title: Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases.
abstract: Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation "well defined strains," encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping. Strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2 × 250 bp Illumina MiSeq technology. Using these methods, we tested the hypothesis that products do contain the quantitative and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species, and un-labeled species. The HTS revealed that many blended products consisted predominantly ofLactobacillus acidophilusandBifidobacterium animalissubsp.lactis. These results highlight the need for reliable methods to determine the correct taxonomy and quantify the relative amounts of mixed microbial populations in commercial probiotic products.
authors.affiliation: Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA.
authors.forename: Wesley
authors.initials: W
authors.lastname: Morovic
authors.affiliation: Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA.
authors.forename: Ashley A
authors.initials: AA
authors.lastname: Hibberd
authors.affiliation: Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Zabel
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University Raleigh, NC, USA.
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
authors.affiliation: Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA.
authors.forename: Buffy
authors.initials: B
authors.lastname: Stahl
keywords: Bifidobacterium; Lactobacillus; high-throughput nucleotide sequencing; labeling; multiplex PCR; probiotics; taxonomy; testing and assessment