Useful Resources

NameDiscriptionLinks
IMG-ABC v.5.0
The largest publicly available database of theoretical predicted and experimentally verified biosynthesis gene clusters from microbial genomes. https://img.jgi.doe.gov/abc-public/
Antismash 6
An tool for detecting and characterising secondary metabolite biosynthesis gene clusters in bacterial and fungal genome. https://antismash.secondarymetabolites.org/
MiBiG 2.0 A repository for known biosynthetic gene clusters with the minimum information. https://mibig.secondarymetabolites.org/
BiG-SCAPE A tool facilitates sequence similarity network analysis of biosynthetic gene clusters and gene cluster families. https://bigscape-corason.secondarymetabolites.org/
PRISM4 A platform for prediction of the chemical structures of genomically encoded antibiotics from bacteria. http://prism.adapsyn.com/
The antiSMASH database A database of microbioal secondary metabolite biosynthetic gene clusters predicted by antiSMASH. https://antismash-db.secondarymetabolites.org/
StreptomeDB 3.0 A compendium of natural products from the genus streptomycetes. http://www.pharmbioinf.uni-freiburg.de/streptomedb/

Literature Links

  • Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res. 2020 Dec 23;31(2):239–50. doi:10.1101/gr.268169.120. PubMed

  • Libis V, Antonovsky N, Zhang M, Shang Z, Montiel D, Maniko J, Ternei MA, Calle PY, Lemetre C, Owen JG, Brady SF. Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences. Nat Commun. 2019 Aug 26;10(1):3848. doi: 10.1038/s41467-019-11658-z. PubMed

  • Wei B, Du AQ, Zhou ZY, Lai C, Yu WC, Yu JB, Yu YL, Chen JW, Zhang HW, Xu XW,Wang H. An atlas of bacterial secondary metabolite biosynthesis gene clusters. Environ Microbiol. 2021 Nov;23(11):6981-6992. doi: 10.1111/1462-2920.15761. PubMed

  • Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep. 2020 Jul 1;37(7):879-892. doi: 10.1039/c9np00050j. PubMed

  • Robey MT, Caesar LK, Drott MT, Keller NP, Kelleher NL. An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2020230118. doi: 10.1073/pnas.2020230118. PubMed

  • Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, Fischbach MA. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell.2014 Sep 11;158(6):1402-1414. doi: 10.1016/j.cell.2014.08.032. PubMed

  • Hiseni P, Rudi K, Wilson RC, Hegge FT, Snipen L. HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data. Microbiome. 2021 Jul 31;9(1):165. doi: 10.1186/s40168-021-01114-w. PubMed

  • Sugimoto Y, Camacho FR, Wang S, Chankhamjon P, Odabas A, Biswas A, Jeffrey PD, Donia MS. A metagenomic strategy for harnessing the chemical repertoire of the human microbiome. Science. 2019 Dec 13;366(6471):eaax9176. doi:10.1126/science.aax9176. PubMed

  • Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, De Los Santos ELC, Yeong M, Cruz-Morales P, Abubucker S, Roeters A, Lokhorst W, Fernandez-Guerra A, Cappelini LTD, Goering AW, Thomson RJ, Metcalf WW, Kelleher NL, Barona-Gomez F, Medema MH. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol. 2020 Jan;16(1):60-68. doi: 10.1038/s41589-019-0400-9. PubMed

  • Gupta VK, Bakshi U, Chang D, Lee AR, Davis JM 3rd, Chandrasekaran S, Jin YS, Freeman MF, Sung J. TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes. mSystems. 2022 Nov 15:e0092522. doi: 10.1128/msystems.00925-22. PubMed

  • Hannigan GD, Prihoda D, Palicka A, Soukup J, Klempir O, Rampula L, Durcak J, Wurst M, Kotowski J, Chang D, Wang R, Piizzi G, Temesi G, Hazuda DJ, Woelk CH, Bitton DA. A deep learning genome-mining strategy for biosynthetic gene cluster prediction. Nucleic Acids Res. 2019 Oct 10;47(18):e110. doi: 10.1093/nar/gkz654. PubMed

  • González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom. 2023 Jan;9(1). doi: 10.1099/mgen.0.000921. PubMed