The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host

Abstract

Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.

Assessments of Probiotic Potentials of Lactiplantibacillus plantarum Strains Isolated From Chinese Traditional Fermented Food: Phenotypic and Genomic Analysis

“…In ancient times, fermentation was a common way for food preservation and processing. At present, fermented food plays an important role in human diets due to its special taste and unique aroma ( Marco et al, 2021 ; Soto-Giron et al, 2021 ). In addition, the health-related properties of fermented food significantly promote their consumption around the world ( Castellone et al, 2021 ).…”

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut

“… 42 Exposure to diverse bacteria via fruit and vegetable consumption could have a significant impact on the genetic diversity of the gut microbiota, in particular during childhood. Interestingly, Soto-Giron et al 16 showed high genetic diversity and specific functions of plant-associated strains of Pseudomonas and Lactobacillus , and specific functions associated with probiotic-linked mechanisms. Limited exposure to diverse microbiota may influence immune system development.…”

“…Fruits and vegetables do not only contain nutrients and bioactive plant secondary metabolites that are known to influence the gut microbial diversity and composition, 13 but also a high diversity of microorganisms. 14 , 15 Therefore, it was hypothesized that fruits and vegetables serve as the main direct sources of environmental microbiota 14 , 16 and may modulate the composition and functionality of our gut microbiomes. 17 However, there has been no study to date to investigate the potential transfer of the natural fruit and vegetable microbiota to the human gut.…”

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“…Fruits and vegetables harbor an immensely diverse microbiome essential for the health and survival of the plant. [10][11][12] This untapped source of microbial diversity has facilitated the development of a novel, safe, Defined Microbial Assemblage ™ (DMA TM ) medical food product, SBD111, for the dietary management of the metabolic processes associated with osteopenia and osteoporosis. SBD111 is composed of four strains of microorganisms isolated from different food sources: Lactobacillus brevis SBS4254, Lactobacillus plantarum SBS4260, Leuconostoc mesenteroides SBS4255, and Pichia kudriavzevii SBS4263, as well as oligofructose and dried blueberry powder.…”