16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome
| Autor: | Jessica Richman, Laurens Kraal, Elisabeth M. Bik, Juan Pablo Cárdenas, Yelena V. Budovskaya, Daniel Almonacid, Francisco J. Ossandon, Zachary Apte, Audrey D. Goddard |
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| Rok vydání: | 2016 |
| Předmět: |
Bacterial Diseases
0301 basic medicine Molecular biology lcsh:Medicine Gene Sequencing Disease Pathology and Laboratory Medicine Biochemistry law.invention Database and Informatics Methods Probiotic Sequencing techniques Salmonella law Reference Values RNA Ribosomal 16S Medicine and Health Sciences DNA sequencing lcsh:Science Multidisciplinary Genomics Bacterial Pathogens Nucleic acids Infectious Diseases Salmonella Enterica Ribosomal RNA Medical Microbiology Pathogens Sequence Analysis Research Article Cell biology Cellular structures and organelles Bioinformatics Clostridium Difficile 030106 microbiology Sequence Databases Reference range Context (language use) Microbial Genomics Computational biology Biology Research and Analysis Methods Microbiology 03 medical and health sciences Enterobacteriaceae Genetics Humans Microbiome Non-coding RNA Microbial Pathogens Biology and life sciences Bacteria Sequence Analysis RNA lcsh:R Gut Bacteria Organisms Correction 16S ribosomal RNA Gastrointestinal Microbiome Molecular biology techniques Biological Databases 030104 developmental biology RNA lcsh:Q Ribosomes |
| Zdroj: | PLoS ONE PLoS ONE, Vol 12, Iss 5, p e0176555 (2017) PLoS ONE, Vol 14, Iss 2, p e0212474 (2019) |
| ISSN: | 1932-6203 |
| Popis: | Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring. More broadly, our method can facilitate epidemiological studies of the microbiome as it relates to overall human health and disease. |
| Databáze: | OpenAIRE |
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