Toward accurate and quantitative comparative metagenomics

S Nayfach, KS Pollard - Cell, 2016 - cell.com
Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles of …

Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases

LWJ Van Den Elsen, HC Poyntz… - Clinical & …, 2017 - Wiley Online Library
The gut microbiota provides essential signals for the development and appropriate function
of the immune system. Through this critical contribution to immune fitness, the gut microbiota …

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

A Vich Vila, F Imhann, V Collij… - Science translational …, 2018 - science.org
Changes in the gut microbiota have been associated with two of the most common
gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome …

Host genetic variation impacts microbiome composition across human body sites

R Blekhman, JK Goodrich, K Huang, Q Sun… - Genome biology, 2015 - Springer
Background The composition of bacteria in and on the human body varies widely across
human individuals, and has been associated with multiple health conditions. While microbial …

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Y Tomofuji, K Sonehara, T Kishikawa, Y Maeda… - Nature …, 2023 - nature.com
Human DNA present in faecal samples can result in a small number of human reads in gut
shotgun metagenomic sequencing data. However, it is presently unclear how much …

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics

NP Marathe, C Pal, SS Gaikwad, V Jonsson… - Water Research, 2017 - Elsevier
Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-
resistant bacteria. In many low and middle income countries, however, large proportions of …

Crewmember microbiome may influence microbial composition of ISS habitable surfaces

A Avila-Herrera, J Thissen, C Urbaniak, NA Be… - PLoS …, 2020 - journals.plos.org
The International Space Station (ISS) is a complex built environment physically isolated from
Earth. Assessing the interplay between the microbial community of the ISS and its crew is …

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

C Urbaniak, MD Morrison, JB Thissen, F Karouia… - Microbiome, 2022 - Springer
Abstract Background The International Space Station (ISS) is a unique and complex built
environment with the ISS surface microbiome originating from crew and cargo or from life …

Investigation of spaceflight induced changes to astronaut microbiomes

MD Morrison, JB Thissen, F Karouia, S Mehta… - Frontiers in …, 2021 - frontiersin.org
The International Space Station (ISS) is a uniquely enclosed environment that has been
continuously occupied for the last two decades. Throughout its operation, protecting the …

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

JM Martí - PLoS computational biology, 2019 - journals.plos.org
Metagenomic sequencing is becoming widespread in biomedical and environmental
research, and the pace is increasing even more thanks to nanopore sequencing. With a …