Evaluating the core microbiota in complex communities: A systematic investigation

Environmental Microbiology, Год журнала: 2017, Номер 19(4), С. 1450 - 1462

Опубликована: Янв. 12, 2017

Summary The study of complex microbial communities poses unique conceptual and analytical challenges, with species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a ‘core’ microbiota approach, focusing only on stable permanent members community, is becoming increasingly popular. Given various ways defining core microbiota, it prudent examine whether definition impacts upon results obtained. Here we used marine sponge microbiotas undertook systematic evaluation degree which different factors define influenced conclusions. Significant differences alpha‐ beta‐diversity were detected using some but not all definitions. However, findings related host specificity environmental quality largely insensitive major changes definition. Furthermore, none applied definitions altered our perception ecological networks summarising interactions among bacteria within sponges. These suggest that, while care should still be taken interpretation, approach surprisingly robust, at least for comparing closely samples.

Язык: Английский

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Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

FEMS Microbiology Reviews, Год журнала: 2016, Номер 40(5), С. 686 - 700

Опубликована: Июнь 29, 2016

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms an unpre-cedented level. The fast development molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, review evaluate some more widely adopted emerging techniques for analysis diversity community composition, inference species interactions from co-occurrence data generated by HTS marker genes. We emphasize importance observational biases properties methods. aim is critically discuss advantages disadvantages established methods, contribute integration HTS-based gene into ecology.

Язык: Английский

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The Vulnerability and Resilience of Reef-Building Corals

Current Biology, Год журнала: 2017, Номер 27(11), С. R528 - R540

Опубликована: Июнь 1, 2017

Язык: Английский

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On the Importance of the Microbiome and Pathobiome in Coral Health and Disease

Frontiers in Marine Science, Год журнала: 2017, Номер 4

Опубликована: Янв. 20, 2017

The term 'microbiome' was first coined in 1988 and given the definition of a characteristic microbial community occupying reasonably well defined habitat which has distinct physio-chemical properties. A more recent also emerged, taking this one step further focusing on diseases host organisms. 'pathobiome' breaks down concept 'one pathogen = disease' highlights role microbiome, specifically certain members within causing pathogenesis. development next generation sequencing allowed large data sets to be amassed describing communities many organisms field coral biology is no exception. However, choices made analytical process interpretation these can significantly affect outcome overall conclusions drawn. In review we explore implications difficulties, as highlighting tools developed other research fields hold substantial potential helping develop deeper understanding microbiome disease corals. We make case that standardisation methods will substantially improve collective gain knowledge across groups. hope acts guide researchers exploring pathobiome jumping off point for future studies.

Язык: Английский

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Rare symbionts may contribute to the resilience of coral–algal assemblages

The ISME Journal, Год журнала: 2017, Номер 12(1), С. 161 - 172

Опубликована: Дек. 1, 2017

The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to success of reef ecosystems in highly oligotrophic environments, but it also their Achilles' heel due its vulnerability local stressors effects climate change. Research during last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, largely exclusive. Deep sequencing now revealed existence rare diversity cryptic Symbiodinium assemblages within holobiont, addition one or few abundant algal members. While contribution most resident species physiology widely recognized, significance low background remains matter debate. In this study, we assessed how coral-Symbiodinium communities assemble components together constitute community by analyzing 892 samples comprising >110 000 unique ITS2 marker gene sequences. Using network modeling, show non-random 'clusters' symbionts. structure follows same principles as bacterial communities, for which functional members (the 'rare biosphere') long been recognized. Importantly, inclusion taxa robustness analyses significant stability host-symbiont overall. As such, highlights potential functions symbionts may provide environmental resilience holobiont.

Язык: Английский

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