Do you know where to find the isolation source of all bacteria?

Question

[Giulia.cosenza]

Do you know where to find the isolation source of all bacteria?

Answer 1

[Michael]

First, when you talk of isolation sources, this term is not well-defined. But I assume you mean geographic sampling location or coordinates of an isolate. Now you need to look for databases that store sample or isolate information. But keep in mind that some samples may not be isolates, they may be lab strains and that bacteria could live in very many places, some other species might have an unknown origin. I think you want something like this: let's have a look at Alcanivorax borkumensis, a species where already the name tells you its origin: https://mmp2.sfb.uit.no/MarRef/records/MMP3138202/ MarRef as part of the MarineMetagenomics Portal. I think this is an excellent resource, but this only works for marine meta-genomics samples or marine species. (Still, the location is not in exact geographic coordinates)

In NCBI, every taxon that has a BioSample may have recorded the sampling location/coordinates. In ENA, the same will be true, but look for example at this entry for Corallococcus: https://www.ebi.ac.uk/biosamples/samples/SAMN10026047 In ENA and in NCBI the location is "United Kingdom" which is pretty useless. Unfortunately, exact geo-locating biological samples has not been a thing until recently.

It is understandable that you want this information. For metagenomics projects, this is essential meta-data. Unfortunately, there are competing standards on how to store this type of information and variable record completeness. In Elixir-Norway, we have a work-package dedicated to biodiversity and we are working on improving and harmonizing meta-data standards for all sorts of studies related to biodiversity. So, for some species, you will have success and it is good to draw attention to the relevance of geographic data and meta-data in particular, but I still doubt that this undertaking is worth the effort for ALL species at the moment.

[Giulia.cosenza]

Thank you Michael! This link

[https://www.ebi.ac.uk/biosamples/samples/SAMN10026047][1]

really helped! In fact the page shows 'isolated from soil' and that is what I was looking for, the source of isolation.

Basically I did a taxonomic analysis on metagenomic sequencing output and I was trying to understand where the bacteria I have obtained come from, so I need those information.

[Michael]

Great, and there is also the term "isolation source" you were looking for in the first place, so I admit I was wrong stating it is not defined (and I should have known :) ). So if it is in annotation, it should be possible to extract it automatically for all samples in ENA at least.

Also, for MarRef, it is annotated that way:

Isolation source Sea water sediment suspension

[Giulia.cosenza]

And how can I extract it automatically for all samples in ENA?

Answer 2

[GenoMax]

Based on the clarification provided (and the example provided) this can be extracted from SRA using Entrezdirect:

$ esearch -db biosample -query SAMN10026047 | efetch            
1: Corallococcus genome_CA054A
Identifiers: BioSample: SAMN10026047; Sample name: Corallococcus CA054A
Organism: Corallococcus terminator
Attributes:
    /strain="CA054A"
    /isolation source="soil"
    /collection date="2016-09-28"
    /geographic location="United Kingdom"
    /sample type="Bacterial Isolate"
    /identified by="Aberystwyth University"
    /type-material="type strain of Corallococcus terminator"
Accession: SAMN10026047 ID: 10026047

Original question was broad without a specific context.