Microbial Species ID Using ANI and Mash

By: Joel Sevinsky

January 22, 2020

Demystifying Webinar Series

For our January 2020 webinar, we discuss how bacterial species identification is conducted using NGS data. Topics focus on both average nucleotide identify (ANI) and Mash, how they are similar, how they are different, and when it is appropriate to use one versus the other.

Click here for slides

Tableau data from presentation

Mash output:

This one has a lot of data so it might be slow to load.

References (Can also be found in this Paperpile folder)

  1. Ondov, B. D. et al. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol. 20, 232 (2019).
  2. Baker, D. N. & Langmead, B. Dashing: fast and accurate genomic distances with HyperLogLog. Genome Biol. 20, 265 (2019).
  3. Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
  4. Yoon, S.-H., Ha, S.-M., Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110, 1281–1286 (2017).
  5. Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
  6. Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761–6771 (2015).
  7. Rodriguez-R, L. M. & Konstantinidis, K. T. Bypassing Cultivation To Identify Bacterial Species: Culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Magazine 9, 111–118 (2014).
  8. Kim, M., Oh, H.-S., Park, S.-C. & Chun, J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64, 346–351 (2014).
  9. Richter, M. & Rosselló-Móra, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 106, 19126–19131 (2009).
  10. Goris, J. et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91 (2007).
  11. Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102, 2567–2572 (2005).
  12. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).