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 …

The best practice for microbiome analysis using R

T Wen, G Niu, T Chen, Q Shen, J Yuan, YX Liu - Protein & Cell, 2023 - academic.oup.com
With the gradual maturity of sequencing technology, many microbiome studies have
published, driving the emergence and advance of related analysis tools. R language is the …

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 …

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

M Wang, AH Ge, X Ma, X Wang, Q **e, L Wang… - Nature …, 2024 - nature.com
Root-associated microbiomes contribute to plant growth and health, and are dynamically
affected by plant development and changes in the soil environment. However, how different …

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease

RS Mehta, JR Mayers, Y Zhang, A Bhosle… - Nature medicine, 2023 - nature.com
For decades, variability in clinical efficacy of the widely used inflammatory bowel disease
(IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and …

[HTML][HTML] 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 **ong, 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 …

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

W Xun, Y Liu, W Li, Y Ren, W **ong, 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 …

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

M Bahram, M Espenberg, J Pärn… - Nature …, 2022 - nature.com
Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and
ozone depleter released by microbes. Yet, microbial players and processes underlying the …

Plant developmental stage drives the differentiation in ecological role of the maize microbiome

C **ong, BK Singh, JZ He, YL Han, PP Li, LH Wan… - Microbiome, 2021 - Springer
Background Plants live with diverse microbial communities which profoundly affect multiple
facets of host performance, but if and how host development impacts the assembly, functions …