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

ABSTRACT

Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.

KEYWORDS:

• Plant microbiome
• fruit
• and vegetable
• metagenome-assembled genomes
• gut microbiome

Acknowledgments

Graphic elements for Figure 1 were obtained from BioRender (https://biorender.com/).

We thank HEDIMED Investigator group for the critical reading of the manuscript.

Disclosure statement

MJSG and GVT are employed by Solarea Bio. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Author contributions

GB and WAW conceived and designed the study. WAW performed bioinformatic and statistical analysis. WAW, TC, and GB wrote the manuscript. WAW, TC, and GB analyzed the data. AA, BW, MJSG, GVT, SV, MK, and HH critically read and commented on the manuscript. GB and HH are involved in project administration and funding acquisition. All authors have read and agreed to the published version of the manuscript.

Data and materials availability

All data are available in the main text or the supplementary materials.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2258565

Additional information

Funding

This research was funded by European Union’s Horizon 2020 under the research and innovation programme under grant agreement No 874864 (HH and GB).