Host-microbiota interactions: from holobiont theory to analysis

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Jan. 11, 2019

In the recent years, holobiont concept has emerged as a theoretical and experimental framework to study interactions between hosts their associated microbial communities in all types of ecosystems. The spread this many branches biology results from fairly realization ubiquitous nature host-associated microbes central role host biology, ecology, evolution. Through special series "Host-microbiota interactions: theory analysis," we wanted promote field research which considerable implications for human health, food production, ecosystem protection. preface, highlight collection articles selected issue that show, use, or debate approach taxonomically ecologically diverse organisms, humans plants sponges insects. We also identify some methodological challenges propose directions future on holobionts.

Language: Английский

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Machine learning and deep learning applications in microbiome research

ISME Communications, Journal Year: 2022, Volume and Issue: 2(1)

Published: Oct. 6, 2022

Abstract The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern influence macroscopic systems including human health, plant resilience, biogeochemical cycling. Such feats have attracted interest scientific community, which has recently turned to machine learning deep methods interrogate microbiome elucidate relationships between its composition function. Here, we provide an overview of how latest studies harness inductive prowess artificial intelligence methods. We start by highlighting that data – being compositional, sparse, high-dimensional necessitates special treatment. then introduce traditional novel discuss their strengths applications. Finally, outlook pipelines, focusing on bottlenecks considerations address them.

Language: Английский

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Characterization of a sponge microbiome using an integrative genome-centric approach

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(5), P. 1100 - 1110

Published: Jan. 28, 2020

Language: Английский

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Sponges to Be Winners under Near-Future Climate Scenarios

BioScience, Journal Year: 2018, Volume and Issue: 68(12), P. 955 - 968

Published: Oct. 18, 2018

Sponges are functionally important components of global benthic environments and have been proposed as potential winners under future climate scenarios. We review the evidence to support this hypothesis by examining individual combined effects ocean warming (OW) acidification (OA) on sponges comparing sponge responses with tolerance thresholds for other organisms. Although generally tolerant OA may even benefit from elevated partial pressure carbon dioxide, they often sensitive seawater temperatures only a few degrees higher than their normal range. Sponge OW more positive response alone. found that less affected or number currently dominant organisms, such corals. Therefore, expected near-future scenarios, although species-specific differences in will likely shift assemblage composition toward resilient species.

Language: Английский

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Host-associated microbiomes drive structure and function of marine ecosystems

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(11), P. e3000533 - e3000533

Published: Nov. 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.

Language: Английский

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A genomic view of the microbiome of coral reef demosponges

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1641 - 1654

Published: Jan. 19, 2021

Abstract Sponges underpin the productivity of coral reefs, yet few their microbial symbionts have been functionally characterised. Here we present an analysis ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 phyla. Compared to MAGs derived from reef seawater, sponge-associated were enriched in glycosyl hydrolases targeting components tissue, mucus macroalgae, revealing a critical role for cycling organic matter. Further, visualisation distribution these genes amongst symbiont taxa uncovered functional guilds matter degradation. Genes utilisation sialic acids glycosaminoglycans tissue found specific lineages that also encoded attachment sponge-derived fibronectins cadherins, suggesting can utilise structural elements tissue. encoding CRISPR restriction-modification systems used defence against mobile genetic symbionts, along with eukaryote-like gene motifs thought be involved maintaining host association. Finally, provide evidence many sponge-enriched are laterally transferred between taxa, they confer selective advantage within niche therefore play ecology evolution.

