How Lactobacillus plantarum shapes its transcriptome in response to contrasting habitats

Abstract

Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.

Fermentation of Wheat Bran and Whey Permeate by Mono-Cultures of Lacticaseibacillus rhamnosus Strains and Co-culture With Yeast Enhances Bioactive Properties

“…Possible mechanisms for microbial bioconversion could be (a) caffeic acid produced by hydroxylation of p-coumaric acid at the meta position similar to Streptomyces caeruleus (Sachan et al, 2006); (b) caffeic acid produced by the o-demethylation of ferulic acid. This pathway was shown in Enterobacter cloacae and Clostridium methoxybenzovorans and in human colonic fermentation of rye bran fortified bread (Micard et al, 2002;Filannino et al, 2014). Filannino et al (2014) had confirmed the ability of some lactic acid bacteria such as Lactobacillus spp.…”

“…This pathway was shown in Enterobacter cloacae and Clostridium methoxybenzovorans and in human colonic fermentation of rye bran fortified bread (Micard et al, 2002;Filannino et al, 2014). Filannino et al (2014) had confirmed the ability of some lactic acid bacteria such as Lactobacillus spp. to convert protocatechuic acid to catechol; p-coumaric to phloteric acid or p-vinylphenol.…”

Bioprocessing of Brewers’ Spent Grain Enhances Its Antioxidant Activity: Characterization of Phenolic Compounds and Bioactive Peptides

“…The free phenolics profile was characterized by the products of microbial metabolism of phenolic acids and their derivatives especially in eBSG and fermented BSG. Dihydroferulic, dihydrocaffeic, and phloretic acids are, in fact, the products of ferulic, caffeic, and coumaric acid reduction, respectively (Filannino et al, 2014). Overall, the highest metabolites concentration was found in eBSG fH46.…”

Abundance, diversity and plant‐specific adaptations of plant‐associated lactic acid bacteria

“…These bacteria appear to have diversified at the strain level (Siezen et al ., ; Broadbent et al ., ). However, in spite of this diversity, generalist LAB have relatively conserved, core metabolic response pathways (Filannino et al ., ). Under this classification, generalist species include L. plantarum , Lactobacillus casei , Lactobacillus brevis , as well as Lactococcus lactis , L. mesenteroides and W. cibaria (Duar et al ., ) (Fig.…”

“…Strains of L. plantarum , L. mesenteroides , L. fermentum , L. brevis and Weissella are able to tolerate high levels of antimicrobial plant phenolic compounds (Filannino et al ., b). Tolerance is likely due to the conversion of these compounds into less toxic metabolites by glycolyl hydrolase, phenolic acid decarboxylase and reductase, and esterase activities (Filannino et al ., ).…”