Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Correlation and association analyses in microbiome study integrating multiomics in health and disease

Y **a - Progress in molecular biology and translational …, 2020 - Elsevier
Correlation and association analyses are one of the most widely used statistical methods in
research fields, including microbiome and integrative multiomics studies. Correlation and …

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

J Chong, P Liu, G Zhou, J **a - Nature protocols, 2020 - nature.com
MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of
common data outputs generated from current microbiome studies. It enables researchers …

Effects of microplastics and carbon nanotubes on soil geochemical properties and bacterial communities

Q Wang, X Feng, Y Liu, W Cui, Y Sun, S Zhang… - Journal of Hazardous …, 2022 - Elsevier
A 100-day soil incubation experiment was conducted to explore the effects of conventional
(high-density polyethylene, HDPE) and biodegradable (polylactic acid, PLA) microplastics …

[HTML][HTML] MetaboAnalystR 3.0: toward an optimized workflow for global metabolomics

Z Pang, J Chong, S Li, J **a - Metabolites, 2020 - mdpi.com
Liquid chromatography coupled to high-resolution mass spectrometry platforms are
increasingly employed to comprehensively measure metabolome changes in systems …

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

L Kang, Y Song, R Mackelprang, D Zhang… - Nature …, 2024 - nature.com
Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse
microorganisms. Understanding these microbial communities is crucial for predicting the …

Distinct community structure and microbial functions of biofilms colonizing microplastics

L Miao, P Wang, J Hou, Y Yao, Z Liu, S Liu… - Science of the Total …, 2019 - Elsevier
Microplastics are frequently detected in freshwater environments, serving as a new factitious
substrate for colonization of biofilm-forming microorganisms. Distinct microbial assemblages …

Decoupling function and taxonomy in the global ocean microbiome

S Louca, LW Parfrey, M Doebeli - Science, 2016 - science.org
Microbial metabolism powers biogeochemical cycling in Earth's ecosystems. The taxonomic
composition of microbial communities varies substantially between environments, but the …

[HTML][HTML] Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota

F Cignarella, C Cantoni, L Ghezzi, A Salter, Y Dorsett… - Cell metabolism, 2018 - cell.com
Multiple sclerosis (MS) is more common in western countries with diet being a potential
contributing factor. Here we show that intermittent fasting (IF) ameliorated clinical course and …

ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

KS Andersen, RH Kirkegaard, SM Karst, M Albertsen - BioRxiv, 2018 - biorxiv.org
Microbial community analysis using 16S rRNA gene amplicon sequencing is the backbone
of many microbial ecology studies. Several approaches and pipelines exist for processing …