A clinician's guide to microbiome analysis

MJ Claesson, AG Clooney, PW O'toole - … Reviews Gastroenterology & …, 2017 - nature.com
Microbiome analysis involves determining the composition and function of a community of
microorganisms in a particular location. For the gastroenterologist, this technology opens up …

Metagenomic analysis using phylogenetic placement—a review of the first decade

L Czech, A Stamatakis, M Dunthorn… - Frontiers in …, 2022 - frontiersin.org
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and
interpret the tsunami of metagenomic sequencing data generated by high-throughput …

Species-level functional profiling of metagenomes and metatranscriptomes

EA Franzosa, LJ McIver, G Rahnavard, LR Thompson… - Nature …, 2018 - nature.com
Functional profiles of microbial communities are typically generated using comprehensive
metagenomic or metatranscriptomic sequence read searches, which are time-consuming …

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

JA Boyd, BJ Woodcroft, GW Tyson - Nucleic Acids Research, 2018 - academic.oup.com
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes
from environmental samples. However, these genomes do not typically represent the full …

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

E Spasov, JM Tsuji, LA Hug, AC Doxey… - The ISME …, 2020 - academic.oup.com
Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in
municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that …

Metagenomic and chemical characterization of soil cobalamin production

X Lu, KR Heal, AE Ingalls, AC Doxey… - The ISME …, 2020 - academic.oup.com
Cobalamin (vitamin B12) is an essential enzyme cofactor for most branches of life. Despite
the potential importance of this cofactor for soil microbial communities, the producers and …

High-resolution characterization of the human microbiome

C Noecker, CP McNally, A Eng, E Borenstein - Translational Research, 2017 - Elsevier
The human microbiome plays an important and increasingly recognized role in human
health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene …

Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems

E Jameson, AC Doxey, R Airs, KJ Purdy… - Microbial …, 2016 - microbiologyresearch.org
Existing metagenome datasets from many different environments contain untapped potential
for understanding metabolic pathways and their biological impact. Our interest lies in the …

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium …

D Li, Z Ren, Y Zhou, L Jiang, M Zheng… - Applied and …, 2023 - Am Soc Microbiol
Exploring nitrifiers in extreme environments is vital to expanding our understanding of
nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation …

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

S Coyotzi, AC Doxey, ID Clark… - Environmental …, 2017 - Wiley Online Library
Denitrification transforms nitrogen applied as fertilizer and emits N2O, which is a potent
greenhouse gas. Very little is known about the identities of abundant and active denitrifiers …