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High complexity and diel dynamics of planktonic microbiome revealed by multi-omics in Taihu, China

ABSTRACT:

Cyanobacterial blooms result from continued short-term succession of planktonic microbiomes, but these short-term variations are little known. Here we address this question with a field diel study in Lake Tai. By integrating untargeted metabolomics—verified by targeted metabolomics—and metagenomics, we reveal the diel cycle of planktonic microbiome in Lake Tai are highly dynamic and complex. First, metabolite abundance and their molecular mass display clear diel changes along with shift in the taxon abundance and biological functions, following the same environmental factors. Some taxa and biological functions (reactions) are highly correlated with the metabolite abundance, and large compounds appear to be more taxon specific. Second, phytoplanktonic and overall planktonic microbiome showed different temporal variation of abundance, opposite levels of abundance and different molecular sizes, and different inter- and intra-specific diversity dynamics. Last, planktonic microbiomes are highly dynamic and complex in inter- and intraspecific diversity in merely one diel cycle, which point to different temperature preference between species, Microcystis aeruginosa and Anabaena sp. This difference was experimentally confirmed in laboratory. Using a multi-omics approach, our study underscores the importance of diel interaction triad between population abundance, biological functions, and environmental factors in leading to microbiome structural change and blooms.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

SUBMITTER: Zeshuang Wang

PROVIDER: MTBLS3038 | MetaboLights | 2022-03-02

REPOSITORIES: MetaboLights

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Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.

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High complexity and diel dynamics of planktonic microbiome revealed by multi-omics in Taihu, China

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