Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria

Abstract

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity.IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.

Topical cream with live lactobacilli modulates the skin microbiome and reduce acne symptoms

“…As expected, the vagina showed the highest relative abundance of Lactobacillus taxa, but the skin turned out to be the second most important niche for these taxa. Moreover, to have a better idea of the phylogenetic diversity of all Lactobacillus taxa present, we also plotted all data on a phylogenetic tree of the Lactobacillus genus complex 18 ( Figure 1c) . These data indicate that taxa typically associated with the human vagina, Lactobacillus crispatus, L. iners, L. gasseri and L. jensenii were also found as the most prevalent lactobacilli on the skin ( Figure 1d and 1e ).…”

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

“…Conjugation is one of the main drivers of horizontal gene transfer and is commonly 310 associated with conjugative plasmids [22,26]. Here, two of the five conjugative regions 311 found were plasmid-associated and the two plasmids found were exactly the same for 312 both L. mudanjiangensis AMBF209 and AMBF249, although these strains were 313 isolated from different household carrot juice fermentations [11]. Previous studies also 314 identified and described conjugative plasmids in other Lactobacillus species, such as 315 Lactobacillus brevis [54], Lactobacillus casei [55], Lactobacillus gasseri [56], Lactobacillus 316 hokkaidonensis [57], L. plantarum [58] and Lactobacillus reuteri [59].…”

“…Furthermore, 56 to allow comparison with other closely related Lactobacillus species and detection of L. 57 mudanjiangensis species-specific properties, all publicly available genome sequences 58 (NCBI Assembly database, 24/07/2018) of L. plantarum group members were included 59 in this comparative genomics study, totaling the number of genomes analyzed to 304 60 ( Table 1). 61 Spontaneously fermented carrot juice [11] Phylogeny of the Lactobacillus plantarum group 62 To obtain a detailed view on the phylogeny of L. mudanjiangensis in relationship to the 63 whole L. plantarum group, a maximum likelihood phylogenetic tree was constructed, 64 based on 612 single-copy core orthogroups, found with Orthofinder (Fig1 and S1 Fig). Maximum likelihood phylogenetic tree of the Lactobacillus plantarum group.…”

“…AMBF197, AMBF209 and AMBF249, which were isolated from three different 256 spontaneous carrot juice fermentations [11]. Since previous phylogenetic analysis of this 257 species, using the 16S rRNA, pheS, and rpoA genes, showed a close genetic relatedness 258 with the members of the L. plantarum group [10], it was decided to study these 259 genomes in relation to the closely related members of the L. plantarum group with a 260 comparative genomics approach.…”

Fermented food metagenomics reveals substrate-associated differences in taxonomy, health-associated- and antibiotic resistance-determinants

“…Due to these potential benefits, and an increasing appreciation that the study of these foods provide valuable fundamental insights into simple microbial communities[17, 18], developing an even greater understanding of the microbiology of these foods has the potential to be of considerable value.…”