Best practices for analysing microbiomes
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …
Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens
Globalization has a dramatic effect on the trade and movement of seeds, fruits and
vegetables, with a corresponding increase in economic losses caused by the introduction of …
vegetables, with a corresponding increase in economic losses caused by the introduction of …
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Background Metagenomics studies provide valuable insight into the composition and
function of microbial populations from diverse environments; however, the data processing …
function of microbial populations from diverse environments; however, the data processing …
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Background Analysis of mixed microbial communities using metagenomic sequencing
experiments requires multiple preprocessing and analytical steps to interpret the microbial …
experiments requires multiple preprocessing and analytical steps to interpret the microbial …
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 …
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a …
Background Cultivation-independent methods, including metagenomics, are tools for the
exploration and discovery of biotechnological compounds produced by microbes in natural …
exploration and discovery of biotechnological compounds produced by microbes in natural …
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes
The functional metagenomic potential of Shark Bay microbial mats was examined for the first
time at a millimeter scale, employing shotgun sequencing of communities via the Illumina …
time at a millimeter scale, employing shotgun sequencing of communities via the Illumina …
iVikodak—A platform and standard workflow for inferring, analyzing, comparing, and visualizing the functional potential of microbial communities
Background: The objectives of any metagenomic study typically include identification of
resident microbes and their relative proportions (taxonomic analysis), profiling functional …
resident microbes and their relative proportions (taxonomic analysis), profiling functional …
Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates
O Müller, T Bang‐Andreasen… - Environmental …, 2018 - Wiley Online Library
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of
formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical …
formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical …
Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health
Intense agricultural practices to meet rising food demands have caused ecosystem
perturbations. For sustainable crop production, biological agents are gaining attention, but …
perturbations. For sustainable crop production, biological agents are gaining attention, but …