Genotypic adaptations associated with prolonged persistence ofLactobacillus plantarumin the murine digestive tract

A large-scale comparative genomics study reveals niche-driven and within-sample intra-species functional diversification in Lacticaseibacillus rhamnosus

Lacticaseibacillus rhamnosus (L. rhamnosus) is widely recognized as a probiotic species, and it exists in a variety of environments including host gut and dairy products. This work aimed at conducting a large-scale comparative genomics analysis of 384 L. rhamnosus genomes (257 whole-sequence or metagenomic-assembled genomes from gut-associated isolates [122 and 135 retrieved from the UHGG and NCBI databases, respectively] and 127 genomes from dairy isolates [34 from the NCBI database; 93 isolated from a cheese sample and sequenced here]). Our results showed that L. rhamnosus had a large and open pan-genome (15,253 pan-genes identified from all 384 genomes; 15,028 pan-genes if the 93 cheese-originated isolates were excluded). The core-gene phylogenetic tree constructed from the 384 L. rhamnosus genomes comprised five phylogenetic branches, with a random distribution of dairy and gut-associated isolates/genomes across the tree. No significant difference was identified in the overall profile of metabolism-related genes between dairy and gut-associated genomes; however, notably, the gut-associated strains/isolates contained more genes coding for specific metabolic pathways and carbohydrate-active enzymes, e.g., lacto-N-biosidase (EC 3.2.1.140; GT20) and lacto-N-biose phosphorylase/galacto-N-biose phosphorylase (EC 2.4.1.211; GH112). Further, we found that there was obvious intra-species diversification of the 93 cheese-originated L. rhamnosus isolates, forming three clades (Clades A, B, and C) in the reconstructed core-gene phylogenetic tree. There were numerous single nucleotide variations (over 10,000) across the three clades. Moreover, significant differences were observed in the content of metabolism-related genes across clades (p < 0.05, Adonis test), characterized by the enrichment in glycoside hydrolases in Clade C and the possession of unique metabolic pathways in each clade. These results implicated genomics/functional diversification of L. rhamnosus in a single food matrix and niche-driven adaptive evolution of isolates from dairy and host gut-associated origins. Our study shed insights into the selection of candidate strains for food industry applications.

Persistence and dynamics of fluorescent Lactobacillus plantarum in the healthy versus inflamed gut

The gastrointestinal tract is the main ecological niche in which Lactobacillus strains may provide health benefits in mammals. There is currently a need to characterize host-microbe interactions in space and time by tracking these bacteria in vivo. We combined noninvasive whole-body imaging with ex vivo fluorescence confocal microscopy imaging to monitor the impact of intestinal inflammation on the persistence of orally administered Lactobacillus plantarum NCIMB8826 in healthy and inflamed mouse colons. We developed fluorescent L. plantarum strains and demonstrated that mCherry is the best system for in vivo imaging and ex vivo fluorescence confocal microscopy of these bacteria. We also used whole-body imaging to show that this anti-inflammatory, orally administered strain persists for longer and at higher counts in the inflamed colon than in the healthy colon. We confirmed these results by the ex vivo confocal imaging of colons from mice with experimental colitis for 3 days after induction. Moreover, extended orthogonal view projections enabled us to localize individual L. plantarum in sites that differed for healthy versus inflamed guts. In healthy colons, orally administered bacteria were localized in the lumen (in close contact with commensal bacteria) and sometimes in the crypts (albeit very rarely in contact with intestinal cells). The bacteria were observed within and outside the mucus layer. In contrast, L. plantarum bacteria in the inflamed colon were mostly located in the lumen and (in less inflamed areas) within the mucus layer. In more intensely inflamed areas (i.e., where the colon had undergone structural damage), the L. plantarum were in direct contact with damaged epithelial cells. Taken as a whole, our results show that fluorescently labeled L. plantarum can be used to study the persistence of these bacteria in inflamed guts using both noninvasive whole-body imaging and ex vivo fluorescence confocal microscopy.

