Minimum information about an uncultivated virus genome (MIUViG)

S Roux, EM Adriaenssens, BE Dutilh, EV Koonin… - Nature …, 2019 - nature.com
We present an extension of the Minimum Information about any (x) Sequence (MIxS)
standard for reporting sequences of uncultivated virus genomes. Minimum Information about …

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

BJ Callahan, PJ McMurdie, SP Holmes - The ISME journal, 2017 - academic.oup.com
Recent advances have made it possible to analyze high-throughput marker-gene
sequencing data without resorting to the customary construction of molecular operational …

Phage puppet masters of the marine microbial realm

M Breitbart, C Bonnain, K Malki, NA Sawaya - Nature microbiology, 2018 - nature.com
Viruses numerically dominate our oceans; however, we have only just begun to document
the diversity, host range and infection dynamics of marine viruses, as well as the subsequent …

Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity …

M Chiarello, M McCauley, S Villéger, CR Jackson - PloS one, 2022 - journals.plos.org
Advances in the analysis of amplicon sequence datasets have introduced a methodological
shift in how research teams investigate microbial biodiversity, away from sequence identity …

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

KE Walters, JBH Martiny - PLoS One, 2020 - journals.plos.org
Bacteria are essential parts of ecosystems and are the most diverse organisms on the
planet. Yet, we still do not know which habitats support the highest diversity of bacteria …

Broadscale ecological patterns are robust to use of exact sequence variants versus operational taxonomic units

SI Glassman, JBH Martiny - MSphere, 2018 - Am Soc Microbiol
Recent discussion focuses on the best method for delineating microbial taxa, based on
either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of …

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

WJ Watterson, M Tanyeri, AR Watson, CM Cham… - Elife, 2020 - elifesciences.org
Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and
yield biased sampling of environmental microbes due to ecological and evolutionary factors …

The microbial rare biosphere: current concepts, methods and ecological principles

F Pascoal, R Costa, C Magalhães - FEMS Microbiology Ecology, 2021 - academic.oup.com
Our ability to describe the highly diverse pool of low abundance populations present in
natural microbial communities is increasing at an unprecedented pace. Yet we currently lack …

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions

N García-García, J Tamames, AM Linz… - The ISME …, 2019 - academic.oup.com
Microdiversity can lead to different ecotypes within the same species. These are assumed to
provide stability in time and space to those species. However, the role of microdiversity in …

Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

J Liu, Z Meng, X Liu, XH Zhang - Marine Life Science & Technology, 2019 - Springer
Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades
have witnessed an upsurge in studies on marine microbial community composition using …