What’s next? Happy to take requests for new databases or features. Let me know what would make TaxSEA more useful for your work. I’m also putting together workshop materials & tutorials, so stay tuned if you’d like to learn how to use TaxSEA in your own microbiome analyses.

Automated BugSigDB integration. TaxSEA now talks more directly to the BugSigDB API and returns a table of PubMed IDs for microbiome signatures most similar to your results, instantly linking your findings to published studies.

New curated signature collections from the literature added:
• Urbanisation-associated microbiomes
• Mucin utilisation
• Gut–brain axis relevant taxa
All available as built-in gene sets for enrichment testing.

TaxSEA now integrates data from BacDive, the Bacterial Diversity Metadatabase, which contains curated phenotypic + metabolic traits for thousands of bacteria. You can test whether your metagenome is enriched for taxa with traits like nitrate reduction, enzyme production etc.

Well done! Look forward to reading it 🎉

Replied above with a link to how I did it on GitHub!

FYI finally tidied this up into something usable github.com/feargalr/bac...

PS shoot me a DM if you want the code I used?. I'll put it together into a GitHub repo but that might not be for a few weeks while I'm busy with other bits.

Mostly fine once I had spent the time to look up a bunch of different bacteria to get a feel for what different entries look like. That was time consuming. Initially I had planned to use an LLM (either local or via the ChatGPT API) to scrape the data I needed but they all kept making things up 😅

Drop me a line if you want to know more. The methodology was also published in Briefings in Bioinformatics earlier this year academic.oup.com/bib/article/...

Link to BioConductor - bioconductor.org/packages/dev...