Title
Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants
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Abstract
The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, r2 = 0.09, p = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a “memoryless” shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.
Keywords
neonatal microbiomeecological processescommunity statesMarkov modelmicrobial community assembly
Object type
Language
English [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:1668266
Appeared in
Title
Frontiers in Microbiology
Volume
13
ISSN
1664-302X
Issued
2022
Publisher
Frontiers Media SA
Date issued
2022
Access rights
Rights statement
© 2022 Zioutis, Seki, Bauchinger, Herbold, Berger, Wisgrill and Berry

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