Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Язык: Английский

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Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Сен. 24, 2019

As many as 22 of the 45 coral species on Florida Reef Tract are currently affected by stony tissue loss disease (SCTLD). The ongoing outbreak was first observed in 2014 Southeast near Miami and early 2019 has been documented from northernmost reaches reef tract Martin County down to Key West. We examined microbiota associated with lesions apparently healthy diseased colonies Montastraea cavernosa, Orbicella faveolata, Diploria labyrinthiformis, Dichocoenia stokesii. Analysis differentially abundant taxa between identified five unique amplicon sequence variants enriched three (all except O. faveolata), namely an unclassified genus Flavobacteriales sequences Fusibacter (Clostridiales), Planktotalea (Rhodobacterales), Algicola (Alteromonadales), Vibrio (Vibrionales). In addition, several groups likely opportunistic or saprophytic colonizers such Epsilonbacteraeota, Patescibacteria, Clostridiales, Bacteroidetes, Rhodobacterales were also SCTLD lesions. This work represents microbiological characterization SCTLD, initial step toward identifying potential pathogen(s) responsible for SCTLD.

Язык: Английский

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A review on monitoring, forecasting, and early warning of harmful algal bloom

Aquaculture, Год журнала: 2024, Номер 593, С. 741351 - 741351

Опубликована: Июль 16, 2024

Язык: Английский

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The role of animal hosts in shaping gut microbiome variation

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1901)

Опубликована: Март 18, 2024

Millions of years co-evolution between animals and their associated microbial communities have shaped diversified the nature relationship. Studies continue to reveal new layers complexity in host–microbe interactions, fate which depends on a variety different factors, ranging from neutral processes environmental factors local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics mathematical modelling disentangle individual contribution ecological microbiome evolution. Within this framework, host are known be among dominant drivers composition animal species. However, extent they shape assembly evolution remains unclear. In review, we summarize our understanding how drive these dynamics conserved vary across taxa. We conclude by outlining key avenues for research highlight need implementation modifications existing theory fully capture host-associated microbiomes. This article part theme issue ‘Sculpting microbiome: determine respond colonization’.

Язык: Английский

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Host-associated microbiomes drive structure and function of marine ecosystems

PLoS Biology, Год журнала: 2019, Номер 17(11), С. e3000533 - e3000533

Опубликована: Ноя. 11, 2019

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to ecosystem level underpins health Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, individual microbial symbionts consortia significantly relevant taxa, little is known about their interactions with vast majority host species. We outline priorities strengthen our current knowledge host-microbiome how they shape argue that such advances will help predict responses species, communities, ecosystems stressors driven by human activity inform future management strategies.

Язык: Английский

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Impacts of microplastics exposure on mussel (Mytilus edulis) gut microbiota

The Science of The Total Environment, Год журнала: 2020, Номер 745, С. 141018 - 141018

Опубликована: Июль 21, 2020

Язык: Английский

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Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment

The Science of The Total Environment, Год журнала: 2020, Номер 717, С. 137209 - 137209

Опубликована: Фев. 8, 2020

In this study, we characterize the structural variation of microbiota Mytilus galloprovincialis at tissue scale, also exploring connection with microbial ecosystem surrounding water. Mussels were sampled within a farm located in North-Western Adriatic Sea and composition was analyzed gills, hemolymph, digestive glands, stomach foot by Next Generation Sequencing marker gene approach. showed distinctive structure, specific declinations level. Indeed, each is characterized distinct pattern dominant families, reflecting peculiar adaptation to respective niche. For instance, gland Ruminococcaceae Lachnospiraceae, being shaped ferment complex polysaccharides dietary origin into short-chain fatty acids, well matching general asset animal gut microbiota. Conversely, gill hemolymph ecosystems are dominated marine microorganisms aerobic oxidative metabolism, consistent role played these tissues as an interface external environment. Our findings highlight putative importance mussel for different aspects host physiology, ultimate repercussions on health productivity.

Язык: Английский

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Host control and the evolution of cooperation in host microbiomes

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июнь 22, 2022

Abstract Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts insufficient drive cooperation in systems like human microbiome, because competition between However, emerge if hosts exert control over symbionts, so long as there constraints limit symbiont counter We test our genomic data two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved predicted under control, tending lose flagella maintain butyrate production when host-associated. Moreover, an analysis retain supports evolution via toll-like receptor 5, which limits work puts mechanisms, including system, at centre microbiome

Язык: Английский

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How different are marine microbial natural products compared to their terrestrial counterparts?

Natural Product Reports, Год журнала: 2021, Номер 39(1), С. 7 - 19

Опубликована: Окт. 16, 2021

Covering: 1877 to 2020A key challenge in natural products research is the selection of biodiversity yield novel chemistry. Recently, marine microorganisms have become a preferred source. But how are microorganism compared those reported from terrestrial microbes? Cluster analysis chemical fingerprints and molecular scaffold 55 817 compounds microorganisms, macro-organisms showed that 76.7% isolated closely related microorganisms. Only 14.3% unique when macro-organism also considered. Studies targeting specific understudied microbial phyla result higher likelihood finding compounds, whereas depth geographic location collection little influence. We recommend targeted strain isolation, incorporating early use genomic sequencing guide selection, innovation culture media cultivation techniques application cheminformatics tools focus on product diversity, rather than dereplication known compounds.

Язык: Английский

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Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture

Frontiers in Sustainable Food Systems, Год журнала: 2022, Номер 6

Опубликована: Июнь 17, 2022

Microorganisms are immense in nature and exist every imaginable ecological niche, performing a wide range of metabolic processes. Unfortunately, using traditional microbiological methods, most microorganisms remain unculturable. The emergence metagenomics has resolved the challenge capturing entire microbial community an environmental sample by enabling analysis whole genomes without requiring culturing. Metagenomics as non-culture approach encompasses greater amount genetic information than approaches. plant root-associated is essential for growth development, hence interactions between microorganisms, soil, plants to understand improve crop yields rural urban agriculture. Although some these currently unculturable laboratory, metagenomic techniques may nevertheless be used identify their functional traits. A detailed understanding organisms should facilitate improvement sustainable production soil soilless Therefore, objective this review provide insights into study microbiota ecology. In addition, different DNA-based role elaborating microbiomes discussed. As biotechnological potentials unlocked through metagenomics, they can develop new, useful unique bio-fertilizers bio-pesticides that not harmful environment.

Язык: Английский

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