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Strain tracking and engraftment


Strain tracking and engraftment persistence analysis are valuable tools to evaluate the efficacy, safety, dynamics and long-term effects of live biotherapeutic products (LBPs), fecal microbiota transplants (FMTs), and probiotics:  

  • Differentiate and track interventional strains from endogenous host strains, even from complex consortia like FMT.
  • Monitor the ability of interventional strains to colonize, persist and modify the host’s microbial community. Discerning endogenous from interventional strains allows assessment of strain-specific behavior.
  • Understanding colonization patterns of interventional strains is necessary for monitoring behavior within the host and assessing therapeutic impact.
  • Engraftment patterns can be correlated to clinical outcomes or other important phenotypes thus guiding next-generation consortia design, dosages or delivery methods.

Strain tracking and engraftment analysis thus serve as indispensable tools, facilitating precision medicine by enabling the customization of microbial interventions based on individual responses and ensuring the optimal therapeutic outcomes for these innovative approaches in the field of microbiome-based therapeutics. 

strain engraftment image

From discovery through clinical validation, strain tracking and engraftment persistence analysis help inform and understand:

  • Efficacy—which is contingent on survival and persistence of interventional strains.
  • Sustained and durable therapeutic benefits of introduced strains.
  • Associations between engraftment and clinical outcomes or other important phenotypes.
  • The effect of dosing and formulation.
  • Strain selection and consortia design.
  • Much more… 

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Zooming in on the clonal level

Few microbiome analysis methods can achieve the high resolution necessary for strain tracking and engraftment persistence analysis. As seen in the figure below, resolving taxonomy at the species or subspecies level will not allow you to accurately assess engraftment since it is not able to distinguish between therapeutic strains and endogenous host strains.

Clinical Microbiomics/CosmosID have developed a robust technique for de novo clonal-level microbiome profiling. This service provides you with information about clonal populations (strains) found in your samples based on variations at the single nucleotide (SNV) level.

species level and clonal level resolutions

Read our case study, based on a publication demonstrating the use our clonal-level microbiome profiling pipeline.¹  

Contact us via the form to learn more!  

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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