Baseline human gut microbiota profile in healthy people and standard reporting template

English version

Autoři: Charles H. King ^aff001; Hiral Desai ^aff001; Allison C. Sylvetsky ^aff003; Jonathan LoTempio ^aff004; Shant Ayanyan ^aff001; Jill Carrie ^aff001; Keith A. Crandall ^aff006; Brian C. Fochtman ^aff001; Lusine Gasparyan ^aff001; Naila Gulzar ^aff001; Paul Howell ^aff007; Najy Issa ^aff003; Konstantinos Krampis ^aff008; Lopa Mishra ^aff009; Hiroki Morizono ^aff005; Joseph R. Pisegna ^aff010; Shuyun Rao ^aff009; Yao Ren ^aff001; Vahan Simonyan ^aff001; Krista Smith ^aff001; Sharanjit VedBrat ^aff007; Michael D. Yao ^aff011; Raja Mazumder ^aff001
Působiště autorů: The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America ^aff001; McCormick Genomic and Proteomic Center, George Washington University, Washington, DC, United States of America ^aff002; The Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America ^aff003; The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America ^aff004; Center for Genetic Medicine, Children’s National Medical Center, George Washington University, Washington, DC, United States of America ^aff005; Computational Biology Institute and The Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America ^aff006; KamTek Inc, Frederick, Maryland, United States of America ^aff007; Department of Biological Sciences, Hunter College, City University of New York, New York, New York, United States of America ^aff008; Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America ^aff009; Division of Gastroenterology and Hepatology VA Greater Los Angeles Healthcare System and Department of Medicine and Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America ^aff010; Washington DC VA Medical Center, Gastroenterology & Hepatology Section, Washington, DC, United States of America ^aff011; Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America ^aff012
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0206484

Souhrn

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI’s Short Read Archive.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Biochemistry – Organisms – Research and analysis methods – Proteins – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – Computer and information sciences – Taxonomy – Data management – Microbiology – Medical microbiology – Bacteria – Microbiome – Microbial genomics – Sequence databases – Biological databases – Metagenomics – Gut bacteria – Bifidobacterium – Bacteroides – Proteomes

Zdroje

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Baseline human gut microbiota profile in healthy people and standard reporting template

Souhrn

Klíčová slova:

Zdroje

PLOS One

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