Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big …

V Aguiar-Pulido, W Huang… - Evolutionary …, 2016 - journals.sagepub.com
Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living
organisms. Changes in the microbiome can impact the health of the environmental niche in …

Microbial functional diversity: from concepts to applications

A Escalas, L Hale, JW Voordeckers… - Ecology and …, 2019 - Wiley Online Library
Functional diversity is increasingly recognized by microbial ecologists as the essential link
between biodiversity patterns and ecosystem functioning, determining the trophic …

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Y Lu, G Zhou, J Ewald, Z Pang, T Shiri… - Nucleic Acids …, 2023 - academic.oup.com
Microbiome studies have become routine in biomedical, agricultural and environmental
sciences with diverse aims, including diversity profiling, functional characterization, and …

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

J Chong, P Liu, G Zhou, J Xia - 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 …

[PDF][PDF] MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

A Dhariwal, J Chong, S Habib, IL King… - Nucleic acids …, 2017 - academic.oup.com
The widespread application of next-generation sequencing technologies has revolutionized
microbiome research by enabling high-throughput profiling of the genetic contents of …

Chemically induced mouse models of acute and chronic intestinal inflammation

S Wirtz, V Popp, M Kindermann, K Gerlach… - Nature protocols, 2017 - nature.com
Inflammatory bowel diseases (IBDs) result in diarrhea and abdominal pain with further
potential complications such as tissue fibrosis and stenosis. Animal models help in …

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size

L Frère, L Maignien, M Chalopin, A Huvet… - Environmental …, 2018 - Elsevier
Abstract Microplastics (< 5 mm) exhibit intrinsic features such as density, hydrophobic
surface, or high surface/volume ratio, that are known to promote microbial colonization and …

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

AM Eren, HG Morrison, PJ Lescault… - The ISME …, 2015 - academic.oup.com
Molecular microbial ecology investigations often employ large marker gene datasets, for
example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial …

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

A Gorvitovskaia, SP Holmes, SM Huse - Microbiome, 2016 - Springer
Background In a series of studies of the gut microbiome,“enterotypes” have been used to
classify gut microbiome samples that cluster together in ordination analyses. Initially, three …

The microbiome and human biology

R Knight, C Callewaert, C Marotz… - Annual review of …, 2017 - annualreviews.org
Over the past few years, microbiome research has dramatically reshaped our understanding
of human biology. New insights range from an enhanced understanding of how microbes …