A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

[HTML][HTML] Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

J Lloyd-Price, C Arze, AN Ananthakrishnan… - Nature, 2019 - nature.com
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect
several million individuals worldwide. Crohn's disease and ulcerative colitis are complex …

Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota

K Hosomi, M Saito, J Park, H Murakami… - Nature …, 2022 - nature.com
The gut microbiome is an important determinant in various diseases. Here we perform a
cross-sectional study of Japanese adults and identify the Blautia genus, especially B …

Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation

S Romano, GM Savva, JR Bedarf, IG Charles… - npj Parkinson's …, 2021 - nature.com
The gut microbiota is emerging as an important modulator of neurodegenerative diseases,
and accumulating evidence has linked gut microbes to Parkinson's disease (PD) …

microeco: an R package for data mining in microbial community ecology

C Liu, Y Cui, X Li, M Yao - FEMS microbiology ecology, 2021 - academic.oup.com
ABSTRACT A large amount of sequencing data is produced in microbial community ecology
studies using the high-throughput sequencing technique, especially amplicon-sequencing …

[PDF][PDF] Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer

A Alam, E Levanduski, P Denz, HS Villavicencio… - Cancer cell, 2022 - cell.com
TH 2 cells and innate lymphoid cells 2 (ILC2) can stimulate tumor growth by secreting pro-
tumorigenic cytokines such as interleukin-4 (IL-4), IL-5, and IL-13. However, the …

Host selection shapes crop microbiome assembly and network complexity

C Xiong, YG Zhu, JT Wang, B Singh, LL Han… - New …, 2021 - Wiley Online Library
Plant microbiomes are essential to host health and productivity but the ecological processes
that govern crop microbiome assembly are not fully known. Here we examined bacterial …

[HTML][HTML] A faecal microbiota signature with high specificity for pancreatic cancer

E Kartal, TSB Schmidt, E Molina-Montes… - Gut, 2022 - gut.bmj.com
Background Recent evidence suggests a role for the microbiome in pancreatic ductal
adenocarcinoma (PDAC) aetiology and progression. Objective To explore the faecal and …

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

W Xun, Y Liu, W Li, Y Ren, W Xiong, Z Xu, N Zhang… - Microbiome, 2021 - Springer
Background The relationship between biodiversity and soil microbiome stability remains
poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on …

Wildfire-dependent changes in soil microbiome diversity and function

AR Nelson, AB Narrowe, CC Rhoades, TS Fegel… - Nature …, 2022 - nature.com
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and
rhizosphere processes. Wildfire season length, and the frequency and size of severe fires …