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Microbiomes Associated with Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity

BY: Louise Vermote, Marko Verce, Fernanda Mozzi, Luc De Vuyst and Stefan Weckx

The Research Group of Industrial Microbiology and Food Biotechnology (IMDO) of the Vrije Universiteit Brussel (VUB), Brussels, Belgium, has recently published a paper in Frontiers in Microbiology on the microbial composition of the surfaces of several fruits and flowers, including white guava, passion fruit, and papaya, sampled in the Tucumán province in Northern Argentina. The researchers have used a shotgun metagenomic sequencing approach. So far, knowledge about the microorganisms present on fruit surfaces and flowers have been obtained using microbiological culturing methods, implying a culturing bias due to the selective culture media and incubation conditions used. The application of metagenomics on this type of sample was novel and avoided those culturing biases, as well as limitations faced when using amplicon-based high-throughput sequencing approaches. A better insight into the fruit surface and flower microbiomes are important to be able to select appropriate microbial strains that could be used as starter cultures to perform fruit and fruit juice fermentation processes. Such fermentation applications could help in avoiding food losses because of low-quality fruits and fruit decay due to overproduction. In addition, producing such fermented fruits and fruit juices is in line with the current trends toward sustainable food production through fermentation and the consumption of healthy, fresh-like, high-nutritional-value, ready-to-eat or -drink fermented foods and beverages.

Figure 1. Principal component analysis of the microbial composition of various fruits and flowers. The plot is based on the relative abundances of all species, detected by fragment recruitment plotting after shotgun metagenomic sequencing. WGF, white guava fruits; MFC, closed medlar flowers; MFO, open medlar flowers; PFA, almost ripe passion fruits; PFR, ripe passion fruits; PAU, unripe papaya fruits; PAA, almost ripe papaya fruits; PAR1 and PAR2, ripe papaya fruits.

The tropical fruit samples investigated showed large differences in microbial community composition, both between and within the selected fruit types. The microbial communities unraveled were mainly composed of bacteria and to a much lesser extent yeasts. Most genera and/or species identified were known inhabitants of flower surfaces, fruit surfaces, and/or the phyllosphere. Species of lactic acid bacteria, acetic acid bacteria, and yeasts, which are suitable for their use in food fermentation processes, were only minor members of these microbial communities.

HPC clusters of VSC and VUB were of utmost importance to perform this research project successfully.

Although a combined taxonomic identification approach was used to process the metagenomic sequence reads (MSRs), relying on different classification methods and fragment recruitment plotting, a large part of the MSRs could not be identified at the species level due to the lack of the corresponding genome sequences in the public databases used. This indicated that either the microorganisms are known but without having their genomes sequenced and/or publicly available, or that yet unknown species were present. Notwithstanding this lack of information in public sequence databases necessary for the current project, these public sequence databases increase in size daily. Together with the large MSR data sets obtained with current DNA sequencing methodologies, shotgun metagenomic sequence data analysis is a computationally intensive task. Hence, the HPC clusters of VSC and VUB were of utmost importance to performing this research project successfully.


The full publication on this topic can be found in Frontiers

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