The 19 sources of annotations in bugphyzza. exp = experimental data; igc = inferred from genome context; tas = traceable author statement; nast = non-traceable author statement.
| Source | Confidence in curation | Evidence | Full source |
|---|---|---|---|
| Asnicar_2021 | medium | igc | Asnicar F, Berry SE, Valdes AM, et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. 2021;27(2):321-332. doi:10.1038/s41591-020-01183-8 |
| BacDive | high | exp | Schober I, Koblitz J, Sardà Carbasse J, et al. BacDive in 2025: the core database for prokaryotic strain data. Nucleic Acids Res. 2025;53(D1):D748-D756. doi:10.1093/nar/gkae959. https://bacdive.dsmz.de (CC BY 4.0) |
| BacMap | low | nas | http://bacmap.wishartlab.com |
| Barcenilla_2000 | high | exp | Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS, Henderson C, Flint HJ. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol. 2000 Apr;66(4):1654-61. doi: 10.1128/aem.66.4.1654-1661.2000. PMID: 10742256; PMCID: PMC92037. |
| Bergey’s Manual | high | exp | https://www.bergeys.org/ |
| Browne_2021 | high | exp | Browne, H.P., Almeida, A., Kumar, N. et al. Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle. Genome Biol 22, 204 (2021). https://doi.org/10.1186/s13059-021-02428-6 |
| Gibson_2018 | high | exp | Gibson B, Wilson DJ, Feil E, Eyre-Walker A. The distribution of bacterial doubling times in the wild. Proc Biol Sci. 2018 Jun 13;285(1880):20180789. doi: 10.1098/rspb.2018.0789. PMID: 29899074; PMCID: PMC6015860. |
| HeaverS_2018 | high | exp | Heaver SL, Johnson EL, Ley RE. Sphingolipids in host-microbial interactions. Curr Opin Microbiol. 2018 Jun;43:92-99. doi: 10.1016/j.mib.2017.12.011. Epub 2018 Jan 12. PMID: 29328957. |
| Hilt_2014 | high | exp | Hilt, E. E., McKinley, K., Pearce, M. M., Rosenfeld, A. B., Zilliox, M. J., Mueller, E. R., … & Schreckenberger, P. C. (2014). Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. Journal of clinical microbiology, 52(3), 871-876. |
| Kegg | medium | igc | https://www.genome.jp/kegg/ |
| Madin_2020 | medium | tas | https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/tree/master/output/prepared_data |
| Microbial Fatty Acid Compositions | high | exp | https://github.com/bovee/fattyacids |
| MiDAS | high | exp | Dueholm, M.S., Nierychlo, M., Andersen, K.S., Rudkjøbing, V., Knudsen, S., the MiDAS Global Consortium, Albertsen, M., Nielsen, P.H. 2021; MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants. BioRxiv. Nierychlo, M., Andersen, K.S., Xu, Y., Green, N., Jiang, C., Albertsen, M., Dueholm, M.S., Nielsen, P.H., 2020. MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge. Water Research 115955. https://doi.org/10.1016/j.watres.2020.115955 |
| OlsenI_2001 | high | exp | Olsen I, Nichols FC. Are Sphingolipids and Serine Dipeptide Lipids Underestimated Virulence Factors of Porphyromonas gingivalis? Infect Immun. 2018 Jun 21;86(7):e00035-18. doi: 10.1128/IAI.00035-18. PMID: 29632248; PMCID: PMC6013676. |
| PATRIC | medium | igc | https://www.patricbrc.org; V3.6.7 |
| ProTraits | medium | igc | http://protraits.irb.hr/ |
| The Microbe Directory | low | nas | https://github.com/dcdanko/MD2 |
| Bergeys_2026 | high | exp | Bergey’s Manual of Systematics of Archaea and Bacteria, genus chapters (Wiley, ISBN 9781118960608), traits extracted from the published abstracts with an LLM in 2026; see sources/bergeys_2026 in https://github.com/waldronlab/bugphyzzExports |
| NCBI_RefSeq | high | igc | Goldfarb T, Kodali VK, Pujar S, et al. NCBI RefSeq: reference sequence standards through 25 years of curation and annotation. Nucleic Acids Res. 2025;53(D1):D243-D257. doi:10.1093/nar/gkae1038. https://ftp.ncbi.nlm.nih.gov/genomes/refseq/ (public domain); see sources/ncbi_assemblies in https://github.com/waldronlab/bugphyzzExports |