Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
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TLDR
A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.Abstract:
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.read more
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The Potential Effect of Oral Microbiota in the Prediction of Mucositis During Radiotherapy for Nasopharyngeal Carcinoma
Xiao-Xia Zhu,Xiao-Jun Yang,Yi-Lan Chao,Hui-Min Zheng,Hua-Fang Sheng,Hai-yue Liu,Yan He,Hongwei Zhou +7 more
TL;DR: Oral microbiota changes correlate with the progression and aggravation of radiotherapy-induced mucositis in patients with nasopharyngeal carcinoma and microbiota-based strategies can be used for the early prediction and prevention of the incidence of severe mucositi during radiotherapy.
Journal ArticleDOI
Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn's disease patients, but not in healthy controls.
Holger Schäffler,Daniel P. R. Herlemann,Daniel P. R. Herlemann,Paul Klinitzke,Peggy Berlin,Bernd Kreikemeyer,Robert Jaster,Georg Lamprecht +7 more
TL;DR: Investigation of whether vitamin D administration has an impact on the bacterial composition in Crohn's disease (CD) compared to healthy controls (HC) found no impact.
Journal ArticleDOI
Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19
TL;DR: In this paper , a functional profile of the gut microbiome in patients with COVID-19 before and after disease resolution was characterized by shotgun metagenomic sequencing on fecal samples from 66 antibiotics-naïve patients with SARS-CoV-2 and 70 non-COVID-2 infected patients.
Journal ArticleDOI
Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China.
TL;DR: The results indicate that the diversity, composition and structure of planktonic bacterial communities are sensitive to water chemistry in the Jiulong River Watershed, and therefore can serve as a good sentinel of environmental changes in this watershed.
Journal ArticleDOI
High-Salt Diet Has a Certain Impact on Protein Digestion and Gut Microbiota: A Sequencing and Proteome Combined Study
Chao Wang,Zixin Huang,Kequan Yu,Ruiling Ding,Keping Ye,Chen Dai,Xinglian Xu,Guanghong Zhou,Chunbao Li +8 more
TL;DR: LC-MS-MS revealed a dynamic change of proteins from the diet, host, and gut microbiota alongside the digestive tract, indicating that high-salt diet may alter the composition of gut microbiota and has a certain impact on protein digestion.
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