Species-level taxonomic profiling of low biomass samples

Microbiome samples with low microbial biomass can be challenging for amplicon-based (e.g., 16S/18S-rRNA) or whole metagenome shotgun sequencing approaches. BaseClear now offers a metagenome-sequencing strategy that simultaneously produces species-level bacterial, archaeal, and fungal profiles for low-biomass samples such as skin, vaginal, oral and scalp swabs. Yet this method is cost-competitive with 16S rRNA gene analysis. 

Metagenome sequencing of low biomass samples

Metagenome sequencing, widely used to obtain the taxonomic profile of microbiomes, typically uses one of the following two strategies. The first strategy is target amplicons of phylogenetic marker genes (e.g., 16S rRNA for bacteria and archaea, and 18S rRNA or ITS for fungi). The second strategy is whole metagenome shotgun sequencing. Although less costly, target amplicon analyses can be limited in taxonomic resolution (i.e. at the genus level) and susceptible to PCR bias in composition and abundance estimates. Moreover it is not possible to capture multiple kingdoms in one analysis that includes bacteria, archaea, fungi and virus. In contrast, sequencing the total DNA with shotgun sequencing resolves species-or strain-level taxonomy, and includes all domains of organisms. However, shotgun sequencing requires a rather high amount of DNA as the starting material, and are usually unable to tackle DNA samples that are low in biomass or dominated by host DNA. Moreover, shotgun sequencing is typically much more costly, due to the much higher sequencing volume required for covering the whole genome (instead of just the marker gene).

Best of both worlds

BaseClear had developed an innovative method that is able to offer the best of both world. We now offer a cost-efficient procedure with accurate species-resolution, multi-kingdom taxonomic profiles for challenging samples like low-biomass and high-host-contaminated microbiomes.

Our shotgun metagenomics analysis of skin & low biomass samples with the proprietary low biomass DNA QC assessment, has been a key to success of clinical trial projects with precious samples often with low microbial DNA. Precious clinical trial samples often don’t have biological replicates, and many times comes with challenges with microbial DNA concentrations. While shotgun metagenomics is a solid method to assess species level taxonomic classification of all microbes, shotgun analysis does have higher DNA concentration specifications. Further, conventional DNA QC methods are incompetent in measuring low DNA concentrations in samples such as skin swabs.

Key benefits of our species-level taxonomic profiling service for low biomass samples:

  • Shotgun metagenome sequencing detects multiple kingdoms (i.e. bacteria, fungi, viruses)
  • Microorganisms can be detected down to species level
  • BaseClear’s proprietary qPCR based QC is a sensitive method, which results in higher successful, valid and reliable shotgun metagenomics taxonomic profiles.

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BaseClear and CHDR collaborate in skin microbiome analysis

The Center for Human Drug Research (CHDR) is collaborating with BaseClear for skin microbiome analyses in the context of clinical trials. “BaseClear partners with us in regards to technical, scientific and logistical aspects. It is a matter of complementary expertise and professional partnership.”

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