Decoupling function and taxonomy in the global ocean microbiome

Science, Journal Year: 2016, Volume and Issue: 353(6305), P. 1272 - 1277

Published: Sept. 15, 2016

Microbial metabolism powers biogeochemical cycling in Earth’s ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes this variation remain largely unknown. We analyzed and functional community profiles to determine factors that shape marine bacterial archaeal across global ocean. By classifying >30,000 microorganisms into metabolic groups, we were able disentangle from variation. find environmental conditions strongly influence distribution groups by shaping niches, only weakly within individual groups. Hence, structure constitute complementary roughly independent “axes variation” shaped markedly different processes.

Language: Английский

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Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Journal Year: 2017, Volume and Issue: 81(4)

Published: Oct. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Language: Английский

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The healthy human microbiome

Genome Medicine, Journal Year: 2016, Volume and Issue: 8(1)

Published: April 27, 2016

Humans are virtually identical in their genetic makeup, yet the small differences our DNA give rise to tremendous phenotypic diversity across human population. By contrast, metagenome of microbiome—the total content microbes inhabiting bodies—is quite a bit more variable, with only third its constituent genes found majority healthy individuals. Understanding this variability “healthy microbiome” has thus been major challenge microbiome research, dating back at least 1960s, continuing through Human Microbiome Project and beyond. Cataloguing necessary sufficient sets features that support health, normal ranges these populations, is an essential first step identifying correcting microbial configurations implicated disease. Toward goal, several population-scale studies have documented both taxonomic compositions functional potentials normally observed microbiomes along possible driving factors such as geography, diet, lifestyle. Here, we review definitions ‘healthy microbiome’ emerged, current understanding diversity, gaps characterization molecular function development ecological therapies be addressed future.

Language: Английский

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Function and functional redundancy in microbial systems

Nature Ecology & Evolution, Journal Year: 2018, Volume and Issue: 2(6), P. 936 - 943

Published: April 12, 2018

Language: Английский

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: Oct. 24, 2016

Abstract The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central Earth’s biogeochemical cycles. However, little is known about how complex in such environments are structured, and inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics aquifer sediments groundwater, reconstruct 2,540 draft-quality, near-complete complete strain-resolved genomes represent the majority bacterial phyla as well 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity representing 36% organisms detected system used document distribution pathways coexisting organisms. Consistent with prior findings indicating metabolic handoffs simple consortia, find few within community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages selected for, altering linkages among major

Language: Английский

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The ecology and biogeochemistry of stream biofilms

Nature Reviews Microbiology, Journal Year: 2016, Volume and Issue: 14(4), P. 251 - 263

Published: March 14, 2016

Language: Английский

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Emergent simplicity in microbial community assembly

Science, Journal Year: 2018, Volume and Issue: 361(6401), P. 469 - 474

Published: Aug. 3, 2018

Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range contexts, from biotechnological applications to what happens our guts. Goldford et al. sampled the microbial soil plants containing hundreds thousands sequence variants. The organisms were passaged after culture low concentrations single carbon sources cross-fed with each other's metabolites; then, resulting sequenced using 16S ribosomal RNA, outcomes modeled mathematically. mix that survived under steady conditions converged reproducibly reflect experimentally imposed rather than initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Language: Английский

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A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Sept. 18, 2020

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it generally accepted that selection, dispersal, diversification and drift are major processes, defining their relative importance very challenging. Here, we present framework to quantitatively infer mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), specificity (0.95–0.98) on simulated communities, which 10–160% higher than those from entire community-based approach. Application of grassland microbial communities response experimental warming reveals dominant roles homogeneous selection (38%) ‘drift’ (59%). Interestingly, decreases over time, enhances primarily imposed Bacillales. In addition, has correlations with drought plant productivity under control. provides an effective robust tool quantify should also be useful for animal

Language: Английский

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Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Language: Английский

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Phage Therapy in the Postantibiotic Era

Clinical Microbiology Reviews, Journal Year: 2019, Volume and Issue: 32(2)

Published: Jan. 15, 2019

Antibiotic resistance is arguably the biggest current threat to global health. An increasing number of infections are becoming harder or almost impossible treat, carrying high morbidity, mortality, and financial cost. The therapeutic use bacteriophages, viruses that infect kill bacteria, well suited be part multidimensional strategies combat antibiotic resistance. Although phage therapy was first implemented a century ago, it brought standstill after successful introduction antibiotics. Now, with rise resistance, experiencing well-deserved rebirth. Among admittedly vast literature recently published on this topic, review aims provide forward-looking perspective its role in modern society. We cover key points crisis then explain biological evolutionary principles support phages, their interaction immune system, comparison therapy. By going through up-to-date reports and, whenever possible, human clinical trials, we examine versatility discuss conventional approaches as novel strategies, including phage-antibiotic combinations, phage-derived enzymes, exploitation mechanisms, bioengineering. Finally, benefits beyond perspective, opportunities for scientific outreach effective education, interdisciplinary collaboration, cultural economic growth, even innovative social media, making case more than just an alternative

Language: Английский

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