Paper says: To all microbiologists everywhere – deposit your strains in public collections – I agree

This is a very very important paper for all people who culture strains of microbes as part of their work: SpringerPlus | Abstract | Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science.

Abstract:

Despite recommendations to release microbial resources to the community post-publication, the reality is far from satisfying. A workshop discussed the need for a coordinated and effective deposition policy for ‘key’ microbial strains and proposes a set of criteria to facilitate their deposition into public service collections. The majority of authors either contacted directly or during submission of manuscripts to several international, mainly European bacteriology journals agreed to this set of ‘key strain’ criteria and to the voluntarily deposition of resources into public resource centres.

Some quotes from the artilce that are very important:

Of 20,200 prokaryotic strains reported in 835 articles in eight European journals in 2008, only 190 strains (0.94%) were deposited in public collections.

Against this background, we recommend a set of selection criteria that would allow all stakeholders to prioritize material for deposition.

There are currently about 2,391 million microbial strains available in the 660 collections listed in the World Data Centre for Microorganisms (http://www.wfcc.info/datacenter.html). There are about 694,000 fungi representing the approximately 100,000 fungal species described (Rossmann 1995), and about 1,024,000 bacteria and archaea representing the 10,600 or so validly named species (http://www.bacterio.net/).

Then they make some recommendations for how to decide what to desposit

The following criteria were agreed:

For Prokaryotes:

– Phylogenetic uniqueness, based on a cutoff point of ≤98% of 16S rRNA gene sequence from its nearest phylogenetic neighbor. This sequence is the gold standard for phylogenetic affiliation of an isolate at the genus level;

– Metabolic uniqueness, based on the presence of a new pathway, modification of an existing pathway, metabolic differences compared to the type strain or novel products including any strains with demonstrated useful properties i.e. production of specific molecule, biopesticide, biofertilizer, degradation of specific compounds, etc. to facilitate biotech exploitation;

– Genomic uniqueness, such as significant differences (≥20%) in genome size, genome architecture or new regulatory mechanisms;

– Resources and parts thereof with fully sequenced genomes (microorganisms, phages, plasmids);

– A second strain of those species for which only the type strain has been described. 79% of new species described in 2009 are based on the type strain only (Stackebrandt 2010);

– Strains associated with significant or new plant and animal diseases in order to ensure reliable reference material is available for diagnostic services and activities;

– Strains from unexplored or extreme environments (e.g. naturally extreme environments, foodstuffs, polluted environments) to reduce the gaps in the holdings, to study adaptation etc….;

For fungi:

– (Ex-) type strains of novel taxa — currently there is not a mandatory process for storing living cultures of the dead dried reference material for fungal types;

– Phylogenetic uniqueness, based on significant differences in the various phylogenetic markers defined for yeasts and fungi (e.g. ITS, D1/D2, SSU, LSU, EF1-alpha, tubulin, etc.);

– Metabolic uniqueness, based on the presence of a new pathway, modification of an existing pathway, metabolic differences compared to the type strain or novel products; including any strains with demonstrated useful properties i.e. production of specific molecule, biopesticide, biofertilizer, degradation of specific compounds, etc. to facilitate biotech exploitation;

– Any strain associated to a complete (or partial) nuclear genome sequence (as a reference and/or as part of future population studies). This includes the genomic uniqueness criteria of the prokaryote list;

– Strains from population studies (to further estimate biodiversity in various niche, environment, substrate etc….);

– Several strains of those species for which only the type strain has been described (to allow delineation of species and to find strains with opposite mating types for genetic experimentation and strain improvement);

– Strains from unexplored or extreme environments (naturally extreme environments, foodstuffs, polluted environments etc.) to reduce the gaps in the holdings, to study adaptation etc.;

– Strains associated with significant or new plant and animal diseases in order to ensure reliable reference material is available for diagnostic services and activities.

They also report on a workshop on a related topic

The workshop participants stressed that:

  • authors should make every reasonable effort to make material available;
  • journals and funding agencies should monitor their policies and have a mechanism for accepting complaints where access to material is denied;
  • journals should introduce a mechanism for active agreement by authors to make material available when they submit an article;
  • microbial resource collections should develop strategies and secure funding for the expected need to expand infrastructure and personnel (Smith et al. 2014).

These recommendations are critical for any microbiology – related field especially the new ones like microbiome studies of various plants and animals and microbial ecology studies of buildings (e.g., microBEnet types of projects).

On a related note, I would like to point out that I and a few others (including the lead author of this paper here) wrote a paper in 2000 emphasizing the need to deposit strains in collections and proposed a mechanism whereby for genome sequencing projects those strains sequenced should be obtained from the collection so that anyone else who wanted to work with the same strain could get it directly from the source.  The paper was: Sequenced strains must be saved from extinction in Nature and alas was published before I become a supporter of Open Access so it is not freely available via Nature.  I have posted the PDF on my web site.  I am poasting the text of the artcile here because I think it is important

Sequenced strains must be saved from extinction

Sir – Many prokaryotic strains used for genome sequencing projects are poorly documented and not generally available.

With improvements in sequencing technology and growing recognition of the value of microbial genome sequence data, the number of microbial genome- sequencing projects is increasing rapidly. There are 56 completed prokaryotic genome sequences (10 strains of Archaea and 46 of Bacteria), and another 210 in progress (see, for example, www.tigr.org and www.integratedgenomics.com).

Of these 266 projects, some of which are performed on organisms not available in pure culture – some endosymbionts, for example – only 51 represent the type strain of the species. (A type strain is made up of living cultures of an organism descended from the nomenclatural type.) Of the rest, 138 represent non-type strains (a non-type strain is often selected only because it happens to be close at hand); 31 projects concern symbionts and environ- mental (uncultured) strains; 32 do not specify a strain; 14 represent prokaryotic species with invalid species names (validly named bacterial species are either on the 1980 approved lists of names, or validated after 1980 by taxonomic description in the International Journal of Systematic and Evolutionary Microbiology, or by validation in that journal: an invalid name has no standing in nomenclature and may be changed subsequently. Only 115 represent the type species of the genus (the typus of the genus included when the genus name was originally validly published) and only 123 are deposited in public culture collections. Mandatory deposition of the type strain of any validly described (culturable) prokaryotic species in a major public culture collection guarantees the availability of the strain and allows cross- referencing of published data.

When there were only a few projects, these taxonomic and preservation issues were not so evident. With the explosion in sequencing and the sequencing of multiple strains of a species (including Escherichia coli, Staphylococcus aureus and other major pathogens), questions of strain identity and safekeeping assume more importance. Deposition of strains in public collections with long-term funding is the only way to ensure their maintenance and their continuing availability to the scientific community. As things stand, it is a real possibility that a strain for which a wealth of genomic data has been generated may become “extinct” through loss of viability.

We propose that the following standards should be adopted by the entire community. First, genome-sequencing project lists and databases should include the name of the strain sequenced and its associated culture collection accession number(s), as well as its origin. Second, the type strain of a species should be used for sequencing unless other factors make this inappropriate. Third, strains for which genome sequences have been, or are being, generated should be deposited in at least two major public biological resource centres, such as the American Type Culture Collection, the German Collection of Microorganisms and Cell Cultures, the Pasteur Institute Collection or the Japanese Collection of Microorganisms.

Naomi Ward*, Jonathan Eisen*, Claire Fraser*, Erko Stackebrandt†

*The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA †German Collection of Microorganisms and Cell Cultures, Mascheroder Weg 1b, D-38124 Braunschweig, Germany

public collection

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.