Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline DOI Creative Commons
Daniel Straub, Nia Blackwell, Adrián Langarica-Fuentes

et al.

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Oct. 23, 2020

One of the major methods to identify microbial community composition, unravel population dynamics, and explore diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing combination with bioinformatics analyses. However, focusing on from contrasting habitats, it was not systematically evaluated i.) which analysis provide results that reflect reality most accurately, ii.) how interpretations studies are biased by different iii.) if optimal workflow can be implemented an easy-to-use pipeline. Here, we compared performance tools (i.e. Mothur, QIIME1, QIIME2, MEGAN) using three mock datasets known composition differed quality, species number abundance distribution even uneven), phylogenetic closely related well-separated sequences). Our showed QIIME2 outcompeted all other investigated sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) estimates (>5% assessment), suggesting this approach able situ accurately. Further 24 obtained four terrestrial freshwater sites revealed dramatic differences resulting for pipelines at genus level. For instance, river water Sphaerotilus only reported when QIIME1 (8% abundance) Agitococcus (2% 3% abundance, respectively), but both genera remained undetected analyzed Mothur MEGAN. Since these abundant taxa probably have implications important biogeochemical cycles (e.g. nitrate sulfate reduction) sites, their detection semi-quantitative enumeration crucial valid interpretations. A high-performance computing conformant constructed allow FAIR (Findable, Accessible, Interoperable, Re-usable) starting raw files, identified our study. presented should considered future studies, thereby facilitating data substantially, while maximizing reliability confidence analysis.

Language: Английский

Keystone taxa as drivers of microbiome structure and functioning DOI
Samiran Banerjee, Klaus Schlaeppi, Marcel G. A. van der Heijden

et al.

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(9), P. 567 - 576

Published: May 22, 2018

Language: Английский

Citations

2098
Microbiome definition re-visited: old concepts and new challenges DOI Creative Commons
Gabriele Berg, Daria Rybakova, Doreen Fischer

et al.

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

Citations

1627
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application DOI Creative Commons
Stéphane Compant, Abdul Samad, Hanna Faist

et al.

Journal of Advanced Research, Journal Year: 2019, Volume and Issue: 19, P. 29 - 37

Published: March 20, 2019

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount information is now available on the structure dynamics microbiota as well functional capacities isolated community members. Due to interesting potential due current challenges in crop production there an urgent need bring microbial innovations into practice. Different approaches microbiome improvement exist. On one hand strains or strain combinations can be applied, however, field success often variable urgently required. Smart, knowledge-driven selection needed use suitable delivery formulations. other hand, farming practices genotype influence thus functioning. Therefore, appropriate breeding leading improved plant-microbiome interactions are avenues increase benefit microbiota. In conclusion, different making new generation inoculants application microbiome-based agro-management lines could lead better microbiome. This paper reviews importance functionalities bacterial discusses concepts regard plant-associated bacteria.

Language: Английский

Citations

1107
Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom DOI Creative Commons
Yuanyuan Xue, Huihuang Chen, Jun R. Yang

et al.

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(9), P. 2263 - 2277

Published: June 13, 2018

Abstract Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate dynamics eukaryotes, explore co-occurrence patterns eukaryotic plankton in subtropical reservoir following cyanobacterial bloom event. Our results showed that event significantly altered community composition diversity without affecting plankton. The similarities both subcommunities declined with increase time-lag, but stronger temporal turnover was observed taxa. Further, species explained higher percentage variation than richness. Both deterministic stochastic processes influenced assembly, pattern (e.g., drift) particularly pronounced for Co-occurrence network analysis revealed keystone taxa mainly belonged which may play fundamental roles persistence. Importantly, covariations between non-rare were predominantly positive, implying multispecies cooperation might contribute stability resilience microbial community. Overall, these findings expand current understanding mechanisms interactions underlying changing aquatic ecosystems.

Language: Английский

Citations

506
Soil microbiomes and one health DOI
Samiran Banerjee, Marcel G. A. van der Heijden

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 21(1), P. 6 - 20

Published: Aug. 23, 2022

Language: Английский

Citations

489
The Role of Lung and Gut Microbiota in the Pathology of Asthma DOI Creative Commons
Weronika Barcik, Rozlyn C. T. Boutin, Milena Sokołowska

et al.

Immunity, Journal Year: 2020, Volume and Issue: 52(2), P. 241 - 255

Published: Feb. 1, 2020

Language: Английский

Citations

477
From hairballs to hypotheses–biological insights from microbial networks DOI Creative Commons

Lisa Röttjers,

Karoline Faust

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 761 - 780

Published: July 25, 2018

Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.

Language: Английский

Citations

476
Initial soil microbiome composition and functioning predetermine future plant health DOI Creative Commons
Zhong Wei, Yian Gu, Ville‐Petri Friman

et al.

Science Advances, Journal Year: 2019, Volume and Issue: 5(9)

Published: Sept. 6, 2019

Soil microbiome composition and functioning determine the outcome of plant-pathogen interactions under natural field conditions.

Language: Английский

Citations

468
Microplastics from mulching film is a distinct habitat for bacteria in farmland soil DOI
Mengjun Zhang,

Yanran Zhao,

Xiao Qin

et al.

The Science of The Total Environment, Journal Year: 2019, Volume and Issue: 688, P. 470 - 478

Published: June 8, 2019

Language: Английский

Citations

463
Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils DOI Creative Commons
Qing‐Lin Chen, Jing Ding, Dong Zhu

et al.

Soil Biology and Biochemistry, Journal Year: 2019, Volume and Issue: 141, P. 107686 - 107686

Published: Nov. 22, 2019

Language: Английский

Citations

425