Answers.Body: <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>
  
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Answers.Body: <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>
  
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Answers.Text: 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.
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Body: <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>
  
Tags: <metagenome><wgs><bacteria>
Title: What would be the best method to obtain every prokaryotic psychrophile genome?
ThreadText: # 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 @username_0  
  
  ---
  
  