Clonal-level Microbiome Profiling™ and engraftment analysis

Some studies require tracking of specific microbial strains over time or across different environments, making clonal-level resolution necessary. In fecal microbiota transplantation experiments, for example, researchers may wish to know which strains in the recipient originated in the donor, even when the donor has endogenous microbes of the same species. Or in studies where strain-level differences are relevant, precise analysis is crucial. Yet many microbiome analysis methods cannot achieve the high resolution necessary for these comparisons. 

Clinical Microbiomics has developed a robust technique for Clonal-level Microbiome Profiling, which provides clients with the most sensitive and accurate microbiome analysis available in the field.

This service provides you with information about clonal populations (i.e. strains) found in your samples based on variations at the single nucleotide (SNV) level. Using this method, you will be able to resolve strains with an average nucleotide identity (ANI) of 99.9%, and our team can help you build trees that organize the strains according to their relatedness and link groups of strains (clades) to clinical information and find the genes accounting for the functional differences. This allows correlations to be supported by clearer hypotheses about the mode of action for a host health outcome. 

Read our case study, based on a publication demonstrating the use our Clonal-level Microbiome Profiling™️ pipeline

Contact us for more information.


¹ Wei, S., Jespersen, M.L., Baunwall, S.M.D. et al. Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report. Microbiome 10, 193 (2022).

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