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The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities.

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PubMed ID: 30687263

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Rocca JD, Simonin M, Blaszczak JR, Ernakovich JG, Gibbons SM, Midani FS, Washburne AD

Front Microbiol. 2018. doi: 10.3389/fmicb.2018.03272

COMMENT: The Microbiome Stress Project is an open-access database of environmental and host-associated 16S rRNA amplicon sequencing studies, that will facilitate cross-study analyses of microbiome responses to natural and anthropogenic stressors. The database will comprise published and unpublished datasets re-processed from the raw sequences into exact sequence variants using a standardized computational pipeline. The article presents the results of a proof-of-concept meta-analysis using a subset data of the database, the most common primer and sequencing platform combination (V4 region of 16S rRNA; Illumina MiSeq). Raw fastq sequence data from the 606 samples were downloaded from NCBI's Sequence Read Archive (SRA) and from an unpublished dataset.

Objectives

To assess microbial community responses to: 1. One stressor in one environment: How consistent are microbiome responses to the same stressor within the same environment?. 2. A range of stressors within an environment: Are there common microbiome responses to different stressors within the same environment?. 3. One stressor across environments: Does a given stressor impose consistent effects on microbiomes across multiple environments, including host-associated and free-living systems?. 4. General trends of microbiome stressor responses: Are there general impacts of stressors on microbiomes across all environments?

Main results

Of the subset of 150 studies randomly screened from the 5,480 full set of studies in our literature search, 96% of the screened studies performed amplicon sequencing, using primarily Illumina (59%) and 454 pyrosequencing (31%) platforms and only 4% performed shotgun metagenomic sequencing. 89% of the studies sequenced the 16S rRNA gene to study the diversity of archaea and bacteria. Of the 16S rRNA gene studies, the V4 hypervariable region was the most frequently sequenced (76% of studies using primer sets: V3-V4, V4, V3-V5, & V4-V5).

We found that warming treatments altered alpha diversity through decreased observed ESV richness (−21%, P < 0.0001) and Shannon-Weiner index (−7.2%, P = 0.0002), and no significant impacts on microbiome evenness (P < 0.0657).

..we expanded the analysis of soil microbiome responses to a wide range of stressors, which also resulted in decreased alpha diversity and increased community dispersion.

We examined copper contamination on 102 samples across the four environments (soil, sludge, gut, and sediment), and found similar decreases in alpha diversity: a 13.1% decrease in observed ESVs (P < 0.0001) and a 2.8% decrease in Shannon-Weiner (P = 0.0002).

These first results suggest that very contrasted stressors in diverse ecosystems lead to similar consequences for microbial community diversity.

Conclusions

With thousands of studies available on the impact of environmental stressors on microbial communities, the Microbiome Stress Project Database is well-poised to allow researchers to tackle key ecological issues regarding the resistance, resilience, and response of microbial communities following exposure to environmental stressors.

Building the database will reveal knowledge gaps in terms of missing or low replication studies of specific stressors or particular environments.

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Contributor

Diana López-Farfán