys_str_mv	AT elizabethkcostello microbiomeassemblyacrossmultiplebodysitesinlowbirthweightinfants AT ericamcarlisle microbiomeassemblyacrossmultiplebodysitesinlowbirthweightinfants AT elisabethmbik microbiomeassemblyacrossmultiplebodysitesinlowbirthweightinfants AT michaeljmorowitz microbiomeassemblyacrossmultiplebodysitesinlowbirthweightinfants AT davidarelman microbiomeassemblyacrossmultiplebodysitesinlowbirthweightinfants
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Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

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