Organism & Taxonomy
Every sample needs an NCBI Taxonomy ID. ENA rejects a sample registration without one, several pipelines use it to pick reference databases, and it is the only machine-readable statement of what was actually sequenced. The Organism column in the sample table is where you set it.
How the lookup works
The Organism field is an autocomplete over a curated list of 71 taxa compiled into the application. It is not a live NCBI query, and it works offline.
This matters more than it sounds. If your organism is not one of the 71, the autocomplete will show no match — that is expected, not a bug. Type the numeric taxId instead (see Entering a taxId by hand).
Behaviour of the search:
- Nothing happens until you type two characters.
- Results are ranked: an exact
taxIdmatch wins outright, then scientific name prefix, common name prefix, word-start matches, substring matches and finally category matches. - The sample-table cell shows up to 6 results; the standalone Organism field used elsewhere shows up to 8.
- Each result shows the scientific name, the taxId in monospace, and its category badge.
- Selecting a result writes both
taxIdandscientificNameto the sample. - A Search NCBI for ”…” link at the bottom of the dropdown opens the NCBI Taxonomy browser pre-filled with what you typed.
Once a taxId is set, the table cell shows it as a small badge on the right-hand edge of the field, so you can scan a column of 96 samples for the odd one out.
What is in the list
The 71 entries are grouped into ten categories.
| Category | Count |
|---|---|
| Environmental Metagenome | 14 |
| Bacteria | 10 |
| Host Organism | 10 |
| Human Metagenome | 9 |
| Animal Metagenome | 7 |
| Other Metagenome | 7 |
| Fungi | 4 |
| Plant Metagenome | 4 |
| Virus | 4 |
| Archaea | 2 |
Metagenomes
For environmental and community samples where no single species can be named, ENA requires a metagenome taxon rather than an organism. The full built-in set:
| Tax ID | Scientific name | Category |
|---|---|---|
| 408170 | human gut metagenome | Human |
| 447426 | human oral metagenome | Human |
| 539655 | human skin metagenome | Human |
| 433733 | human lung metagenome | Human |
| 1202446 | human vaginal metagenome | Human |
| 749907 | human nasopharyngeal metagenome | Human |
| 1202531 | human urogenital metagenome | Human |
| 1076179 | human milk metagenome | Human |
| 428 | human metagenome | Human |
| 410661 | mouse gut metagenome | Animal |
| 1510822 | pig gut metagenome | Animal |
| 1510823 | chicken gut metagenome | Animal |
| 749906 | bovine gut metagenome | Animal |
| 1510824 | fish gut metagenome | Animal |
| 1510825 | insect gut metagenome | Animal |
| 1510826 | invertebrate gut metagenome | Animal |
| 410658 | soil metagenome | Environmental |
| 449393 | freshwater metagenome | Environmental |
| 408172 | marine metagenome | Environmental |
| 412755 | sediment metagenome | Environmental |
| 717931 | freshwater sediment metagenome | Environmental |
| 443218 | marine sediment metagenome | Environmental |
| 527639 | wastewater metagenome | Environmental |
| 527640 | activated sludge metagenome | Environmental |
| 527641 | sludge metagenome | Environmental |
| 556182 | groundwater metagenome | Environmental |
| 652676 | hydrothermal vent metagenome | Environmental |
| 1169740 | cold seep metagenome | Environmental |
| 1034836 | permafrost metagenome | Environmental |
| 939928 | glacier metagenome | Environmental |
| 556180 | rhizosphere metagenome | Plant |
| 1348798 | phyllosphere metagenome | Plant |
| 1169741 | root metagenome | Plant |
| 939929 | compost metagenome | Plant |
| 412532 | air metagenome | Other |
| 1169742 | dust metagenome | Other |
| 652107 | biogas fermenter metagenome | Other |
| 718308 | bioreactor metagenome | Other |
| 1379530 | food metagenome | Other |
| 1437825 | fermentation metagenome | Other |
| 256318 | metagenome | Other |
Isolates and hosts
| Tax ID | Scientific name | Common name |
|---|---|---|
| 9606 | Homo sapiens | human |
| 10090 | Mus musculus | house mouse |
| 10116 | Rattus norvegicus | Norway rat |
