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Microb Ecol. 2018 Feb;75(2):529-542. doi: 10.1007/s00248-017-1068-x. Epub 2017 Sep 13.

Development of a Stable Lung Microbiome in Healthy Neonatal Mice.

Author information

1
Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85716, Neuherberg, Germany.
2
Department of Internal Medicine V, University of Munich, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.
3
Institute of Lung Biology and Disease (ILBD), Helmholtz Center Munich, Comprehensive Pneumology Center (CPC-M), Munich, Germany.
4
Division of Experimental Asthma Research, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Member of the German Center for Lung Research (DZL), Parkallee 1-40, 23845, Borstel, Germany.
5
Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Niemannsweg 11, 24105, Kiel, Germany.
6
Research Unit Scientific Computing, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85716, Neuherberg, Germany.
7
Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85716, Neuherberg, Germany. schloter@helmholtz-muenchen.de.
8
ZIEL Institute for Food and Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany. schloter@helmholtz-muenchen.de.

Abstract

The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.

KEYWORDS:

16S rRNA-based barcoding; Core microbiome; Delftia; Murine lung microbiome; Rhodococcus

PMID:
28905200
DOI:
10.1007/s00248-017-1068-x

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