A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly availab...
| Main Authors: | , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Nature Publishing Group
2017
|
| Online Access: | http://hdl.handle.net/1721.1/110118 https://orcid.org/0000-0002-3059-5784 |
| _version_ | 1826212789512830976 |
|---|---|
| author | Hahn, Aria S. Altman, Tomer Hanson, Niels W. Kim, Dongjae Relman, David A. Dill, David L. Konwar, Kishori Mohan Hallam, Steven |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Hahn, Aria S. Altman, Tomer Hanson, Niels W. Kim, Dongjae Relman, David A. Dill, David L. Konwar, Kishori Mohan Hallam, Steven |
| author_sort | Hahn, Aria S. |
| collection | MIT |
| description | Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools. |
| first_indexed | 2024-09-23T15:38:15Z |
| format | Article |
| id | mit-1721.1/110118 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:38:15Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1101182022-09-29T15:10:56Z A geographically-diverse collection of 418 human gut microbiome pathway genome databases Hahn, Aria S. Altman, Tomer Hanson, Niels W. Kim, Dongjae Relman, David A. Dill, David L. Konwar, Kishori Mohan Hallam, Steven Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Konwar, Kishori Mohan Hallam, Steven Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools. Alexander Graham Bell Canada (Graduate Scholarships-Doctoral Program (CGS D)) Tula Foundation University of British Columbia. Faculty of Graduate and Postdoctoral Studies Stanford University. School of Medicine (Dean's Funds) National Institutes of Health (U.S.) (Biotechnology Training Grant, grant number 5T32 GM008412) King Abdullah University of Science and Technology (research grant under the KAUST Stanford Academic Excellence Alliance program) National Institutes of Health (U.S.) (NIH/NIGMS 5R01GM099534) Thomas C. and Joan M. Merigan Endowment 2017-06-21T15:17:27Z 2017-06-21T15:17:27Z 2017-04 2016-08 Article http://purl.org/eprint/type/JournalArticle 2052-4463 http://hdl.handle.net/1721.1/110118 Hahn, Aria S., Tomer Altman, Kishori M. Konwar, Niels W. Hanson, Dongjae Kim, David A. Relman, David L. Dill, and Steven J. Hallam. “A Geographically-Diverse Collection of 418 Human Gut Microbiome Pathway Genome Databases.” Scientific Data 4 (April 11, 2017): 170035. https://orcid.org/0000-0002-3059-5784 en_US http://dx.doi.org/10.1038/sdata.2017.35 Scientific Data Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Nature |
| spellingShingle | Hahn, Aria S. Altman, Tomer Hanson, Niels W. Kim, Dongjae Relman, David A. Dill, David L. Konwar, Kishori Mohan Hallam, Steven A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title | A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title_full | A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title_fullStr | A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title_full_unstemmed | A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title_short | A geographically-diverse collection of 418 human gut microbiome pathway genome databases |
| title_sort | geographically diverse collection of 418 human gut microbiome pathway genome databases |
| url | http://hdl.handle.net/1721.1/110118 https://orcid.org/0000-0002-3059-5784 |
| work_keys_str_mv | AT hahnarias ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT altmantomer ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT hansonnielsw ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT kimdongjae ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT relmandavida ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT dilldavidl ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT konwarkishorimohan ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT hallamsteven ageographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT hahnarias geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT altmantomer geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT hansonnielsw geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT kimdongjae geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT relmandavida geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT dilldavidl geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT konwarkishorimohan geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases AT hallamsteven geographicallydiversecollectionof418humangutmicrobiomepathwaygenomedatabases |