Baseline human gut microbiota profile in healthy people and standard reporting template Article Swipe
Charles H. King
,
Hiral Desai
,
Allison C. Sylvetsky
,
Jonathan LoTempio
,
Shant Ayanyan
,
J. Finno Carrie
,
Keith A. Crandall
,
Brian Fochtman
,
Lusine Gasparyan
,
Naila Gulzar
,
Paul Howell
,
Najy Issa
,
Konstantinos Krampis
,
Lopa Mishra
,
Hiroki Morizono
,
Joseph R. Pisegna
,
Shuyun Rao
,
Yao Ren
,
Vahan Simonyan
,
Krista Smith
,
Sharanjit VedBrat
,
Michael Yao
,
Raja Mazumder
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1101/445353
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1101/445353
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. 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 abundances the study also generated a list of 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.
Related Topics
Concepts
Human Microbiome Project
Metagenomics
Microbiome
Dysbiosis
Biome
Human microbiome
Biology
Workflow
Computational biology
Phylum
Fecal bacteriotherapy
Population
Annotation
Bioinformatics
Ecology
Computer science
Genetics
Medicine
Gene
Clostridium difficile
Environmental health
Ecosystem
Antibiotics
Database
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/445353
- https://www.biorxiv.org/content/biorxiv/early/2018/10/16/445353.full.pdf
- OA Status
- green
- Cited By
- 16
- References
- 67
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2896009274
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2896009274Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/445353Digital Object Identifier
- Title
-
Baseline human gut microbiota profile in healthy people and standard reporting templateWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2018Year of publication
- Publication date
-
2018-10-16Full publication date if available
- Authors
-
Charles H. King, Hiral Desai, Allison C. Sylvetsky, Jonathan LoTempio, Shant Ayanyan, J. Finno Carrie, Keith A. Crandall, Brian Fochtman, Lusine Gasparyan, Naila Gulzar, Paul Howell, Najy Issa, Konstantinos Krampis, Lopa Mishra, Hiroki Morizono, Joseph R. Pisegna, Shuyun Rao, Yao Ren, Vahan Simonyan, Krista Smith, Sharanjit VedBrat, Michael Yao, Raja MazumderList of authors in order
- Landing page
-
https://doi.org/10.1101/445353Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2018/10/16/445353.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2018/10/16/445353.full.pdfDirect OA link when available
- Concepts
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Human Microbiome Project, Metagenomics, Microbiome, Dysbiosis, Biome, Human microbiome, Biology, Workflow, Computational biology, Phylum, Fecal bacteriotherapy, Population, Annotation, Bioinformatics, Ecology, Computer science, Genetics, Medicine, Gene, Clostridium difficile, Environmental health, Ecosystem, Antibiotics, DatabaseTop concepts (fields/topics) attached by OpenAlex
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16Total citation count in OpenAlex
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2025: 1, 2024: 2, 2023: 2, 2022: 6, 2021: 3Per-year citation counts (last 5 years)
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67Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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