Microbiome Benchmarking Software development Best practices Metagenomics Amplicon sequencing Marker-gene sequencing 1. Introduction “What we observe is not nature itself, but nature exposed to our method of questioning.”-Werner Heisenberg Microbial communities have colonized and influence practically every ...
However, although probiotic use has been greatly popularized among the general public, there are conflicting clinical results for many probiotic strains and formulations. Emerging insights from microbiome research enable an assessment of gut colonization by probiotics, strain-level activity, interactions ...
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome’s ecological balance, commonly by antibiotics, can cause and exace...
Our strain-level analysis reinforced the consistency of CRC-associated microbial signatures in old- and young-onset CRC. Additionally, the similar prediction accuracy of our microbiome-based models for CRC status in both old- and young-onset patients underscores the consistency of microbial signatures ...
G. Current challenges and best-practice protocols for microbiome analysis. Brief. Bioinform. 22, 178–193. https://doi.org/10.1093/bib/bbz155 (2019). Article CAS PubMed Central Google Scholar Andrews, S. S. FastQC: A quality control tool for high throughput sequence data. https://doi....
Equally important are the identification and stratification of relevant cohorts to support cross-study comparisons and consolidate research findings (e.g., The Quadram Institute website released for best practice in microbiome research [114]). Robust human studies must be conducted in real-life ...
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issue
Our Bodies’ Best Buddies About Microbiome Digest January 17, 2025 Posted on January 16, 2025 by Svetlana Ugarcina Perovic Starting the new year with a new digest out, full of interesting findings.Check it out and see you at MVIF next week! It's a new year! …and a new #MVIF...
The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from th
M. et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio 6, e00037 (2015). Article PubMed PubMed Central CAS Google Scholar Dickson, R. P. et al. Spatial variation in the healthy human lung microbiome ...