Current understanding of the human microbiome

Nature Medicine, Journal Year: 2018, Volume and Issue: 24(4), P. 392 - 400

Published: April 1, 2018

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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Microbiome definition re-visited: old concepts and new challenges

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

Published: June 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.

Language: Английский

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NCBI Taxonomy: a comprehensive update on curation, resources and tools

Database, Journal Year: 2020, Volume and Issue: 2020

Published: Jan. 1, 2020

Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications every sequence in the nucleotide protein databases of International Nucleotide Sequence Database Collaboration. Since last review this resource 2012, it has undergone several improvements. Most notable is shift from a single SQL database to series linked tied framework data called NameBank. This means that relations among elements can be adjusted more detail, resulting expanded annotation synonyms, ability flag with specific nomenclatural properties, enhanced tracking publications improved scientific authorities types. Additionally, practices utilized by NCBI curators major taxonomic groups are described, terms peculiar explained, external resources acknowledged updates tools other documented. URL: https://www.ncbi.nlm.nih.gov/taxonomy

Language: Английский

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Fungal Diversity Revisited: 2.2 to 3.8 Million Species

Microbiology Spectrum, Journal Year: 2017, Volume and Issue: 5(4)

Published: July 28, 2017

The question of how many species Fungi there are has occasioned much speculation, with figures mostly posited from around half a million to 10 million, and in one extreme case even sizable portion the spectacular number 1 trillion. Here we examine new evidence various sources derive an updated estimate global fungal diversity. rates patterns description 1750s show no sign approaching asymptote accelerated 2010s after advent molecular approaches delimitation. Species recognition studies (semi-)cryptic hidden morpho-species complexes suggest weighted average ratio about order magnitude for recognized before such studies. New also comes extrapolations plant:fungus ratios, information now being generated environmental sequence studies, including comparisons fieldwork data same sites. We further draw attention undescribed awaiting discovery biodiversity hot spots tropics, little-explored habitats (such as lichen-inhabiting fungi), material collections study. conclude that commonly cited 1.5 is conservative actual range properly estimated at 2.2 3.8 million. With 120,000 currently accepted species, it appears best just 8%, worst scenario 3%, named so far. Improved estimates hinge particularly on reliable statistical phylogenetic analyze rapidly increasing amount data.

Language: Английский

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Where less may be more: how the rare biosphere pulls ecosystems strings

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(4), P. 853 - 862

Published: Jan. 10, 2017

Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which typically composed a high number relatively rare species. Recent studies have demonstrated that can an over-proportional role in biogeochemical cycles and may be hidden driver microbiome function. In this review, we provide ecological overview the biosphere, including causes rarity impacts on ecosystem functioning. We discuss how preponderant local biodiversity turnover with potentially bound to phylogenetically conserved features. microbes therefore overlooked keystone regulating functioning host-associated, terrestrial aquatic environments. conclude review recommendations guide scientists interested investigating rapidly emerging research area.

Language: Английский

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The microbiome and human cancer

Science, Journal Year: 2021, Volume and Issue: 371(6536)

Published: March 25, 2021

Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors immunotherapy, engineerable to treat metastases. Despite these findings, the number of microbes known directly cause carcinogenesis remains small. Critically evaluating building frameworks such evidence light modern biology is an important task. In this Review, we delineate between causal complicit trace common themes their influence through host's immune system, herein defined as immuno-oncology-microbiome axis. We further review intratumoral approaches manipulate gut or tumor microbiome while projecting next phase experimental discovery.

Language: Английский

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Towards the sustainable discovery and development of new antibiotics

Nature Reviews Chemistry, Journal Year: 2021, Volume and Issue: 5(10), P. 726 - 749

Published: Aug. 19, 2021

An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast current level investment their development, particularly fields natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry modes action are desperately needed worldwide tackle public health menace posed antimicrobial resistance. Here, our consortium presents a strategic blueprint substantially improve ability discover develop new antibiotics. We propose both short-term long-term solutions overcome most urgent limitations various sectors research funding, aiming bridge gap between academic, industrial political stakeholders, unite interdisciplinary expertise order efficiently fuel translational pipeline benefit future generations.

Language: Английский

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Global diversity and biogeography of bacterial communities in wastewater treatment plants

Nature Microbiology, Journal Year: 2019, Volume and Issue: 4(7), P. 1183 - 1195

Published: May 13, 2019

Language: Английский

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Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality

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

Published: June 17, 2020

Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, effects GCFs microbial diversity unclear despite that soil microorganisms play critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show rare species are more sensitive than common species, while do not always lead reduction diversity. GCFs-induced shifts alpha can be predominately explained by changed pH. In addition, impacts functionality community structure biomass rather Altogether, our findings fundamentally different from previous knowledge for well-studied plant animal communities, crucial policy-making conservation hotspots under changes.

Language: Английский

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