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 …

Analysis of microbial compositions: a review of normalization and differential abundance analysis

H Lin, SD Peddada - NPJ biofilms and microbiomes, 2020 - nature.com
Increasingly, researchers are discovering associations between microbiome and a wide
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on …

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic

E Kadosh, I Snir-Alkalay, A Venkatachalam, S May… - Nature, 2020 - nature.com
Somatic mutations in p53, which inactivate the tumour-suppressor function of p53 and often
confer oncogenic gain-of-function properties, are very common in cancer,. Here we studied …

Establishing microbial composition measurement standards with reference frames

JT Morton, C Marotz, A Washburne, J Silverman… - Nature …, 2019 - nature.com
Differential abundance analysis is controversial throughout microbiome research. Gold
standard approaches require laborious measurements of total microbial load, or absolute …

QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data

M Estaki, L Jiang, NA Bokulich… - Current protocols in …, 2020 - Wiley Online Library
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the
popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully …

Quantitative microbiome profiling links gut community variation to microbial load

D Vandeputte, G Kathagen, K D'hoe, S Vieira-Silva… - Nature, 2017 - nature.com
Current sequencing-based analyses of faecal microbiota quantify microbial taxa and
metabolic pathways as fractions of the sample sequence library generated by each …

[HTML][HTML] Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data

H Lin, M Eggesbø, SD Peddada - Nature communications, 2022 - nature.com
It is well-known that human gut microbiota form an ecosystem where microbes interact with
each other. Due to complex underlying interactions, some microbes may correlate …

American gut: an open platform for citizen science microbiome research

D McDonald, E Hyde, JW Debelius, JT Morton… - Msystems, 2018 - Am Soc Microbiol
Although much work has linked the human microbiome to specific phenotypes and lifestyle
variables, data from different projects have been challenging to integrate and the extent of …

Gut microbiota and cardiovascular disease: opportunities and challenges

N Kazemian, M Mahmoudi, F Halperin, JC Wu… - Microbiome, 2020 - Springer
Coronary artery disease (CAD) is the most common health problem worldwide and remains
the leading cause of morbidity and mortality. Over the past decade, it has become clear that …

Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma

JR Björk, LA Bolte, A Maltez Thomas, KA Lee… - Nature Medicine, 2024 - nature.com
Multiple clinical trials targeting the gut microbiome are being conducted to optimize
treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these …