Current understanding of the human microbiome

JA Gilbert, MJ Blaser, JG Caporaso, JK Jansson… - Nature medicine, 2018 - nature.com
Our understanding of the link between the human microbiome and disease, including
obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding …

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

M Pammi, J Cope, PI Tarr, BB Warner, AL Morrow… - Microbiome, 2017 - Springer
Background Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and
microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the …

Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle

E Pasolli, F Asnicar, S Manara, M Zolfo, N Karcher… - Cell, 2019 - cell.com
The body-wide human microbiome plays a role in health, but its full diversity remains
uncharacterized, particularly outside of the gut and in international populations. We …

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

MR Olm, CT Brown, B Brooks, JF Banfield - The ISME journal, 2017 - academic.oup.com
The number of microbial genomes sequenced each year is expanding rapidly, in part due to
genome-resolved metagenomic studies that routinely recover hundreds of draft-quality …

[HTML][HTML] Anvi'o: an advanced analysis and visualization platform for 'omics data

AM Eren, ÖC Esen, C Quince, JH Vineis, HG Morrison… - PeerJ, 2015 - peerj.com
Advances in high-throughput sequencing and 'omics technologies are revolutionizing
studies of naturally occurring microbial communities. Comprehensive investigations of …

Microbial strain-level population structure and genetic diversity from metagenomes

DT Truong, A Tett, E Pasolli, C Huttenhower… - Genome …, 2017 - genome.cshlp.org
Among the human health conditions linked to microbial communities, phenotypes are often
associated with only a subset of strains within causal microbial groups. Although it has been …

Clades of huge phages from across Earth's ecosystems

B Al-Shayeb, R Sachdeva, LX Chen, F Ward, P Munk… - Nature, 2020 - nature.com
Bacteriophages typically have small genomes and depend on their bacterial hosts for
replication. Here we sequenced DNA from diverse ecosystems and found hundreds of …

Schrödinger's microbes: tools for distinguishing the living from the dead in microbial ecosystems

JB Emerson, RI Adams, CMB Román, B Brooks… - Microbiome, 2017 - Springer
While often obvious for macroscopic organisms, determining whether a microbe is dead or
alive is fraught with complications. Fields such as microbial ecology, environmental health …

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

R Berni Canani, N Sangwan, AT Stefka… - The ISME …, 2016 - academic.oup.com
Dietary intervention with extensively hydrolyzed casein formula supplemented with
Lactobacillus rhamnosus GG (EHCF+ LGG) accelerates tolerance acquisition in infants with …

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study

BB Warner, E Deych, Y Zhou, C Hall-Moore… - The Lancet, 2016 - thelancet.com
Background Gut bacteria might predispose to or protect from necrotising enterocolitis, a
severe illness linked to prematurity. In this observational prospective study we aimed to …