| 9913 | Bos taurus | cattle |
| 9823 | Sus scrofa | pig |
| 9031 | Gallus gallus | chicken |
| 7955 | Danio rerio | zebrafish |
| 7227 | Drosophila melanogaster | fruit fly |
| 6239 | Caenorhabditis elegans | nematode |
| 3702 | Arabidopsis thaliana | thale cress |
| 562 | Escherichia coli | — |
| 1280 | Staphylococcus aureus | — |
| 287 | Pseudomonas aeruginosa | — |
| 1313 | Streptococcus pneumoniae | — |
| 1351 | Enterococcus faecalis | — |
| 1423 | Bacillus subtilis | — |
| 1773 | Mycobacterium tuberculosis | — |
| 210 | Helicobacter pylori | — |
| 1639 | Listeria monocytogenes | — |
| 573 | Klebsiella pneumoniae | — |
| 2287 | Methanobacterium formicicum | — |
| 2162 | Methanobrevibacter smithii | — |
| 4932 | Saccharomyces cerevisiae | baker’s yeast |
| 5476 | Candida albicans | — |
| 5061 | Aspergillus niger | — |
| 5141 | Neurospora crassa | — |
| 2697049 | Severe acute respiratory syndrome coronavirus 2 | SARS-CoV-2 |
| 11676 | Human immunodeficiency virus 1 | — |
| 10298 | Human alphaherpesvirus 1 | HSV-1 |
| 12814 | Respiratory syncytial virus | — |
Entering a taxId by hand
Anything outside the list is entered as a bare number.
- Look the organism up at NCBI Taxonomy and copy its numeric ID.
- Type only the digits into the Organism cell — no name, no prefix.
- Click or tab away. On blur, SeqDesk checks whether the number is one of the 71. If it is, the matching name is filled in. If it is not, the taxId is stored and a placeholder scientific name is written.
The placeholder text differs by surface, because two components implement the field:
| Surface | Placeholder written to scientificName |
|---|---|
| Sample table cell | Unknown (TaxID: 1358) |
| Standalone organism field | Unknown organism (TaxID: 1358) |
SeqDesk never verifies a taxId. There is no call to NCBI, no checksum, no
range check. A typo such as 9066 instead of 9606 is accepted silently and
will only surface as an ENA rejection weeks later. Paste, do not retype.
You can overwrite the placeholder name afterwards — nothing depends on the
Unknown … text — but leaving it in place is a useful marker that the entry was
never confirmed against the curated list.
Why the taxId matters
| Consumer | What it uses the taxId for |
|---|---|
| ENA submission | Every registered sample must carry a valid NCBI taxonomy ID; ENA also cross-checks it against the checklist type |
| MIxS checklists | An environmental metagenome taxon is what makes an environment package appropriate |
| Pipelines | Taxonomic classification and reference database selection |
| Assemblies and bins | Downstream records inherit the sample’s organism context |
The most common real mistake is using a host species where a metagenome is meant.
If you sequenced a stool sample, the organism is human gut metagenome (408170),
not Homo sapiens (9606). ENA will accept 9606 — and then your submission
describes a human genome.
Where taxonomy can be edited
| Location | When |
|---|---|
| The order wizard’s Samples step | While creating the order |
| The order’s sample table | While the order is DRAFT |
| Study metadata surfaces | Any time, for samples in that study |
Once the order is submitted, the organism becomes read-only along with the rest of the sample data — see Sequencing Order Lifecycle.
Troubleshooting
| Symptom | Cause | Fix |
|---|---|---|
| No dropdown appears | Fewer than two characters typed | Type at least two characters |
| ”No matches. Enter a valid NCBI Taxonomy ID” | Your organism is not in the 71-entry list | Type the numeric taxId instead |
The cell shows Unknown (TaxID: …) | A taxId outside the built-in list was entered | Expected. Confirm the number at NCBI |
| The taxId badge is empty after typing a name | A free-text name was typed and never matched | Only a selection from the dropdown, or a bare number, sets taxId |
| ENA rejects the sample’s organism | The taxId does not exist, or conflicts with the checklist | Re-check the ID at NCBI and see ENA troubleshooting |
Next
- Samples & Metadata — the rest of the sample record.
- Study Metadata & MIxS — choosing the checklist that goes with your organism.