NCIMB culture collection deposits & services reflect growing microbiome research activity

NCIMB’s NGS services manager Dr Daniel Swan examines how developments in microbiome and probiotics research have been reflected in activity at NCIMB, from additions to their culture collection to provision of whole genome sequencing and metagenomics services.

NCIMB Ltd is custodian of the UK’s National Collection of Industrial, Food and Marine Bacteria. That might sound like an eclectic mix, but over the past 70 years the content of the collection has become increasingly diverse, and it now includes bacteria for a huge range of ecological niches. The collection has always reflected what is ‘hot’ in applied microbiology research, as new species are named and deposited.  Our culture collection is a fantastic resource of genetic diversity, and the deposits tell fascinating stories through the research they are associated with.

Scientists are now developing a far more detailed understanding of the true importance of microbial communities to human health, and significantly, also to diseases that may not originally have been suspected to have a microbiological origin. For example, recent research has associated changes in human gut bacteria with conditions including obesity and recurrent infection. Concordant with this, one of the trends that we have started to see, is an increase in the deposits made to the culture collection associated with microbiome research, both in humans, animals and even plants. For example, there has been much concern about colony collapse disorder in bee populations and we have seen a number of deposits to the collection of strains isolated from honeybees and their guts, as attempts are made to remedy this with beneficial microbes.

We were also delighted to be able to add a strain isolated from human breast milk to the collection last year:  the bacteriocin-producing strain NCIMB 15251 Lactobacillus gasseri was isolated from human milk and deposited at NCIMB by scientists from the Gut Microbes and Health research team at the Quadram Institute. The action of bacteriocins, and their role in modulation of the bacterial environment, is part of the complex system that defines gut health.

Another significant development in the evolution of our culture collection was the addition of strains isolated from the human gut. Researchers from the Host-Microbiota Interactions Laboratory at the Wellcome Sanger Institute have deposited more than 20 strains, including many novel species and genera. The work that this research group are doing in culturing and isolating novel gut bacteria is making a significant contribution to the understanding of gut microbiota and its compositional diversity, showing that even in a system that is so extensively studied, new bacterial discoveries are being made, and we are delighted to be able to make these strains available to the wider research community.

As our understanding of the microbiome and its relation to human health develops, researchers are seeking to modify these systems with beneficial microbes, for example, with the use of prebiotic and probiotic products. But there are also important safety issues that must be considered – such as ensuring that any strains used in any products are not themselves pathogenic, or resistant to antibiotics. Companies involved in the development of these kinds of products must convince regulators of the safety profile of their strains, and we are increasingly providing next-generation sequencing and bioinformatics to support this process.  This extends to making sure that people have a true understanding of their strain, taking it beyond a simple taxonomic designation. Genome sequencing can show if a strain is truly novel, as well as pinpointing problematic genes such as toxins, virulence factors or genes encoding for antimicrobial resistance, all of which are undesirable in a therapeutic product. The human gut is reported to be one of the most favourable ecological niches for horizontal gene transfer, so screening for these elements is a crucial step in the development of any probiotic products. We can even assay the genome of strains to look for other features that may be of interest to researchers, such as the production of bacteriocins or other natural products.

As always, our microbiological expertise extends beyond genome sequencing and bioinformatics, and we undertake lab-based assessment of strains to understand their sensitivity to antibiotics, as well as to see if strains are resistant to the gastric environment and test their potential for aggregation – two desirable factors for potential probiotics.

At NCIMB we love to support the application of microorganisms for good through the development of both our culture collection and the range of services that we provide. Although humankind has been benefiting from the activity of microorganism for most of our history as a species, there is so much more to learn about what they can do for us.

NCIMB Ltd is custodian of the National Collection of Industrial, Food and Marine Bacteria and offers a range of next-generation sequencing and bioinformatics services for microbiome and bacterial community analysis as well as screening for candidate probiotic strains.