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

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  • Aliphatic amine: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)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 propionate
  • Other: 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:

Pathway Reference
pdu operon https://pubmed.ncbi.nlm.nih.gov/27242734/
Arginine to putrescine https://pubmed.ncbi.nlm.nih.gov/30183487/
Putrescine to spermidine https://pubmed.ncbi.nlm.nih.gov/30183487/
tma operon https://pubmed.ncbi.nlm.nih.gov/25873372/
AAA reductive branch https://pubmed.ncbi.nlm.nih.gov/29168502/
Caffeate respiration https://pubmed.ncbi.nlm.nih.gov/23315745/
Gallic acid metabolism https://pubmed.ncbi.nlm.nih.gov/30054365/
Indoleacetate to scatole https://pubmed.ncbi.nlm.nih.gov/30310076/
P-cresol synthesis gene cluster https://pubmed.ncbi.nlm.nih.gov/11231288/
Phenylacetate to toluene https://pubmed.ncbi.nlm.nih.gov/29556105/
hydroxybenzoate to phenol https://academic.oup.com/femsec/article/94/9/fiy125/5042942
Carnitine caiTABCDE gene cluster https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2958.1994.tb00470.x
Proline to 5-aminovalerate gene cluster https://pubmed.ncbi.nlm.nih.gov/20937090/
Threonine to propionate https://pubmed.ncbi.nlm.nih.gov/9484901/
Acetate to butyrate gene cluster https://pubmed.ncbi.nlm.nih.gov/17241242/
Acetyl-CoA pathway https://pubmed.ncbi.nlm.nih.gov/27733845/
Acrylate to propionate gene cluster https://pubmed.ncbi.nlm.nih.gov/24553467/
Aminobutyrate to butyrate https://pubmed.ncbi.nlm.nih.gov/27994578/
eut operon https://pubmed.ncbi.nlm.nih.gov/20234377/
Fumarate to succinate https://pubmed.ncbi.nlm.nih.gov/28049145/
Glutamate to butyrate gene cluster https://pubmed.ncbi.nlm.nih.gov/27994578/
Glycine reductase https://pubmed.ncbi.nlm.nih.gov/11271425/
Leucine reductive branch https://pubmed.ncbi.nlm.nih.gov/15654892/
Lysine degradation gene cluster https://pubmed.ncbi.nlm.nih.gov/26620920/
PFOR-II pathway https://pubmed.ncbi.nlm.nih.gov/32301184/
Pyruvate to acetate-formate https://pubmed.ncbi.nlm.nih.gov/20622067/
Succinate to propionate https://pubmed.ncbi.nlm.nih.gov/24553467/
porA pathway https://pubmed.ncbi.nlm.nih.gov/31831639/
Arginine to Hcarbonate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300872/
Glycine cleavage https://pubmed.ncbi.nlm.nih.gov/8375392/
Histidine to glutamate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429618/
Hydroxy-L-proline to proline https://pubmed.ncbi.nlm.nih.gov/32180548/
bai operon https://www.nature.com/articles/s41586-020-2396-4
sulfate to sulfide https://pubmed.ncbi.nlm.nih.gov/10792666/

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