FARME

Functional Antibiotic Resistance Metagenomic Element
Content
Description	Compilation of publicly available predicted proteins and DNA elements that confer Antibiotic Resistance, regulatory elements and mobile genetic elements.
Data types; captured	Antimicrobial resistance genes and DNA Elements
Organisms	Bacteria
Contact
Primary citation	PMID 28077567
Access
Website	staff.washington.edu/jwallace/farme/
Download URL	Download
Miscellaneous
Bookmarkable; entities	yes

FARME also known as Functional Antibiotic Resistance Metagenomic Element is a database that compiles publicly available DNA elements and predicted proteins that confer antibiotic resistance, regulatory elements and mobile genetic elements. It is the first database to focus on functional metagenomics. This allows the database to understand 99% of bacteria which cannot be cultured, the relationship between environmental antibiotic resistance sequences and antibiotic genes derived from cultured isolates.^[1] This information was derived from 20 metagenomics^[2]^[3]^[4] projects from GenBank. Also from GenBank are the protein sequence predictions and annotations.

References

^ Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M. (2017). "FARME DB: a functional antibiotic resistance element database". Database. 2017: baw165. doi:10.1093/database/baw165. ISSN 1758-0463. PMC 5225399. PMID 28077567.
^ Forsberg, K. J.; Reyes, A.; Wang, B.; Selleck, E. M.; Sommer, M. O. A.; Dantas, G. (2012-08-30). "The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens". Science. 337 (6098): 1107–1111. Bibcode:2012Sci...337.1107F. doi:10.1126/science.1220761. ISSN 0036-8075. PMC 4070369. PMID 22936781.
^ Moore, Aimée M.; Patel, Sanket; Forsberg, Kevin J.; Wang, Bin; Bentley, Gayle; Razia, Yasmin; Qin, Xuan; Tarr, Phillip I.; Dantas, Gautam (2013-11-13). "Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes". PLOS ONE. 8 (11): e78822. Bibcode:2013PLoSO...878822M. doi:10.1371/journal.pone.0078822. ISSN 1932-6203. PMC 3827270. PMID 24236055.
^ Parsley, L. C.; Consuegra, E. J.; Kakirde, K. S.; Land, A. M.; Harper, W. F.; Liles, M. R. (2010-04-09). "Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial, Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage". Applied and Environmental Microbiology. 76 (11): 3753–3757. Bibcode:2010ApEnM..76.3753P. doi:10.1128/aem.03080-09. ISSN 0099-2240. PMC 2876469. PMID 20382816.

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[1] Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M. (2017). "FARME DB: a functional antibiotic resistance element database". Database. 2017: baw165. doi:10.1093/database/baw165. ISSN 1758-0463. PMC 5225399. PMID 28077567.

[2] Forsberg, K. J.; Reyes, A.; Wang, B.; Selleck, E. M.; Sommer, M. O. A.; Dantas, G. (2012-08-30). "The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens". Science. 337 (6098): 1107–1111. Bibcode:2012Sci...337.1107F. doi:10.1126/science.1220761. ISSN 0036-8075. PMC 4070369. PMID 22936781.

[3] Moore, Aimée M.; Patel, Sanket; Forsberg, Kevin J.; Wang, Bin; Bentley, Gayle; Razia, Yasmin; Qin, Xuan; Tarr, Phillip I.; Dantas, Gautam (2013-11-13). "Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes". PLOS ONE. 8 (11): e78822. Bibcode:2013PLoSO...878822M. doi:10.1371/journal.pone.0078822. ISSN 1932-6203. PMC 3827270. PMID 24236055.

[4] Parsley, L. C.; Consuegra, E. J.; Kakirde, K. S.; Land, A. M.; Harper, W. F.; Liles, M. R. (2010-04-09). "Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial, Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage". Applied and Environmental Microbiology. 76 (11): 3753–3757. Bibcode:2010ApEnM..76.3753P. doi:10.1128/aem.03080-09. ISSN 0099-2240. PMC 2876469. PMID 20382816.

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See also

References