Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

RM Bowers, NC Kyrpides, R Stepanauskas… - Nature …, 2017 - nature.com
We present two standards developed by the Genomic Standards Consortium (GSC) for
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …

A new view of the fish gut microbiome: advances from next-generation sequencing

M Ghanbari, W Kneifel, KJ Domig - Aquaculture, 2015 - Elsevier
The fish gut microbiota contributes to digestion and can affect the nutrition, growth,
reproduction, overall population dynamics and vulnerability of the host fish to disease; …

Estuarine plastisphere as an overlooked source of N2O production

X Su, L Yang, K Yang, Y Tang, T Wen, Y Wang… - Nature …, 2022 - nature.com
Abstract “Plastisphere”, microbial communities colonizing plastic debris, has sparked global
concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has …

Primer, pipelines, parameters: issues in 16S rRNA gene sequencing

I Abellan-Schneyder, MS Matchado, S Reitmeier… - Msphere, 2021 - Am Soc Microbiol
Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies
investigating microbiomes. However, comparative studies on differences in procedures are …

Continental-scale pollution of estuaries with antibiotic resistance genes

YG Zhu, YI Zhao, B Li, CL Huang, SY Zhang, S Yu… - Nature …, 2017 - nature.com
Antibiotic resistance genes (ARGs) have moved from the environmental resistome into
human commensals and pathogens, driven by human selection with antimicrobial agents …

Antibiotic resistome and its association with bacterial communities during sewage sludge composting

JQ Su, B Wei, WY Ou-Yang, FY Huang… - … science & technology, 2015 - ACS Publications
Composting is widely used for recycling of urban sewage sludge to improve soil properties,
which represents a potential pathway of spreading antibiotic resistant bacteria and genes to …

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

SF Stoddard, BJ Smith, R Hein, BRK Roller… - Nucleic acids …, 2015 - academic.oup.com
Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of
microbial communities. rRNA genes are often co-located as part of an rrn operon, and …

Nitrifying niche in estuaries is expanded by the plastisphere

X Su, X Huang, Y Zhang, L Yang, T Wen… - Nature …, 2024 - nature.com
The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered
global concerns. Recent geochemical evidence has pointed out its potential role in …

Patterns and processes of microbial community assembly

DR Nemergut, SK Schmidt, T Fukami… - Microbiology and …, 2013 - Am Soc Microbiol
Recent research has expanded our understanding of microbial community assembly.
However, the field of community ecology is inaccessible to many microbial ecologists …

The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses

T Větrovský, P Baldrian - PloS one, 2013 - journals.plos.org
16S ribosomal RNA currently represents the most important target of study in bacterial
ecology. Its use for the description of bacterial diversity is, however, limited by the presence …