Language
English
Publication Date
1-16-2024
Journal
Journal of Clinical Investigation
DOI
10.1172/JCI170859
PMID
37962956
PMCID
PMC10786686
PubMedCentral® Posted Date
1-16-2024
PubMedCentral® Full Text Version
Post-print
Abstract
Targeted metagenomic sequencing is an emerging strategy to survey disease-specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.
Keywords
Humans, Dysbiosis, Gastrointestinal Microbiome, RNA, Ribosomal, 16S, Microbiota, Diarrhea, Gastroenterology, Infectious disease, Bacterial infections
Published Open-Access
yes
Recommended Citation
Wu, Qinglong; Badu, Shyam; So, Sik Yu; et al., "The Pan-Microbiome Profiling System taxa4meta Identifies Clinical Dysbiotic Features and Classifies Diarrheal Disease" (2024). Faculty and Staff Publications. 5644.
https://digitalcommons.library.tmc.edu/baylor_docs/5644
Included in
Allergy and Immunology Commons, Biological Phenomena, Cell Phenomena, and Immunity Commons, Pathology Commons