gutSMASH documentation¶
Using gutSMASH¶
gutSMASH is a tool that indentifies bacterial metabolic gene clusters involved in specialized primary metabolism.
Content¶
About¶
gutSMASH is an algorithm that enables to systematically evaluate the metabolic potential of anaerobic bacteria by predicting both known and putative Metabolic Gene Clusters (MGCs). This tool is specifically designed to uncover MGCs that are involved in specialized primary metabolism from the gut microbiome that have been associated to microbe-microbe and host-microbe interactions. Moreover, gutSMASH also predicts energy-capturing-related MGCs, to evaluate the mechanisms bacteria employ to harvest energy. To be able to detect these MGCs, gutSMASH uses detection rules logic as antiSMASH, that are Pfam combination defining of a specific reaction. For more information on how to use gutSMASH you can also visit our online documenation in: https://gutsmash.bioinformatics.nl/help.html
How to run gutSMASH¶
- You can try out gutSMASH by using our online webserver: https://gutsmash.bioinformatics.nl/
- or download and install the gutSMASH command line version from here: https://github.com/victoriapascal/antismash/tree/gutsmash
How to cite¶
If you have found gutSMASH useful, please cite our preprint on the algorithm: https://www.biorxiv.org/content/10.1101/2021.02.25.432841v1, and/or the article describing the gutSMASH web server: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab353/6279837
Glossary¶
Gene Cluster Classes¶
The anaerobic metabolic pathways that gutSMASH predicts can be divided into different gene cluster classes based on their product:
Aliphatic amine
: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)npAA
: non-proteinogenic amino acids (e.g.: Proline to 5-aminovalerate)Aromatic
: derivatives of benzene (e.g.: P-cresol pathway, Caffeate respiration)SCFA
: fatty acids with 5 carbon atoms maximum (e.g.: Acetate to butyrate pathway, Threonine to propionate)SCFA-other
: a SCFA is produced in combination with another molecule. For instance, the pdu operon, releases propanol and propionateOther
: pathways that don’t fit in any other categories are classified in here (e.g.: bai operon)E-MGC
: related to energy-capturing mechanisms (e.g.: Ech complex, Rnf complex)Putative
: gene clusters of unknown function
Gene Cluster Types¶
gutSMASH uses some abbreviations internally to refer to the different types of primary metabolic clusters:
Energy-capturing-related gene clusters (E-MGCs):
Pathway | Reference |
---|---|
Rnf complex | https://pubmed.ncbi.nlm.nih.gov/23269825/ |
Tetrathionate to thiosulfate | https://pubmed.ncbi.nlm.nih.gov/10231485/ |
DMSO/TMAO reductase | https://pubmed.ncbi.nlm.nih.gov/1917829/ |
Nitrate reductase | https://pubmed.ncbi.nlm.nih.gov/2674654/ |
Ech complex | https://pubmed.ncbi.nlm.nih.gov/30850546/ |
Formate dehydrogenase | https://pubmed.ncbi.nlm.nih.gov/26443736/ |
Glycerol-3-P dehydrogenase | https://pubmed.ncbi.nlm.nih.gov/26443736/ |
NADH dehydrogenase I | https://pubmed.ncbi.nlm.nih.gov/26443736/ |
Help¶
You can find more technical information in our help or github page:
You can contact us for any further question at gutsmash.contact@gmail.com