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PLoS ONE issues expression of concern when company won’t share bacterial strain

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plosoneThe editors of PLoS ONE have issued an expression of concern for a 2014 article on a form of nitrogen-fixing bacteria called Bacillus pumilus.

The reason: The company that provided the strain of microbe used in the research won’t let other researchers look at the organism.

The article is titled “Bacillus pumilus Reveals a Remarkably High Resistance to Hydrogen Peroxide Provoked Oxidative Stress,” and it came from a group led by Stefan Handtke, of the University of Greifswald, in Germany.

Here’s the notice:

Following publication of this article, a reader made a request for the Bacillus pumilus Jo2 strain employed in this study.

The PLOS ONE policy governing the sharing of materials and data that applies to articles submitted before March 3, 2014, requires that authors agree to make freely available any materials and data described in their publication that may be reasonably requested for the purpose of academic, non-commercial research.

The journal evaluated the request and concluded that it falls within the requirements of the policy above. The journal has contacted the authors, who indicated that Henkel, the company that provided the strain, will not share the strain or its genome sequence with other researchers and that they were not aware of this restriction on the availability of the strain at the time at which the study was conducted. This is not in line with the journal’s policy and the authors’ declaration of adherence to its requirements.

The editors are issuing this Expression of Concern to alert readers about the fact that the Bacillus pumilus Jo2 strain employed in this study is not available, and thus that the article is in breach of the journal’s editorial policy.

And here’s the abstract of the article in question:

Bacillus pumilus is characterized by a higher oxidative stress resistance than other comparable industrially relevant Bacilli such as B. subtilis or B. licheniformis. In this study the response of B. pumilus to oxidative stress was investigated during a treatment with high concentrations of hydrogen peroxide at the proteome, transcriptome and metabolome level. Genes/proteins belonging to regulons, which are known to have important functions in the oxidative stress response of other organisms, were found to be upregulated, such as the Fur, Spx, SOS or CtsR regulon. Strikingly, parts of the fundamental PerR regulon responding to peroxide stress in B. subtilis are not encoded in the B. pumilus genome. Thus, B. pumilus misses the catalase KatA, the DNA-protection protein MrgA or the alkyl hydroperoxide reductase AhpCF. Data of this study suggests that the catalase KatX2 takes over the function of the missing KatA in the oxidative stress response of B. pumilus. The genome-wide expression analysis revealed an induction of bacillithiol (Cys-GlcN-malate, BSH) relevant genes. An analysis of the intracellular metabolites detected high intracellular levels of this protective metabolite, which indicates the importance of bacillithiol in the peroxide stress resistance of B. pumilus.

Written by amarcus41

July 16th, 2014 at 9:30 am

Comments
  • ed goodwin July 16, 2014 at 9:46 am

    Plos seems to be following the half measure weak process of the established journals. Expression of concerns are the wimps way of saying “we know there is a problem” but WE ARE NOT GOING TO DO WHAT IS RIGHT: RETRACTION.

  • lar July 16, 2014 at 10:01 am

    “the article is in breach of the journal’s editorial policy.”

    And why, pray tell, did PLoS ONE not see fit to retract this article? If the authors breached the journal’s policy, and as a result submitted an article describing unreproducible studies, what is the justification for keeping it around?

    • KK July 16, 2014 at 11:05 am

      it may be difficult to have a concrete editorial policy with thousands of editorial board members!!

  • Eibl July 16, 2014 at 10:32 am

    These things happen all the time. It is almost impossible that a journal really sticks to its rules. I can understand that sometimes a research lab does not work any longer on an old, for example, human tumor cell line and the responsible persons moved on with their careers, or that too many scientists ask for a free supply of a widely used cell line. I know so many bad examples and antibodies “cooked” (and ruined) before sending them to a competitor, but I also know a few good examples, where the institution asked for some handling fees and a rigorous MTA (material transfer agreement), which needed to be checked and slightly modified by the university’s lawers. In that case the handling fees for thawing and growing and checking the original cells was really OK. But it was also understandable in the 1990s when labs invested lot of human and financial ressources to make one or several K.O. mouse strains that they never even thought of sharing any of them with their competitors. Some people said: To have or not to have (the K.O. mouse strain). I am sure the official policy of most journals was similar that published “material” should be shared, but almost nobody shared an expensive new K.O. mouse strain. I hope the company retracts the article itself – or shares the bacterial strain. Otherwise the journal should retract the article later. It is just dishonest behaviour to not stick to the honor rules.

    • ed goodwin July 16, 2014 at 10:46 am

      All publishers should adhere to one strict rule: Tell us everything or we are not going to the vehicle for
      your manuscript with secrets and if we find out that we were duped, we will, without exception retract it period.

      Further, you might consider your publication as a commercial advertisement rather than use the cloak of science.

  • BB July 16, 2014 at 12:03 pm

    The scope of PLos ONE is rather unspecific, so would be careful not to blame them prematurely. This is a much more common problem in the material science, and in fact most major journals of that field now have explicit rules about this. Altogether there is not much to discuss, if no one can access to this strain, then the results of this paper can not be validated or implemented by external investigators, thus it has no use for the scientific community, and should not have been published. This article should be pulled for good, mainly as otherwise it will serve as a green light for other academic researchers with far too cordial ties to commercial entities, that they can start publishing their own “proprietary” findings.

  • Dan Zabetakis July 16, 2014 at 4:37 pm

    The expression of concern is unlikely to be the last we hear about this.

    In the paper they write “Bacillus pumilus Jo2 (DSM 14395)…” which seems to indicate that the strain is available from the DSMZ depository. Except when I had a quick look there was no entry for 14395 (or else I couldn’t find it). I also note that none of the authors are employed by that company (one author was previously employed by them). There is no explanation as to how the company can stop the distribution of the strain.

    Clearly some further investigation is called for.

  • Deidentified July 16, 2014 at 7:03 pm

    There is one other reference to DSM 14395 and that is from google patents:

    http://www.google.nl/patents/DE102012201297A1?cl=en

    “A method according to any one of claims 1 to 4, characterized in that it is the microorganism is Bacillus pumilus DSM 14395th”. Some of the names from the paper overlap. The micro-organism catalog for DSMZ doesn’t show anything, as you note.

    From the paper itself, it merely states “Bacillus pumilus Jo2 (DSM 14395) was used for all experiments
    described in this study.” (the statement that the strain came from Henkel is relayed by Plos). The only relationship I can see to Henkel is found elsewhere in the paper. “Probe design was performed on the chromosome sequence of B. pumilus Jo2 (Sequence Intellectual Property of Henkel KGaA). ”

    It would seem strange for a company that refuses to share a strain or a FASTA file to deposit the sequence with DSM. Perhaps this particular bug was not deposited with DSM after all. Perhaps someone should notify DSMZ that someone is pretending bugs are DSMZ deposited, or is purposefully obfuscating DSMZ numbers to prevent followup?

    • Deidentified July 16, 2014 at 7:10 pm

      More of the story comes from http://www.microbialcellfactories.com/content/13/1/46

      There’s a table that describes where the strains come from. I find:

      “B. pumilus Jo2 Wild type Henkel AG & Co. KGaA”

      Which tells me the history of this strain is that of a wild-type isolate found/owned by the company. I suppose this paper may have to be moved to a different journal.

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