Researchers are limited only by their imagination and available technological resources, but technology is continuing to gain ground.
Over the years, the way knowledge has been pieced together about the function and location of genes has generally depended on the manipulation, observation, and sequencing of specific loci. Technological advances, however, have given us the ability to apply Next Generation Sequencing (NGS) on a micro scale – for example, to provide simple and economical Whole Genome Sequencing (WGS) for bacteria. When combined with bioinformatics, it is possible to generate thorough, personalized information about the entirety of a given bacterial genome, including regions of interest (ROIs), single nucleotide polymorphisms (SNPs), individual genes of interest (such as the antibiotic-resistant gene), and step-by-step pathways of bacterial passage.
What makes this possible?
It’s true that common methods of sequencing generally do not accommodate such complex data. One feature of the Illumina MiniSeq system is the ability to simultaneously multiplex up to 25 million clusters to provide a more inclusive outlook of DNA or RNA of one or hundreds of samples of bacterial cultures. The resulting benefits for researchers include the ability to bypass the tedious steps involved in bacterial cloning, and to have a cost-effective method of maintaining diversity in bacterial cultures. This diversity is crucial, especially for researchers interested in the genetic drift that occurs during bacterial passage. In addition, the MiniSeq system is highly sensitive and recognizes small variants within the genome as well as other genetic changes, like rearrangements, so the significance of the data is not compromised even when the sample input is much higher.
The idea of gathering data by running multiple parallel sequences at once may seem overwhelming. However, biotechnological services can be provided to simplify results by creating reports that compare and contrast all of the sequences. This can not only show detailed variations between clusters, but can also shed light on how the individual loci displaying genetic drift ended up in their position. At The Sequencing Center, part of the value we offer clients who are working with bacterial WGS comes in the form of a highly detailed and personalized report that covers the sequencing process, the resulting data, and a step-by-step guide to replicating the results. This unique pathway analysis also includes SNPs and provides valuable insight to where genes of interest are located, what may have caused them to arise (in the case of an antibiotic resistant gene, for example), and how this outcome may be reproduced.
WGS is effectively changing the outlook of research that entails the mapping of both known and novel organisms’ genomes, as well as making it both feasible and economical to generate accurate reference data and make cross-sample comparisons. Paired with expert analysis and step-by-step replication guidelines, bacterial WGS represents a formidable new instrument in the genetic researcher’s tool kit.