Our microbiome methods

Microbiome and microbes

Microbes are microscopic organisms that include fungi, viruses and bacteria. They play a crucial role in various environments, such as those found in soil or in many parts of the human body. These microbes form complex collective communities known as microbiomes.

Here at Salient, we work with a variety of clients of different sizes, using cutting edge methods and technologies to analyse microbiomes and generate the highest quality data for our clients and customers. The fundamental output of microbiome analysis is a taxonomic profile, which lists the types of microbe present in the sample and how much there is of each – but there is a lot more that can be learned from further analyses of this data. Today, we're going into a little more detail about microbiome analysis services and methods.

Microbiome analysis methods

At Salient we work closely with our clients to select the best approach possible, creating a bespoke service that works on a case-by-case basis. We use a variety of analysis methods, such as:

Shotgun sequencing

Together, all of the genomes from the different microbes making up a microbiome are called the metagenome. In shotgun sequencing the whole metagenome is broken into small fragments and the genetic code of these fragments is read. This means that all of the available genetic data is sampled, giving us information about which species are present as well as what genes they are carrying.

Shotgun sequencing can either be deep or shallow. Deep sequencing produces a very large number of reads, so the data has better coverage and depth. This means more of the metagenome is sampled, allowing for detection of rarer species, better discrimination of closely related strains, and greater confidence when detecting variant sequences. Shallow sequencing generates fewer reads but is less expensive. We will help you decide what sequencing depth is appropriate for your samples.

16S (amplicon) sequencing

Amplicon sequencing uses PCR amplification to focus the sequencing efforts on particular regions of the metagenome. The usual target is the 16S ribosomal RNA gene, which contains variable regions that can be used to identify different types of bacteria and archaea. However, the same principle can also be applied to fungi, or to other genes that might provide useful strain-specific information. Amplicon sequencing is typically the cheapest way to generate a profile of a microbiome, though the data is not as rich as from shotgun sequencing.

Long-read sequencing

The sequencing methods above typically use short-read sequencing technologies, which analyse fragment lengths of 150-600 base-pairs. We also have long-read sequencing capabilities which have advantages in some applications. For example, long-read sequencing can be applied to amplicon sequencing to provide better taxonomic resolution, and it provides complementary information to short-read sequencing for de novo genome assembly projects.

Bioinformatics

The taxonomic profile generated by either sequencing approach can then be analysed further to give meaningful insights into the microbiome and how it may be behaving. For example, the presence of particular species or patterns of microbial growth can be analysed for indications of disease; the levels of key metabolic pathways can be inferred; shifts in the microbiome composition and diversity can be quantified. Our bioinformatics team will work with you to generate the actionable insights you need, with services ranging from machine-learning approaches to disease prediction, to de novo genome assembly, to generation of easy to understand, publication-quality charts and figures.

qPCR

Quantitative Polymerase Chain Reaction (qPCR) is a technique used to amplify and quantify a target DNA sequence: if the target sequence is present in a sample millions of copies are made which can be detected using fluorescent dyes or probes. Common applications include pathogen detection, profiling key microbiome members, detecting genetic mutations or variations, and studying gene expression patterns by quantifying mRNA levels. This method is best suited to quantification of a smaller set of defined targets, but is extremely cost effective and highly sensitive. Using a highly automated workflow we can rapidly design and validate novel qPCR assays for use in contexts such as academic research projects, clinical trials, or custom microbe detection kits.

Metabolomics

We can also provide metabolomic and proteomic services to complement our sequencing and qPCR-based approaches. Metabolomic and proteomic studies use technologies such as chromatography, mass spectrometry, and nuclear magnetic resonance to measure the levels of small metabolite molecules and proteins in a sample, giving a direct measure of how the microbiome or human host tissue is behaving. Some of the more common applications are to study how certain drugs can affect metabolism, analysing the effect of environmental change on metabolic processes, or identifying molecules such as immune markers that can indicate disease states and be used to monitor responses to treatments.

Our full address is: Salient Bio The Biscuit Factory 100 Drummond Rd London SE16 4DG

Clinical Review: The information on this page has been reviewed for clinical accuracy by Dr. Marta Ciechonska Ph.D, microbiologist.