A clinician's guide to microbiome analysis
Microbiome analysis involves determining the composition and function of a community of
microorganisms in a particular location. For the gastroenterologist, this technology opens up …
microorganisms in a particular location. For the gastroenterologist, this technology opens up …
Metagenomic analysis using phylogenetic placement—a review of the first decade
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 …
interpret the tsunami of metagenomic sequencing data generated by high-throughput …
Species-level functional profiling of metagenomes and metatranscriptomes
Functional profiles of microbial communities are typically generated using comprehensive
metagenomic or metatranscriptomic sequence read searches, which are time-consuming …
metagenomic or metatranscriptomic sequence read searches, which are time-consuming …
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes
from environmental samples. However, these genomes do not typically represent the full …
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
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 …
municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that …
Metagenomic and chemical characterization of soil cobalamin production
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 …
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 …
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
Existing metagenome datasets from many different environments contain untapped potential
for understanding metabolic pathways and their biological impact. Our interest lies in the …
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 …
nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation …
Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity
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 …
greenhouse gas. Very little is known about the identities of abundant and active denitrifiers …