In Vitro Gut Modeling as a Tool for Adaptive Evolutionary Engineering of Lactiplantibacillus plantarum

Research and marketing of probiotics demand holistic strain improvement considering both the biotic and abiotic gut environment. Here, we aim to establish the continuous in vitro colonic fermentation model PolyFermS as a tool for adaptive evolutionary engineering. Immobilized fecal microbiota from adult donors were steadily cultivated up to 72 days in PolyFermS reactors, providing a long-term compositional and functional stable ecosystem akin to the donor’s gut. Inoculation of the gut microbiota with immobilized or planktonic Lactiplantibacillus plantarum NZ3400, a derivative of the probiotic model strain WCFS1, led to successful colonization. Whole-genome sequencing of 45 recovered strains revealed mutations in 16 genes involved in signaling, metabolism, transport, and cell surface. Remarkably, mutations in LP_RS14990, LP_RS15205, and intergenic region LP_RS05100<LP_RS05095 were found in recovered strains from different adaptation experiments. Combined addition of the reference strain NZ3400 and each of those mutants to the gut microbiota resulted in increased abundance of the corresponding mutant in PolyFermS microbiota after 10 days, showing the beneficial nature of these mutations. Our data show that the PolyFermS system is a suitable technology to generate adapted mutants for colonization under colonic conditions. Analysis thereof will provide knowledge about factors involved in gut microbiota colonization and persistence.

IMPORTANCE Improvement of bacterial strains in regard to specific abiotic environmental factors is broadly used to enhance strain characteristics for processing and product quality. However, there is currently no multidimensional probiotic strain improvement approach for both abiotic and biotic factors of a colon microbiota. The continuous PolyFermS fermentation model allows stable and reproducible continuous cultivation of colonic microbiota and provides conditions akin to the host gut with high control and easy sampling. This study investigated the suitability of PolyFermS for adaptive evolutionary engineering of a probiotic model organism for lactobacilli, Lactiplantibacillus plantarum, to an adult human colonic microbiota. The application of PolyFermS controlled gut microbiota environment led to adaptive evolution of L. plantarum strains for enhanced gut colonization characteristics. This novel tool for strain improvement can be used to reveal relevant factors involved in gut microbiota colonization and develop adapted probiotic strains with improved functionality in the gut.

Genomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut

The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate, Lactobacillus plantarum P-8, a well-studied probiotic bacterium, was consumed by healthy human volunteers and rats. Then, the persistence and genomic stability of P-8 in the host gut were surveyed. qPCR results revealed that after the consumption of one dose, P-8 could be detected in the host gastrointestinal tract for 4–5 weeks. By contrast, after 4 successive weeks of consumption, P-8 could be detected for up to 17 weeks after consumption ceased. In total, 92 P-8 derived strains were isolated from fecal samples and their genomes were sequenced and analyzed. Comparative genomic analysis detected 19 SNPs, which showed the characteristics of neutral evolution in the core genome. In nearly half of samples (n = 39, 42%), the loss of one to three plasmids was observed. The frequent loss of plasmids indicated reductive evolution in the accessory genome under selection pressure within the gastrointestinal tract. We also observed a 609-bp 23S rRNA homologous fragment that may have been acquired from other species after intake. Our findings offer insight into the complex reactions of probiotics to the gut environment during survival in the host. The in vivo genomic dynamics of L. plantarum P-8 observed in this study will aid the commercial development of probiotics with more stable characteristics.

