Microbial culture collections can help researchers during a research hiatus

Many academic, government agency, and industry research laboratories around the world are taking a break from lab work due to the COVID-19 health crisis. Although researchers who are not involved in COVID-19 research are ordering few supplies including microbe strains, other resources offered by culture collections can be helpful for manuscript and grant writing, and planning future lines of research. Here’s some ideas gathered from several US culture collections.

1.     Culture collections can provide updated information about strains you are already using. This is especially important if you received the strain from the collection years ago. Species names change due to taxonomic revisions, and you don’t want to use an obsolete species name in your manuscript. Examples: 

• Since 2016, hundreds of yeast species names have changed due to taxonomic revisions. A large proportion of basidiomycete species have been revised, and also many former Candida species have been changed to line up with their equivalent teleomorph genus. 
• Just last week (April 15, 2020), industrially important lactic acid bacteria genus Lactobacillus was divided into 24 genera (Zheng et al. 2020, IJSEM ijsem004107). This is so recent that culture collections that distribute these species may not have updated these genus and species names in their online catalogs yet. 

Online strain catalogs may have other new information about strains you received a few years ago, such as citation in other people’s publications or patents, DNA sequences, and new phenotype data. As you write your manuscripts, check in with the culture collections for updated information about the strains you are using.

• First stop: Look at the online catalog of the collection you ordered the strain from. There may be new information posted. Strain catalogs cross reference the strain ID number in other collections. 
• If the same strain is available from other collections (such as type strains and other frequently used strains), check the other collections' online catalogs too – different collections post different categories of information.
• Kyria Boundy-Mills, curator of the Phaff Yeast Culture Collection said, “We have updated about 300 species names in the last four years, but the strain ID number stays the same. One example: genus Rhodosporidium no longer exists. Look up the strain ID number in our online strain catalog (phaffcollection.ucdavis.edu) to confirm the current species name before you submit your manuscript. Also check recent taxonomy publications in case we missed an update.”
• Brandy Russell, curator of the Arbovirus Reference Collection said, “If you are having difficulty working with a viral isolate obtained from us we are always happy to consult. We may have found other cell types that work better for replication for that particular isolate. If additional sequencing of the isolate has been performed since you received it from us, we are happy to provide you with an updated product insert”

2.     Culture collections can help you select strains for your future research. Curators have extensive knowledge about the organisms in general, the specific strains held in the collection, and the associated data. If you tell them what question you are studying, or strain properties you desire, collection curators can guide you to some useful strains. For example:

• Curators can help you find strains with phenotypes or mutant genotypes related to the property you are studying.
• Collection curators can help you select strains or species whose genome has already been sequenced. 
• Inside secret: Many curators are willing to help researchers find strains in other culture collections to supplement what is not available from their own collection.
• The catalogs of over 130 culture collections around the world have been combined into one catalog: the Global Catalog of Microorganisms (http://gcm.wfcc.info). You may find a strain available from a collection you didn’t know about. Prices and distribution policies differ greatly among different collections.
• Boundy-Mills said, “Several years ago, we helped a researcher find yeasts able to perform a certain function at low pH. Based on our knowledge of the collection, we selected a variety of yeast strains that were originally isolated from low pH environments such as fruits. The best performing strain was originally isolated from citrus fruit juice. Other strains of that same species isolated from less acidic environments did not perform as well. Another example: A researcher wanted to compare fungicide resistance genes in strains of an environmental yeast species collected before vs. after agricultural pesticides were commonly used. We were able to provide several strains collected many decades ago.”
• Russell said, “We have a large number of unpublished isolates and can help you select isolates in addition to those found in the published literature.”

3.     Culture collection websites have new strains and new data, which may inspire some new research ideas. Collections preserve and distribute organisms of course, but they also act as a repository for information about those organisms. 

• Culture collections acquire new strains continually, sometimes as large sets. Last year, 13 people associated with 12 different US culture collections co-authored the publication, “Preserving US microbe collections sparks future discoveries”. (J Appl Microbiol, doi:10.1111/jam.14525). This paper lists 26 sizeable sets of strains that were deposited into 10 different culture collections. Check in with your favorite collections for newly acquired strains -- you may find some pleasant surprises.
• The genome sequences of 2,199 strains in the E. coli Reference Center are now incorporated into NCBI’s Pathogen Detection pipeline, which includes a screen for virulence and antibiotic resistance genes.  It can be accessed here: https://www.ncbi.nlm.nih.gov/pathogens/isolates#/search/PSU.  This table can be searched so researchers can identify isolates with specific combinations of genes they are interested in.  This table can also be sorted, identifying things such as the isolate with the most number of resistance genes. Current record holder: a calf isolate carrying 28 antibiotic resistance genes!
• Boundy-Mills said, “The Phaff Yeast Culture Collection online catalog recently added a searchable field for the substrate category, which may be particularly informative for microbiome analysis. You can now generate lists of yeasts in the Phaff collection that originated from certain types of buildings, dairy products, food fermentations, flower nectar, decaying wood, insects, trees, air, water, and many other categories.”

The participating collections in the US Culture Collection Network (USCCN.org) hope these ideas help researchers continue their innovative studies using microbial culture collections, now and for years to come. Now is a good time to reach out to culture collection curators to explore ideas.

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Authors:

Kyria Boundy-Mills, Phaff Yeast Culture Collection, University of California Davis

Brandy Russell, Arbovirus Reference Collection, Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Arboviral Diseases Branch

Edward Dudley, E. coli Reference Center, Pennsylvania State University