Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling.

Juliana M Ansari,Olivia Harriott,Scott Kohlhepp,Christine Colasacco,Elli Emmanouil,Adriana Calderaro

doi:10.1371/journal.pone.0213841

Juliana M Ansari, Olivia Harriott + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0213841

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Journal: PloS one	Publication Date: Mar 22, 2019
Citations: 37	License type: CC BY 4.0

Affiliation: Fairfield University

Abstract

Probiotic products are becoming more prevalent as awareness of the role of beneficial microbes in health increases. Ingredient labels of these products often omit identifications at the strain level, making it difficult to track down applicable published research. In this study, we investigated whether products labeled with the same species name contained different strains of those species. From 21 commercially available probiotic supplements and beverages, we cultured five main species: Bacillus coagulans, Bacillus subtilis, Lactobacillus plantarum, Lactobacillus rhamnosus, and the yeast Saccharomyces boulardii. To confirm the identity of each bacterial isolate, we applied standard molecular approaches: 16S rRNA gene sequencing and Matrix Assisted Laser Desorption Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS). Phenotypic profiling and identification were performed with the Biolog Microbial Identification system. All of the bacterial isolates were correctly identified by at least one approach. Sequencing the 16S rRNA gene led to 82% of species identifications matching the product label, with 71% of isolates identified by MALDI-TOF MS and 60% identified correctly with the Biolog system. Analysis of the Biolog phenotypic profiles revealed different patterns of carbon source usage by each species, with sugars preferentially utilized by all except B. subtilis. To assess the strain-level differences, we compared strains of the same species and found variability in carbohydrate utilization and tolerance to environmental stressors (salt, acidity, antibiotics). By demonstrating that products listing the same species often contain strains with different 16S sequences and phenotypes, this study highlights that current labels of probiotic supplements do not sufficiently convey the strain diversity in these products.

Highlights

A widespread awakening in the public and medical community’s interest in beneficial bacteria for promoting health is underway
We selected a variety of probiotic supplements and beverages to adequately represent the selection of products available to consumers
Pure cultures of bacteria and yeast were isolated from 15 probiotic supplements, six probiotic beverages, and four environmental sources (Chaas fermented beverage, fruit fly gut, kale, and leaves) to serve as “wild” microbes for comparison

Summary

Introduction

A widespread awakening in the public and medical community’s interest in beneficial bacteria for promoting health is underway. Accelerated by the ease and affordability of rapid DNA sequencing technology, an avalanche of studies in animal models and humans has linked the microbiome (the microbial community inhabiting the human body) body to a wide range of diseases. This mounting knowledge of the human microbiome has stimulated interest in bacteria that confer a health benefit to the host (probiotics) or foods that selectively enhance growth of certain beneficial microbes (prebiotics). Candidate probiotic bacteria such as Akkermansia municiphila and Faecalibacterium prausnitzii, often termed “ generation probiotics,” have been identified from human microbiome studies but are not yet commercially available [3]

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