3rd Party Upload File Format

Bacteria names are moving targets and unreliable for analysis by themselves. The only reliable way to identify a bacteria is by taxon number.

Taxon numbers are supplied in:

  • uBiome files (no longer in business)
  • Thryve Alive files
    • FastQ Files from any provider may be uploaded to Thryve to obtain taxon numbers.
  • biomesight has indicated that they are adding them to their downloads

The microbiome.com site is built off of taxon numbers and not names.

Support for non-taxon number uploads has ended. The data has too much risk of being inaccurate or incomplete because the data has to go thru textual data mining which rarely exceeds 85% accuracy. These diminishes the power of the uploads for research and analysis. Each variation of an upload files runs about $5,000 of time (at my typical billing rates) to implement and then test.

The existing non-taxon number uploads will continue to be available on an “As Is” basis with no support or enhancements.

Contact your 16s provider!

Many providers should be able to add taxon numbers to their reports easily. All of the data is freely available. Your provider may need to get a software update from the manufacturer of their lab equipment.

The recommended minimum format for a CSV or Json file is simple:

  • Taxon
  • Count In Sample
  • Count as percentage OR Count per million

Names, hierarchies and other information may be included. This extra data will be ignored and only the taxon and counts used.

Some examples of supported uploads:

tax_name,tax_rank,count,count_norm,taxon,parent
Bacteroidaeota,phylum,536380,536380,976,68336
Actinobacteria,class,10,525790,1760,201174
Bacteroidales,order,525600,525600,171549,200643
Bacillaeota,phylum,339560,339560,1239,1783272

and

taxon_id,rank,name,parent,count
459786,genus,Oscillibacter,Oscillospiraceae,3091
216572,family,Oscillospiraceae,Clostridiales,3091
186802,order,Clostridiales,Clostridia,32864
186801,class,Clostridia,Firmicutes,32889

and

{
"download_time_utc": "8/24/2019 12:00:00 AM",
"sequencing_revision": "1234567",
"site": "gut",
"sampling_time": "1/1/2022 12:00:00 AM",
"notes": "http://microbiomeprescription.azurewebsites.net:Ubiome - Example",
"ubiome_bacteriacounts": [
{
"taxon": 131567,
"parent": 1,
"count": 75946,
"count_norm": 1003216,
"tax_name": "cellular organisms",
"tax_rank": "no_rank"
},
{
"taxon": 1,
"parent": 1,
"count": 75946,
"count_norm": 1003216,
"tax_name": "root",
"tax_rank": "root"
},

or

"taxon_id","rank","name","parent","count","rank_count","perc"
"200643","class","Bacteroidia","Bacteroidetes","27541","52379","0.5258023253593997"
"186801","class","Clostridia","Firmicutes","19766","52379","0.37736497451268636"
"201174","class","Actinobacteria","Actinobacteria","1419","52379","0.02709100975581817"
"31969","class","Mollicutes","Tenericutes","402","52379","0.007674831516447431"

or

"taxon_id","rank","name","parent","count","tags","health_effects","associated_diseases"
"53443","species","Blautia hydrogenotrophica","Blautia","1236","","",""
"572511","genus","Blautia","Lachnospiraceae","4241","commensal,probiotic","Help improve the gut microbiota, reduces the growth of bad bacteria, reduces the risk of host vs. graft rejection. It also has anti-inflammatory and immune modulating effects.","Rarely associated with human infections, only one case of human necrotizing fasciitis reported."
"186803","family","Lachnospiraceae","Clostridiales","10777","commensal,probiotic","Members of this family may protect against colon cancer in humans by producing butyric acid. It also offers protection against C. difficile infections and obesity. A reduction in these bacteria have found a consistent finding among patients with liver cirrhosis and non-alcoholic fatty liver disease. Furthermore, a reduction in these bacteria have found in patients with irritable bowel disease ( IBD).","Metabolic dysfunctions, Diabetes, Multiple sclerosis, Major depressive disorder, Autism, Inflammatory bowel disease ( IBD), Nonalcoholic fatty liver disease."
"186802","order","Clostridiales","Clostridia","18762","","",""
"186801","class","Clostridia","Firmicutes","18763","commensal,path