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

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
doi: 10.1371/journal.pone.0206484


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 and NCBI’s Short Read Archive.

Klíčová slova:

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


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