Host–microbiota maladaptation in colorectal cancer

A Janney, F Powrie, EH Mann - Nature, 2020 - nature.com
Colorectal cancer (CRC) is a heterogeneous disease of the intestinal epithelium that is
characterized by the accumulation of mutations and a dysregulated immune response. Up to …

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 …

Advances and challenges in metatranscriptomic analysis

M Shakya, CC Lo, PSG Chain - Frontiers in genetics, 2019 - frontiersin.org
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …

Human gut microbiome: function matters

A Heintz-Buschart, P Wilmes - Trends in microbiology, 2018 - cell.com
The human gut microbiome represents a complex ecosystem contributing essential
functions to its host. Recent large-scale metagenomic studies have provided insights into its …

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

A Heintz‐Buschart, U Pandey, T Wicke… - Movement …, 2018 - Wiley Online Library
Background Increasing evidence connects the gut microbiota and the onset and/or
phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial …

The use of next generation sequencing for improving food safety: Translation into practice

B Jagadeesan, P Gerner-Smidt, MW Allard, S Leuillet… - Food …, 2019 - Elsevier
Abstract Next Generation Sequencing (NGS) combined with powerful bioinformatic
approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of …

Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential

L Wampach, A Heintz-Buschart, JV Fritz… - Nature …, 2018 - nature.com
The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear
whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and …

SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline

J Tamames, F Puente-Sánchez - Frontiers in microbiology, 2019 - frontiersin.org
The improvement of sequencing technologies has facilitated generalization of metagenomic
sequencing, which has become a standard procedure for analyzing the structure and …

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

S Kieser, J Brown, EM Zdobnov, M Trajkovski… - BMC …, 2020 - Springer
Background Metagenomics studies provide valuable insight into the composition and
function of microbial populations from diverse environments; however, the data processing …

A guide to human microbiome research: study design, sample collection, and bioinformatics analysis

XB Qian, T Chen, YP Xu, L Chen, FX Sun… - Chinese Medical …, 2020 - mednexus.org
The purpose of this review is to provide medical researchers, especially those without a
bioinformatics background, with an easy-to-understand summary of the concepts and …