Mass spectrometry-based metabolomics in microbiome investigations

A Bauermeister, H Mannochio-Russo… - Nature Reviews …, 2022‏ - nature.com
Microbiotas are a malleable part of ecosystems, including the human ecosystem.
Microorganisms affect not only the chemistry of their specific niche, such as the human gut …

The microbiome and human cancer

GD Sepich-Poore, L Zitvogel, R Straussman, J Hasty… - Science, 2021‏ - science.org
BACKGROUND Historical accounts linking cancer and microbes date as early as four
millennia ago. After establishment of the germ theory of infectious diseases, clinical research …

Greengenes2 unifies microbial data in a single reference tree

D McDonald, Y Jiang, M Balaban, K Cantrell… - Nature …, 2024‏ - nature.com
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …

Sangerbox: a comprehensive, interaction‐friendly clinical bioinformatics analysis platform

W Shen, Z Song, X Zhong, M Huang, D Shen, P Gao… - Imeta, 2022‏ - Wiley Online Library
In recent decades, with the continuous development of high‐throughput sequencing
technology, data volume in medical research has increased, at the same time, almost all …

Majorbio Cloud: a one‐stop, comprehensive bioinformatic platform for multiomics analyses

Y Ren, G Yu, C Shi, L Liu, Q Guo, C Han, D Zhang… - IMeta, 2022‏ - Wiley Online Library
The rapid developments of high‐throughput sequencing technology in the last decade
allowed the emergence of multiomics analyses. Analytic platforms for high‐throughput omics …

OmicStudio: a composable bioinformatics cloud platform with real‐time feedback that can generate high‐quality graphs for publication

F Lyu, F Han, C Ge, W Mao, L Chen, H Hu, G Chen… - Imeta, 2023‏ - pmc.ncbi.nlm.nih.gov
OmicStudio focuses on speed, quality together with flexibility. Generally, OmicStudio can not
only meet the users' demand of ordinary bioinformatics data analysis, statistics, and …

Insulin-regulated serine and lipid metabolism drive peripheral neuropathy

MK Handzlik, JM Gengatharan, KE Frizzi… - Nature, 2023‏ - nature.com
Diabetes represents a spectrum of disease in which metabolic dysfunction damages
multiple organ systems including liver, kidneys and peripheral nerves,. Although the onset …

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

X Zhou, R Baumann, X Gao, M Mendoza, S Singh… - Cell, 2022‏ - cell.com
Changes in gut microbiota have been associated with several diseases. Here, the
International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of …

Microbiome differential abundance methods produce different results across 38 datasets

JT Nearing, GM Douglas, MG Hayes… - Nature …, 2022‏ - nature.com
Identifying differentially abundant microbes is a common goal of microbiome studies.
Multiple methods are used interchangeably for this purpose in the literature. Yet, there are …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022‏ - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …