The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Abstract

Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.

Keywords: food microbiome; human microbiome; lactic acid bacteria; sprobiotics.

Figure 1.

Bubble plot showing prevalence (% of samples) of LAB genera and species in different fermented foods, as obtained from 16S rRNA gene sequencing studies reported in FoodMicrobionet (Parente et al. 2019). A taxon was considered present if its relative abundance was > 0.5%. For lactobacilli, species were grouped into taxonomic groups, as reported by Salvetti et al. (2018).

Figure 2.

Number of LAB reference genomes in NCBI grouped at (A) genera and (B) species level. In (B), only species with at least 10 genomes deposited in NCBI on December 2019 are shown.

Figure 3.

Pie charts showing isolation source for public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. NA, Not Available. According to the taxonomy update proposed by Zheng et al. (2020), the names of the genera reported would change as follows: Lb. brevis = Levilactobacillus brevis; Lb casei, Lb. paracasei and Lb. rhamnosus = Lacticaseibacillus spp.; Lb. fermentum and Lb. reuteri = Limosilactobacillus spp.; Lb. sakei and Lb. curvatus = Latilactobacillus spp.; Lb. plantarum and Lb. pentosus = Lactiplantibacillus spp.; Lb. salivarius = Ligilactobacillus.

Figure 4.

Heat plot showing prevalence of genes involved in resistance to the GIT passage and engraftment in the gut in public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. Eps, genes involved in exopolysaccharides production; ure, urease; bsh, bile-salt hydrolase; luxS, S-ribosylhomocysteine lyase. A list of the genes included and their NCBI accession numbers are reported in Supplementary Table S4. Color bar indicates assignment to the different taxonomic groups, as reported by Salvetti et al. (2018). For the taxonomy update proposed by Zheng et al. (2020), see Figure 3 legend.