The Pure Probiotic Initiative: Strain authenticaiton: Genetics and beyond

By Kelly C. Heim, Ph.D.

The Human Microbiome Project, a federally funded research program similar to the Human Genome Project, has identified more than 10,000 microbial species in the human body.1 Ongoing isolation and commercialization of probiotic organisms, together with strain-specific clinical research, continues to expand the practitioner’s repertoire. With so many new options, confidence in the identity of strains listed on a product label is more important than ever before.2

Identity testing for nutritional ingredients involves chromatographic and spectroscopic methods that are extremely reliable for vitamins, minerals and botanicals. However, probiotics are different—they are living, active organisms with adaptable biochemical compositions. Since their chemical makeup can change spontaneously, conventional ingredient test methods are not definitive. Fortunately, amidst the dynamic biochemical motions within a probiotic cell, the most informative and demarcating constituent stands quite still.

This steadfast principle is DNA—the genetic material that determines the bacterium’s distinctive structure and function. The sequence of probiotic DNA is different for every genus and species, and is the blueprint from which its functional health benefits materialize. Therefore, proof of genetic identity is indispensable in the sourcing of these organisms for clinical use. Of paramount importance is routine genetic validation of raw ingredients to ensure that probiotic products deliver the intended health benefits.

Since a probiotic genome contains thousands of genes, it is impossible for microbiologists to sequence its entirety on a routine basis. However, a small strip of DNA in the genome, known as the ribosomal RNA gene, bears a sequence that typifies genus and species, providing a convenient “bar code” for identification. Microbial genetics laboratories have carried the routine sequencing of this gene to methodological perfection, enabling precise identification. Upon every reception of raw probiotic material, Pure Encapsulations sends samples to these independent laboratories for this analysis, which utilizes the most updated instrumentation, software and genetic expertise.

The classification of bacteria extends beyond genus and species. Within a species, many unique strains may exist (Figure 1). The medical significance of strain designation is straightforward, as constitutional nuances can impact function. A familiar analogy is the striking multiplicity of breeds within Felis catus –the domestic cat. Despite a genomic kinship, the breeds display extraordinary heterogeneity in physical and functional attributes. In the case of bacteria, these differences are less overt. They are seldom apparent under a microscope, and are rarely detectable in a gene sequence. However, bacterial strains display unique patterns of lipids in their membranes, forming a signature that can be detected by chromatography. Known as fatty acid methyl ester analysis (FAME), this analysis can reveal a strain-specific signature that matches an authoritative reference.

Figure 1. The complete name of a probiotic organism typically consists of genus, species and strain. Genus and species are the most basic descriptors, while strain denotes a minor variation within the species.


Recognized as quintessential tools in the taxonomic fingerprinting of bacteria, FAME analysis and DNA sequencing are utilized by microbiologists all over the world. As part of a comprehensive program of probiotic quality assurance, Pure Encapsulations requires positive authentication from both tests. This commitment to excellence in probiotic sourcing, manufacturing and testing ensures confidence in the accuracy of every label and the reliability of every finished product.


  1. Aagaard K, Petrosino J, Keitel W, et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J. 2012 Nov 19.
  2. Yeung PS, Sanders ME, Kitts CL, et al. Species-specific identification of commercial probiotic strains. J Dairy Sci. 2002 May;85(5):1039-51.