antiSMASH database

Hunt for interesting metabolites with antiSMASH database

Wednesday 07 Nov 18

Contact

Kai Blin
Postdoc
DTU Biosustain
+45 93 51 13 06

Contact

Tilmann Weber
Professor
DTU Biosustain
+45 24 89 61 32
Scientists who treasure hunt for interesting bacterial metabolites using the online tool antiSMASH now have the opportunity to use an antiSMASH database with pre-calculated results of nearly 25,000 bacterial genomes. This database will ease the discovery of antibiotics, pesticides, and anti-cancer drugs.

The antiSMASH tool can help researchers find bacterial genes responsible for the biosynthesis of interesting metabolites such as new antibiotics, pesticides, and anti-cancer drugs. A new database that collects results from the antiSMASH tool eases the comparison of thousands of bacterial genomes when it comes to metabolites.

“Many scientists search for bacterial metabolites, because they look for new antibiotics. In our group, we look for new antibiotics against multi-drug resistant bacteria like Klebsiella pneumoniae or Acinetobacter baumannii. Society desperately needs new antibiotics against these bacteria, which cause severe septicaemia, urinal infections and pneumonia,” says Kai Blin, Researcher and Scientific Software Engineer at The Novo Nordisk Foundation Center for Biosustainability at Technical University of Denmark (DTU).

The database does not only work for discovering new antibiotics. The food and pharmaceutical industries also use this tool in order to ensure that bacteria used as for instance probiotics do not produce toxic compounds.

The newest improvements of the database have now been published in Nucleic Acid Research.

Metabolites are often not produced
"Using the antiSMASH database, users can avoid doing this job manually, which would take days or weeks"
Kai Blin, Scientific Software Engineer at The Novo Nordisk Foundation Center for Biosustainability

Interesting metabolites are not directly involved in the normal growth, development, or reproduction of the microorganism. But the metabolites often play an important role in the organism’s defence systems against predators.

In the industry, these microbial metabolites can be used as medicines, flavourings, and pigments. Often, microorganisms do not produce interesting metabolites automatically when they are assessed in the lab, which makes the valuable compounds “invisible” to the scientists – unless they look in the DNA.

“For instance, if you know that a certain bacterium produces a metabolite, but at the same time the organism cannot be cultured and, hence, studied further, you can look for the same hidden metabolite in other bacteria via the database,” Kai Blin says.

Find interesting metabolites fast

The scientists have built and improved the antiSMASH online tool over the last 7 years, and it now runs more than 100,000 tasks pr. year and has over 2500 citations.

But the scientists discovered that many antiSMASH-users ran the same genomes, looking for the same results. This was very time consuming for the user, since each run takes up to several hours. Therefore, the researchers and software engineers decided to build the antiSMASH database, which collects all the precomputed results.

“This means that the user can have the results right away and doesn’t have to wait for hours or do this job manually, which would take days or weeks,” says Kai Blin.

Look through 25,000 genomes in a jiffy

The interesting metabolites are encoded by so-called biosynthetic gene clusters, BGCs, which the database is trained to identify. antiSMASH uses a rule-based cluster detection approach to identify 45 different types of interesting metabolites.

The newest version of the antiSMASH database contains 6,200 full bacterial genomes, an 58 % increase compared to version 1. Also, 18,576 so-called draft genomes have been added.

Quite importantly, the update also contains various query options to access the BGS’s. The software engineers have also added a redundancy filter to version 2, which means that instead of giving results for hundreds of strains with almost identical sequences, the database only shows results from the best quality genome. The database is open source, free and easy to use, even for non-programmers.

Resources:

Visit the antiSMASH database here.

Paper: Kai Blin et al., 'The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters', Nucleic Acids Research, gky1060, https://doi.org/10.1093/nar/gky1060

Genome Mining Workshop

iimena workshop September 2018

 

In September 2018, a workshop was held at The Novo Nordisk Foundation Center for Biosustainability at Technical University of Denmark by organizers from the iimena NNF Challenge grant.

The aim of this workshop was to enable the next generation of researcher to perform genome mining studies using antiSMASH software and critically interpret bioinformatics software results. 30 early career scientists, mainly microbiologists, from eight different countries participated.

Also, the young scientists were trained in the NORINE database, a leading resource for an important class of natural products called “non-ribosonally peptides”. NORINE is developed by scientists at University of Lille (France), who were co-organizers of the workshop.

The organizers plan on holding the workshop again in 2-3 years. Interested in participating in the next workshop? Then contact Professor Tilmann Weber.

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