Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms

Abstract

For thousands of years, humans have safely consumed microorganisms through fermented foods. Many of these bacteria are considered probiotics, which act through diverse mechanisms to confer a health benefit to the host. However, it was not until the availability of whole-genome sequencing and the era of genomics that mechanisms of probiotic efficacy could be discovered. In this review, we explore the history of the probiotic concept and the current standard of integrated genomic techniques to discern the complex, beneficial relationships between probiotic microbes and their hosts.

Fig. 1

Seminal milestones contributing to the functional characterization of probiotic lactic acid bacteria

Fig. 2

With the advent of genome sequencing, integrated genomic techniques including proteomics, transcriptomics and functional genomics have collectively characterized the mechanism of probiotic host-interactions. These analyses rely on access to annotated sequence data from whole genome sequencing. Genetic systems for deletions and mutational knockouts allow for phenotyping specific genetic loci. Proteomic approaches involve the characterization of proteins expressed, secreted, and/or attached to the cell wall. In this way, proteins are isolated, characterized by mass spectrometry, and mapped back to the proteome and corresponding genome for functional analysis. Finally, transcriptomic profiling using DNA microarrays, RNA sequencing, and RT-qPCR can measure the transcriptional responses of both bacteria and host cells in response to one another, via measurement of mRNA

Fig. 3

a Probiotic microbes delivered orally must survive varying environments encountered through gastrointestinal transit, including acidic gastric juices (pH ~2) in the stomach, and bile in the small intestines. b At the intestinal epithelia, probiotics have been reported to adhere in high numbers, leading to competitive exclusion of pathogens. The growth of certain probiotics can be stimulated by the presence of complex prebiotic oligosaccharides. Additionally, some probiotics produce bacteriocins and other antimicrobial agents which may antagonize pathogens in the lumen. c Probiotics bound in the mucus and epithelial layers are proximal to dendritic cells of the mucosal immune system, leading to immunomodulation

Fig. 4

Identification of pili structures in Lactobacillus rhamnosus GG (I) and Bifidobacterium breve UCC2003 (II). Images were obtained using transmission electron microscopy on negatively stained, immunogold-labeled anti-SpaC pili in L. rhamnosus (I) and anti-Flp ₂₀₀₃ pili in B. breve (II). Reprinted with permission from Kankainen et al. (2009), copyright © 2009 National Academy of Sciences, USA; and O’Connell Motherway et al. (2011), copyright © 2011 National Academy of Sciences USA

Fig. 5

Bacteriocins produced by LAB are grouped into three classes based on structure and function: class I (lantibiotics), class II, and bacteriolysins. Class I lantibiotics, such as nisin, can have two modes of action. First, they bind lipid II to prevent peptidoglycan subunit transport, disrupting peptidoglycan synthesis and cell division. Second, they dock at lipid II to create pores in the cytoplasmic membrane of the bacteria. Class II bacteriocins, such as sakacin, often contain amphiphilic helical structures which can insert into the cell membrane, leading to cell lysis. Bacteriolysins, such as lyostaphin, are large hydrolases which directly degrade the peptidoglycan cell wall. Reprinted with permission of Macmillan Publishers, Ltd, from Cotter et al. (2005), copyright © 2005 Nature Publishing Group