Language: Английский

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Neutrality in the Metaorganism

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(6), P. e3000298 - e3000298

Published: June 19, 2019

Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, metaorganism. Natural selection should favor hosts that shape community composition these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal often pose selective environments, which only subset environmentally available able colonize. How assemble after colonization form complex microbiota is less clear. Neutral models based on assumption alternatives in selectively equivalent thus entirely shaped random population dynamics dispersal. Here, we use neutral model as null hypothesis assess microbiata host organisms, does not rely invoking any adaptive processes underlying microbial assembly. We show overall structure from wide range particular including previously understudied invertebrates, many cases consistent with expectations. Our approach allows identify individual deviating expectation therefore interesting candidates for further study. Moreover, using simulated communities, demonstrate transient states may play role deviations expectation. findings highlight consideration temporal changes critical in-depth understanding microbiota-host interactions.

Language: Английский

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Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: April 2, 2020

Abstract Background The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts following metagenomics have shed light global ocean microbial diversity function, yet microbiota of polar regions has not been included in such analyses. Results Here a metagenomic study seawater samples ( n = 60) collected from different depths at 28 locations zones was performed, together with metagenomes Tara Oceans. More than 7500 (19%) seawater-derived operational taxonomic units could be identified Oceans datasets, more 3,900,000 protein-coding gene orthologs had no hits Ocean Microbial Reference Gene Catalog. Analysis 214 metagenome assembled genomes (MAGs) recovered microbiomes, revealed strains that prevalent while nearly undetectable temperate seawater. Metabolic pathway reconstruction for these microbes suggested versatility saccharide lipids biosynthesis, nitrate sulfate reduction, CO 2 fixation. Comparison between microbiomes antibiotic resistance genes were enriched functions like DNA recombination Antarctic. Conclusions Our data highlight occurrence dominant locally unique functional traits environmental adaption, provide foundation analyzing microbiome complete perspective.

Language: Английский

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Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

mSystems, Journal Year: 2018, Volume and Issue: 3(6)

Published: Oct. 30, 2018

Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In Sponge Microbiome Project, sequences amounted to 20 30% total microbiome certain HMA genera with classes/clades SAR202, Caldilineae, and Anaerolineae being most prominent. We performed metagenomic single-cell genomic analyses elucidate functional gene repertoire symbionts Aplysina aerophoba. Eighteen draft genomes were reconstructed placed into phylogenetic context which six investigated in detail. Common features related central energy carbon converting pathways, amino acid fatty metabolism, respiration. Clade-specific metabolic included a massively expanded for carbohydrate degradation Caldilineae genomes, but only utilization by SAR202. While import cofactors vitamins, SAR202 harbor genes encoding components involved cofactor biosynthesis. A number relevant symbiosis further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, secondary metabolite clusters. visualized extracellular matrix at ultrastructural resolution fluorescence situ hybridization-correlative light electron microscopy (FISH-CLEM) method. Carbohydrate potential was reported previously "Candidatus Poribacteria" SAUL, typical sponges, we propose here that collectively engage dissolved organic matter, both labile recalcitrant. Thus, microbes may not provide nutrients host, they also contribute matter (DOM) recycling primary productivity reef ecosystems via pathway termed loop. IMPORTANCEChloroflexi represent widespread, yet enigmatic few cultivated members. used approaches characterize marine sponges. The results this study suggest clade-specific specialization have from seawater. Considering abundance dominance sponges many benthic environments, predict role biogeochemical cycles is larger than thought.

Language: Английский

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Coral Reef Microorganisms in a Changing Climate

iScience, Journal Year: 2020, Volume and Issue: 23(4), P. 100972 - 100972

Published: March 9, 2020

Coral reefs are one of the most diverse and productive ecosystems on planet, yet they have suffered tremendous losses due to anthropogenic disturbances predicted be adversely affected habitats under future climate change conditions. can viewed as microbially driven that rely efficient capture, retention, recycling nutrients in order thrive oligotrophic waters. Microorganisms play vital roles maintaining holobiont health ecosystem resilience environmental stress; however, also key players positive feedback loops intensify coral reef decline, with cascading effects biogeochemical cycles marine food webs. There is an urgent need develop a fundamental understanding complex microbial interactions within their role acclimatization, it important include microorganisms conservation secure for these unique environments.

Language: Английский

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