Analyses of intestinal microbiota: culture versus sequencing

A Hiergeist, J Gläsner, U Reischl, A Gessner - ILAR journal, 2015 - academic.oup.com
Analyzing human as well as animal microbiota composition has gained growing interest
because structural components and metabolites of microorganisms fundamentally influence …

Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data

KD Curry, Q Wang, MG Nute, A Tyshaieva, E Reeves… - Nature …, 2022 - nature.com
Abstract 16S ribosomal RNA-based analysis is the established standard for elucidating the
composition of microbial communities. While short-read 16S rRNA analyses are largely …

[HTML][HTML] Selection of microorganisms capable of polyethylene (PE) and polypropylene (PP) degradation

M Wróbel, S Szymańska, T Kowalkowski… - Microbiological …, 2023 - Elsevier
Microorganisms degrade microplastics, but their potential is still not fully exploited, eg, due
to inadequate selection of microorganisms. We developed an effective selection method of …

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

B Brooks, BA Firek, CS Miller, I Sharon, BC Thomas… - Microbiome, 2014 - Springer
Background The source inoculum of gastrointestinal tract (GIT) microbes is largely
influenced by delivery mode in full-term infants, but these influences may be decoupled in …

Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp.

EJC Gálvez, A Iljazovic, L Amend, TR Lesker… - Cell Host & Microbe, 2020 - cell.com
Prevotella spp. are a dominant bacterial genus within the human gut. Multiple Prevotella
spp. co-exist in some individuals, particularly those consuming plant-based diets …

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

PD Schloss, ML Jenior, CC Koumpouras, SL Westcott… - PeerJ, 2016 - peerj.com
Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA
genes by the Sanger sequencing method and have instead adopted highly parallelized …

Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'

TE Brewer, KM Handley, P Carini, JA Gilbert… - Nature …, 2016 - nature.com
Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the
world, they are under-represented in both isolate collections and genomic databases. Here …

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

K Bergauer, A Fernandez-Guerra… - Proceedings of the …, 2018 - National Acad Sciences
The phylogenetic composition of the heterotrophic microbial community is depth stratified in
the oceanic water column down to abyssopelagic layers. In the layers below the euphotic …

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

BJ Tully, CG Wheat, BT Glazer, JA Huber - The ISME journal, 2018 - academic.oup.com
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may
influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of …

Status of the archaeal and bacterial census: an update

PD Schloss, RA Girard, T Martin, J Edwards, JC Thrash - MBio, 2016 - Am Soc Microbiol
ABSTRACT A census is typically carried out for people across a range of geographical
levels; however, microbial ecologists have implemented a molecular census of bacteria and …