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Choosing the Right Bacterial Strains for Your Lab

Posted in: Protein Expression and Analysis
Cartoon of bacteria to represent choosing bacterial strains for research

Choosing the Right Bacterial Strains for Your Lab

Whether you’re simply seeking competent E. coli for a transformation experiment or building a panel intended for a whole project, it’s vital that you pick the right bacterial strains for your experiment.

Whatever your intended use, it can be easy to miss critical variables when planning what bacterial strains to use, but this short read will teach you how to effectively single out the strains you need while avoiding potential pitfalls.

Common Uses of Bacteria in the Lab

There are almost endless reasons why a particular bacterial species or strain may need to be grown in the lab.

Some bacteria strains are workhorses for genetic laboratories and are often modified to be efficient vectors for producing recombinant proteins. Some are well-described model organisms that may be used to study fundamental cellular processes. Others have niche applications such as controls for experimental validation. We’ve got the lowdown on strain selection right here.

A Step-by-Step Guide to Strain Selection

Understanding Strain IDs

Before you begin, to help you navigate supplier catalogs you should make sense of the way strains are named. The “main” strain designation is the one assigned by the authors who first described it. For example, the type strain of Bacillus subtilis is named B. subtilis “Marburg”.

Authors are required to deposit strains that represent a new species, subspecies, or genetic variant in at least two publicly accessible culture collections in different countries. These culture collections act as central repositories of strain material, which can distribute authentic specimens for research purposes. Confusingly, different collections will list the same strains with different catalog IDs of their own!

Culture Collection Catalog IDs

For example, in the case of B. subtilis Marburg, the strain ID used by the American Type Culture Collection (ATCC) is ‘ATCC 6051’ but it is listed by the German Collection of Microorganisms and Cell Cultures as ‘DSM 10’.

However, some strains are curated by culture collections to fulfill a particular purpose by commission. For example, the ATCC ‘Global Priority Superbugs’ collection was sourced directly from clinical isolates harboring emerging antimicrobial resistance genes. In cases like this, the culture collection catalog ID could be considered the primary strain ID.

Keeping Track of IDs

This can complicate strain sourcing and it’s important to be aware that you may be looking at the same strain under two separate collection IDs. If possible, it’s good practice to keep a record of different IDs for the same strain. Usually, a collection will list IDs used elsewhere, but such lists are not always comprehensive. The best place to double-check strain IDs is The Bacterial Diversity Metadatabase (BacDive), which lists the original strain designation alongside the IDs used by different collections.

Considerations when Selecting a Supplier

Generally, the largest repositories of microbial strains are national culture collections.

Aside from the American and German culture collections previously mentioned, some of the more well-known culture collections to search include:

  • National Collection of Type Cultures (NCTC, Public Health England);
  • Culture Collection University of Gothenburg (CCUG);
  • Japanese Collection of Microorganisms (JCM);
  • Belgian Coordinated Collection of Microorganisms (BCCM).

There are many other national and private collections, and these can vary greatly in terms of:

  • catalogue size;
  • level of strain characterization;
  • sample formats available;
  • pricing;
  • permitted uses of strain materials.

If your organization doesn’t have a “go-to” supplier for strains and you need to pick one, it’s worthwhile investigating different collections and considering these factors to pick the best one for your needs.

What Paperwork Do You Need?

One crucial aspect to consider is the Material Transfer Agreement (MTA) that you would be required to enter into before using a collection’s strains. This legal document outlines what you’re allowed to do with the strain materials, and different collections can have different restrictions in place.

Be sure to read any MTA carefully before opting for a supplier to make sure you’re not falling foul of the conditions.

Can You “Borrow” a Strain from a Partner Laboratory?

For some specific applications, it could be that the strain you need hasn’t been deposited in a collection yet. Or you might just be looking to obtain specimens from a specific source or with particular characteristics, regardless of whether they have been typed and properly described.

If you’re wondering whether you can simply ask for a sample from a colleague or a partner laboratory, the short answer is “yes”—but with some caveats.

If the strain you’re seeking is derived from material already deposited in a collection, then you will likely need to arrange permission from the collection in question, in the process entering a new MTA. This can be complex and time-consuming and is often worth avoiding by just sourcing directly from the collection.

Otherwise, the sharing of the strain is at the discretion of the source laboratory, subject to any national or international restrictions on biosecurity or sharing biological resources. However, it is still good practice to make sure both labs have an MTA in place


The first thing to consider when picking a strain is—what do you need from it? Some factors that might help you narrow the search could be:

  • the phenotype of the strain;
  • the source or date of isolation;
  • the genotype of the strain;
  • the Biosafety classification of the strain.

Phenotype and Strain Source

The diversity that can be found within some bacterial species compared with others can vary and choosing an “outlier” strain could confound your experiment.

This can also be affected by the source of the strain. For example, in terms of optimal conditions for growth or resistance profile to antibiotics, “wild-type” strains of the same species isolated from a clinical sample and from the environment could be very different.

In cloning applications, the growth rate of an organism can be particularly important as the plasmid yield after a certain time will vary with the doubling time of the strain being used. If you need to harvest or process your cells during the exponential phase of growth, it is vital that you consider how the growth rate of a strain affects your overall process.


If selecting a competent strain for transformation, the genotype notation associated with a strain can give you an indication of whether a strain is suitable for your application. These follow a strict nomenclature, describing the presence or absence of certain genes (e.g., lacA). The symbols in Table 1 indicate the different type of mutation.

Table 1. Mutation notation symbols in genotype nomenclature




Deletion of a gene


Insertion of a gene


Constitutive mutation (i.e., uncontrolled expression)


Mutation conferring antibiotic resistance

Biosafety Classification

This last point is particularly important. The hazards associated with working with a species may vary between bacterial strains. For example, although most labs are permitted to work with most E. coli strains, more virulent strains such as E. coli O157:H7 require increased biosafety controls.

Type Strains

If you have no requirements other than the species, it is better to select a well-characterized strain. The more information available, the easier it may be to contextualize your results or troubleshoot.

Typically, the “type strains” of species are among the best studied. These are the strains that possess all the phenotypic and genotypic characters used in the taxonomic description of a species. However, do exercise caution, as type strains are not always the most representative of a species as a whole.

If you intend to use your strains as controls for a specific procedure or product (e.g., for antimicrobial susceptibility testing or validating a particular instrument), many strains are recommended by the manufacturer or regulatory guidelines as “quality control” or “reference” strains.

Where to Find Advice

If you’re still struggling to find bacterial strains that match your requirements, the BacDive record for a strain summarizes phenotypic data and can link you to any available NCBI genome assemblies.

In a pinch—ask! Curators at the collections are often able to select bacterial strains from your catalog that match your requirements or help you find the information you need to make your selection.

We’ve put some examples of specific bacterial strains commonly used for different procedures or experimental applications in Table 2 to help you get started.

Table 2. Commonly used strains and their applications



Escherichia coli

B/K-12 Strains (e.g. MG1655)

Large-scale pharmaceutical production of recombinant proteins

Caulobacter crescentus


Model organism for the study of bacterial cell cycles

Mycoplasma genitalium


Studies of reduced-genome organisms (e.g., synthetic biology applications or studying biochemical pathways)

Aliivibrio fischeri


Model organism for studies of quorum sensing, bioluminescence, and bacteria–animal symbiosis

Geobacillus stearothermophilus


Thermophile used as a control in verifying sterilization processes 

Do you have any tips for hunting bacterial strains? Let us know and share your experience in the comments below!

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