Performance and application of 16S rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory

DL Church, L Cerutti, A Gürtler, T Griener… - Clinical microbiology …, 2020 - Am Soc Microbiol
This review provides a state-of-the-art description of the performance of Sanger cycle
sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical …

Bacterial endophyte colonization and distribution within plants

SL Kandel, PM Joubert, SL Doty - Microorganisms, 2017 - mdpi.com
The plant endosphere contains a diverse group of microbial communities. There is general
consensus that these microbial communities make significant contributions to plant health …

Global diversity and biogeography of bacterial communities in wastewater treatment plants

L Wu, D Ning, B Zhang, Y Li, P Zhang, X Shan… - Nature …, 2019 - nature.com
Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification
to protect public and environmental health. However, the diversity of microorganisms and …

Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities

ES Cameron, PJ Schmidt, BJM Tremblay, MB Emelko… - Scientific reports, 2021 - nature.com
Amplicon sequencing has revolutionized our ability to study DNA collected from
environmental samples by providing a rapid and sensitive technique for microbial …

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

D Dodd, MH Spitzer, W Van Treuren, BD Merrill… - Nature, 2017 - nature.com
The human gut microbiota produces dozens of metabolites that accumulate in the
bloodstream,, where they can have systemic effects on the host. Although these small …

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

AE Pérez-Cobas, L Gomez-Valero… - Microbial …, 2020 - microbiologyresearch.org
Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

HB Hassler, B Probert, C Moore, E Lawson… - Microbiome, 2022 - Springer
Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in
species delineation, and now widely in microbiome studies. However, the gene suffers from …

Structure and function of the bacterial root microbiota in wild and domesticated barley

D Bulgarelli, R Garrido-Oter, PC Münch, A Weiman… - Cell host & …, 2015 - cell.com
The microbial communities inhabiting the root interior of healthy plants, as well as the
rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic …

Insights from 20 years of bacterial genome sequencing

M Land, L Hauser, SR Jun, I Nookaew… - Functional & integrative …, 2015 - Springer
Since the first two complete bacterial genome sequences were published in 1995, the
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …

Oscillospira and related bacteria – From metagenomic species to metabolic features

U Gophna, T Konikoff… - Environmental …, 2017 - Wiley Online Library
Oscillospira is an under‐studied anaerobic bacterial genus from Clostridial cluster IV that
has resisted cultivation for over a century since the first time it was observed. In recent years …