<p>I ended up copying the GenBank (primary) column from the REBASE search results into an excel sheet. From there, I created a file with one accession per line called <code>Psych_Accessions.txt</code>. I then ran the following command using NCBI's command line tools.</p>
<pre><code>epost -db nuccore -input Psych_Accessions.txt -format acc | efetch -format fasta &gt; psych_genomes.fasta
</code></pre>

CC BY-SA 4.0
2023-07-04T00:21:03.493Z
2023-07-04T00:21:03.493Z
donkey
<p>The database to use is BactoTraits. This will help either in the entirety or at least provide a solid starting point. Its here</p>
<p><a href="https://www.sciencedirect.com/science/article/pii/S1470160X21007123" rel="nofollow noreferrer">BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities</a>
by Aurélie Cébron (2021) Ecological Indicators 130</p>
<blockquote>
<p>We have created a user-friendly database of bacterial functional traits, thanks to the properties of <strong>19,455 bacterial strains</strong>. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and <strong>temperature</strong>, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations.</p>
</blockquote>
<p>Thus it's nearly 20000 species so your batteria should be there.</p>
<p>You can download the exact database <a href="https://ordar.otelo.univ-lorraine.fr/record?id=10.24396/ORDAR-53" rel="nofollow noreferrer">here</a>. This is Univ de Lorraine's site, France. Its 9.4MB and called</p>
<blockquote>
<p>BactoTraits_databaseV2_Jun2022.csv</p>
</blockquote>
<p>The supplementary information in the paper gives all the details for interpreting the database columns.</p>
<p>Given your skills in development you should have no trouble converting the <strong>csv</strong> format into a functional database and interrogating/querying it. My understanding of the paper is that the authors are microbiologists rather than coders, which in context is perfect.</p>
<hr />
<p>Linking NCBI</p>
<p>BactoTraits contains two strain designations</p>
<ul>
<li>DSM no. (<a href="https://www.dsmz.de/collection/catalogue/microorganisms/catalogue" rel="nofollow noreferrer">https://www.dsmz.de/collection/catalogue/microorganisms/catalogue</a>)</li>
<li>ATCC no. for example  ATCC BAA 1260 is <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=364410" rel="nofollow noreferrer">here on NCBI</a> <em>Granulibacter bethesdensis</em>, which checks out on BactoTraits and is DSM 17861</li>
<li>txid364410[Organism:exp]  is the SRA number from the above link ... so its all there, and here <a href="https://www.ncbi.nlm.nih.gov/sra/?term=txid364410%5BOrganism:exp%5D" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/sra/?term=txid364410[Organism:exp]</a></li>
</ul>
<p>So ATCC links to NCBI links to the SRA and genome.</p>
<p>DSM are not necessarily available on NCBI, but ATCC will there. NCBI do have lots of databases for download, a database comprising ATCC to NCBI genome ... dunno, but <em>Entrez</em> will be able to link the ATCC (American Type Culture Collection)</p>

CC BY-SA 4.0
2023-07-02T03:09:52.570Z
While this is a great database for getting the names of psychrophiles, I was hoping for something that would tie temperature optima to NCBI project numbers or other direct genomic artifacts to make it easier to download. I will keep this question open for a bit longer before marking your answer.
donkey
CC BY-SA 4.0
2023-07-02T04:08:05.977Z
Comment answered about below the line @donkey
M__
CC BY-SA 4.0
2023-07-02T02:21:26.523Z
2023-07-02T04:07:39.093Z
2023-07-02T04:07:39.093Z
M__
<p>I am interested in running an analysis on the genome of every psychrophilic bacteria. Here defined as bacteria that have an optimal growth temperature at less than 15°C.</p>
<p>What would be the best way to go about collecting these?</p>
<p>I have yet to find a &quot;growth temperature&quot; filter on databases like NCBI. Though REBASE does include that (however obtaining the genomes from that site does not seem straightforward).</p>
<p>Thank you</p>

<metagenome><wgs><bacteria>
What would be the best method to obtain every prokaryotic psychrophile genome?
# What would be the best method to obtain every prokaryotic psychrophile genome?

(Asked by: username_0 on 2023-07-02)

I am interested in running an analysis on the genome of every psychrophilic bacteria. Here defined as bacteria that have an optimal growth temperature at less than 15°C.

What would be the best way to go about collecting these?

I have yet to find a "growth temperature" filter on databases like NCBI. Though REBASE does include that (however obtaining the genomes from that site does not seem straightforward).

Thank you

**Tags:** metagenome, wgs, bacteria

---

## 2 answers

### Answer by username_0 on 2023-07-04. Score: 2 | Accepted answer

I ended up copying the GenBank (primary) column from the REBASE search results into an excel sheet. From there, I created a file with one accession per line called Psych_Accessions.txt. I then ran the following command using NCBI's command line tools.
epost -db nuccore -input Psych_Accessions.txt -format acc | efetch -format fasta > psych_genomes.fasta


---

### Answer by username_1 on 2023-07-02. Score: 2

The database to use is BactoTraits. This will help either in the entirety or at least provide a solid starting point. Its here

[BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities](https://www.sciencedirect.com/science/article/pii/S1470160X21007123)
by Aurélie Cébron (2021) Ecological Indicators 130

> We have created a user-friendly database of bacterial functional traits, thanks to the properties of **19,455 bacterial strains**. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and **temperature**, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations.

Thus it's nearly 20000 species so your batteria should be there.

You can download the exact database [here](https://ordar.otelo.univ-lorraine.fr/record?id=10.24396/ORDAR-53). This is Univ de Lorraine's site, France. Its 9.4MB and called

> BactoTraits\_databaseV2\_Jun2022.csv

The supplementary information in the paper gives all the details for interpreting the database columns.

Given your skills in development you should have no trouble converting the **csv** format into a functional database and interrogating/querying it. My understanding of the paper is that the authors are microbiologists rather than coders, which in context is perfect.

---

Linking NCBI

BactoTraits contains two strain designations

* DSM no. (<https://www.dsmz.de/collection/catalogue/microorganisms/catalogue>)
* ATCC no. for example ATCC BAA 1260 is [here on NCBI](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=364410) *Granulibacter bethesdensis*, which checks out on BactoTraits and is DSM 17861
* txid364410[Organism:exp] is the SRA number from the above link ... so its all there, and here [https://www.ncbi.nlm.nih.gov/sra/?term=txid364410[Organism:exp]](https://www.ncbi.nlm.nih.gov/sra/?term=txid364410%5BOrganism:exp%5D)

So ATCC links to NCBI links to the SRA and genome.

DSM are not necessarily available on NCBI, but ATCC will there. NCBI do have lots of databases for download, a database comprising ATCC to NCBI genome ... dunno, but *Entrez* will be able to link the ATCC (American Type Culture Collection)

> **Comments:**
> **username_0**: While this is a great database for getting the names of psychrophiles, I was hoping for something that would tie temperature optima to NCBI project numbers or other direct genomic artifacts to make it easier to download. I will keep this question open for a bit longer before marking your answer.  
> **username_1**: Comment answered about below the line @donkey  

---