Genomic resequencing combined with quantitative proteomic analyses elucidate the survival mechanisms of Lactobacillus plantarum P-8 in a long-term glucose-limited experiment

Lactobacillus plantarum, commonly isolated from plant material, is widely used to produce various types of fermented foods. However, nutrient-limiting conditions are often encountered during industrial applications. The present study aimed to investigate the response of L. plantarum P-8 to glucose-limited conditions in a long-term experiment. Genotypic and proteomic changes in L. plantarum P-8 were monitored over 3 years in glucose-limited and glucose-normal media using whole-genome resequencing and tandem mass tag-based quantitative proteomic analysis. Results showed that L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (via glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation. This study demonstrates the feasibility of experimental evolution of L. plantarum P-8, while whole-genome resequencing of adapted isolates provided clues toward bacterial functions involved and a deeper mechanistic understanding of the adaptive response of L. plantarum to glucose-limited conditions.

SIGNIFICANCE

We have conducted a 3-year experiment monitoring genotypic and proteomic changes in Lactobacillus plantarum P-8 in glucose-limited and glucose-normal media. Whole-genome resequencing and tandem mass tag-based quantitative proteomics were performed for analyzing genomic evolution of L. plantarum P-8 in glucose-limited and glucose-normal conditions. In addition, differential expressed proteins in all generations between these two conditions were identified and functions of these proteins specific to L group were predicted. L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation.

The potential of lactic acid bacteria to colonize biotic and abiotic surfaces and the investigation of their interactions and mechanisms

Lactic acid bacteria (LAB) are a heterogeneous group of Gram-positive bacteria that comprise several species which have evolved in close association with humans (food and lifestyle). While their use to ferment food dates back to very ancient times, in the last decades, LAB have attracted much attention for their documented beneficial properties and for potential biomedical applications. Some LAB are commensal that colonize, stably or transiently, host mucosal surfaces, inlcuding the gut, where they may contribute to host health. In this review, we present and discuss the main factors enabling LAB adaptation to such lifestyle, including the gene reprogramming accompanying gut colonization, the specific bacterial components involved in adhesion and interaction with host, and how the gut niche has shaped the genome of intestine-adapted species. Moreover, the capacity of LAB to colonize abiotic surfaces by forming structured communities, i.e., biofilms, is briefly discussed, taking into account the main bacterial and environmental factors involved, particularly in relation to food-related environments. The vast spread of LAB surface-associated communities and the ability to control their occurrence hold great potentials for human health and food safety biotechnologies.

Stress Physiology of Lactic Acid Bacteria

Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.

Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome

Lactobacillus plantarum WCFS1 is one of the best studied Lactobacilli, notably as its genome was unravelled over 12 years ago. L. plantarum WCFS1 can be grown to high densities, is amenable to genetic transformation and highly robust with a relatively high survival rate during the gastrointestinal passage. In this review, we present and discuss the main insights provided by the functional genomics research on L. plantarum WCFS1 with specific attention for the molecular mechanisms related to its interaction with the human host and its potential to modify the immune system, and induce other health-related benefits. Whereas most insight has been gained in mouse and other model studies, only five human studies have been reported with L. plantarum WCFS1. Hence NCIMB 8826 (the parental strain of L. plantarum WCFS1) in human trials as to capitalize on the wealth of knowledge that is summarized here.

Microbial bioinformatics for food safety and production

In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.

The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology

The food industry is constantly striving to develop new products to fulfil the ever changing demands of consumers and the strict requirements of regulatory agencies. For foods based on microbial fermentation, this pushes the boundaries of microbial performance and requires the constant development of new starter cultures with novel properties. Since the use of ingredients in the food industry is tightly regulated and under close scrutiny by consumers, the use of recombinant DNA technology to improve microbial performance is currently not an option. As a result, the focus for improving strains for microbial fermentation is on classical strain improvement methods. Here we review the use of these techniques to improve the functionality of lactic acid bacteria starter cultures for application in industrial-scale food production. Methods will be described for improving the bacteriophage resistance of specific strains, improving their texture forming ability, increasing their tolerance to stress and modulating both the amount and identity of acids produced during fermentation. In addition, approaches to eliminating undesirable properties will be described. Techniques include random mutagenesis, directed evolution and dominant selection schemes.

Functional genomics of lactic acid bacteria: from food to health

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.