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  Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa

Johnke, J., Dirksen, P., & Schulenburg, H. (2020). Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa. Environmental Microbiology, 22(4), 1265-1279. doi:10.1111/1462-2920.14932.

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1462-2920.14932.pdf (Publisher version), 2MB
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Johnke, Julia, Author
Dirksen, Philipp1, Author           
Schulenburg, Hinrich1, Author           
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1Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2600692              

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Free keywords: C. elegans
 Abstract: Summary Microbiome communities are complex assemblages of bacteria. The dissection of their assembly dynamics is challenging because it requires repeated sampling of both host and source communities. We used the nematode Caenorhabditis elegans as a model to study these dynamics. We characterized microbiome variation from natural worm populations and their substrates for two consecutive years using 16S rDNA amplicon sequencing. We found conservation in microbiome composition across time at the genus, but not amplicon sequencing variant (ASV) level. Only three ASVs were consistently present across worm samples (Comamonas ASV10859, Pseudomonas ASV7162 and Cellvibrio ASV9073). ASVs were more diverse in worms from different rather than the same substrates, indicating an influence of the source community on microbiome assembly. Surprisingly, almost 50% of worm-associated ASVs were absent in corresponding substrates, potentially due to environmental filtering. Ecological network analysis revealed strong effects of bacteria–bacteria interactions on community composition: While a dominant Erwinia strain correlated with decreased alpha-diversity, predatory bacteria of the Bdellovibrio and like organisms associated with increased alpha-diversity. High alpha-diversity was further linked to high worm population growth, especially on species-poor substrates. Our results highlight that microbiomes are individually shaped and sensitive to dramatic community shifts in response to particular competitive species.

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Language(s): eng - English
 Dates: 2019-08-132020-01-272020-02-072020-04
 Publication Status: Published in print
 Pages: -
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 Identifiers: DOI: 10.1111/1462-2920.14932
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Title: Environmental Microbiology
  Other : Environmental Microbiology and Environmental Microbiology Reports
Source Genre: Journal
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Publ. Info: Oxford, England : Blackwell Science
Pages: - Volume / Issue: 22 (4) Sequence Number: - Start / End Page: 1265 - 1279 Identifier: ISSN: 1462-2912
CoNE: https://pure.mpg.de/cone/journals/resource/959328105031