Next generation sequencing: revolutionising microbiology

The development of next generation sequencing (NGS) has revolutionised genomic research, but what exactly are the benefits of NGS, and what value can it offer our customers? NCIMB’s NGS Services Manager, Dr Daniel Swan, takes a brief look back at the development of sequencing technologies and highlights some of the applications.

Microbiologists have always exploited new technologies in order to understand the impact and processes of bacterial systems. In 1977, Carl Woese revolutionised microbial taxonomy, using rRNA genes as a marker to classify archaea as a separate domain from bacteria. The same year marked the development of DNA sequencing by Fred Sanger. By the early 1990s “Sanger sequencing” had led to the study of microbial communities through sequencing of the 16S ribosomal DNA gene, and this was followed by the first bacterial genome sequence (Haemophilus influenza) in 1995.

The impact of Sanger sequencing on modern biology has been huge.
Its automation enabled production scale sequencing, and a major landmark was reached in 2000 when, after 13 years and an investment of $2.7bn, the human genome was completed.

As the technology matured and costs reduced, Sanger sequencing technology started to become more widely used for routine analysis, and 16S sequencing became accepted as the “gold standard” for bacterial identification. This is still a core NCIMB service for our pharma customers who require identification of unknown isolates to Good Manufacturing Practice (GMP) standards.

Sequencing: The next generation

NGS platforms were launched commercially in 2005, and this development opened the floodgates to new applications, an increased understanding of microbial biodiversity, and an industry brimming with genome data.

The term “next-generation sequencing” refers to a number of different technologies, that all have one thing in common – they offer a step change in the scale of data production from a single machine. A state of the art, automated Sanger sequencing platform, running at full capacity can generate 1,536 DNA sequences a day – a total of 1,536,000 bases (1.5Mb). The first NGS platform gave a single lab the ability to analyse 20,000,000 bases (20Mb) in 5.5 hours, using a machine with a much smaller footprint. The development in throughput has continued at a rapid pace and at NCIMB we can produce 14Gb of data in a single run, a huge advance again from early NGS machines.

In addition, the old adage of ‘Better, faster, cheaper – pick two’ was a poor predictor for sequencing as NGS has delivered all three – better accuracy, higher throughput and lower costs. The lower cost is a combination of both the underlying technologies used (clonal amplification of DNA strands on immobilised surfaces; super-sensitive methods of detecting the bases added during sequencing) and also the massive uptake of the new platforms as science became hungry for sequence data.

NGS – An enabling technology

The rapid throughput of NGS allows genomic diversity to be looked at across thousands of individuals, and this has a myriad of applications. Within the microbiology community, it has enabled researchers to understand the minimum genome required for bacterial life. With respect to clinical applications, NGS has enabled rapid responses to outbreaks of pathogens, and much more finely grained taxonomic classification
of serovars.

The link between the human microbiome and human health has been in the news recently, with improved understanding set to revolutionise the treatment of conditions like recurrent Clostridium difficile infection. These leaps in understanding of the microbial ecology of the human gut have only really been possible as a result of NGS.

NGS has also revolutionised environmental microbiology, providing new insights into the diversity of extreme marine environments and soil microbe communities.

NGS services at NCIMB

Much of our NGS work focuses on understanding the makeup of bacterial whole genomes. Whole-genome sequencing is the ultimate in organism characterisation. It allows us to take a deep dive into a strain, and one application we are very interested in, is screening strains for the production of industrially or clinically important secondary metabolites. We offer this as a service to customers, and also work in collaboration with other researchers to explore the potential of our own culture collection.

Another critical application of whole-genome sequencing is in characterising probiotic products for human or animal use. Screening genomes for the presence of anti-microbial resistance genes and virulence factors is essential, as it is crucial that strains used do not facilitate the spread of resistance or pose other health risks.

We also use our experience in microbial ecology to sequence and understand the makeup and effects of microbial communities in environments, with 16S sequencing at NGS scale. This has applications in environmental monitoring programmes and we use it to analyse samples from niches as diverse as oil and gas reservoirs and production facilities, soil, and the human gut. In the case of the oil and gas industry, community analysis can help operating companies assess the likelihood of reservoir souring and corrosion, and take preventative steps to safeguard the environment and potentially avoid much greater costs.

Importantly, at NCIMB, we have the bioinformatics capability and expertise to get the most from your NGS data, no matter what your research or commercial aim. You can find more information visit our NGS web pages.

ABOUT THE AUTHOR

Dr Daniel Swan joined NCIMB in 2017. Daniel is an experienced bioinformatician who has been generating and analysing DNA sequence data since 1995. He is responsible for developing and maintaining the analysis infrastructure that supports NCIMB’s NGS platforms as well as providing NGS and bioinformatics consultation for R&D partners. He is passionate about sequencing all of the reference strains in the NCIMB collection.