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. 2023 Aug 18;12(16):3102.
doi: 10.3390/foods12163102.

Microbiome of Free-Living Amoebae (FLA) Isolated from Fresh Organic Produce: Potential Risk to Consumers?

Lara Soler  1 , Yolanda Moreno  1 , Laura Moreno-Mesonero  1   2 , Inmaculada Amorós  1 , José Luís Alonso  1 , María Antonia Ferrús  2
Affiliations

Microbiome of Free-Living Amoebae (FLA) Isolated from Fresh Organic Produce: Potential Risk to Consumers?

Lara Soler et al. Foods. .

Abstract

In response to growing global interest in organic agriculture, this study delves into the microbial landscape of organically grown raw produce with a focus on food safety. Vegetables that are consumed raw are potential vehicles for the transmission of any type of microorganism capable of causing human disease. Free-living amoebae (FLA) are ubiquitous protozoa found in many ecosystems and can serve as hosts to pathogenic bacteria. So far, data regarding the FLA bacterial microbiome in fresh produce remain scarce and are non-existent for those of organic origin. Thus, the aim of this preliminary work is to characterize the microbiome of FLA in commonly consumed raw vegetables to know their possible implications for consumers. A total of 40 organic cabbage, lettuce, spinach, and strawberry samples were analyzed. FLA were found in all samples, and their bacterial microbiome was obtained via amplicon sequencing using the Illumina MiSeq platform and pair-end protocol. Acanthamoeba spp. and Vermamoeba vermiformis were identified via qPCR in 65.0% and 25.0% of the samples, respectively. Regarding the bacterial microbiome of FLA, the most abundant genera were Pseudomonas (1.8-17.8%) and Flavobacterium (1.7-12.6%). Bacteria not previously related to FLA, such as Prosthecobacter or Cellvibrio, are described in this work. Importantly, several bacterial genera found within the FLA microbiome were identified as potential human pathogens, including Pseudomonas, Flavobacterium, Arcobacter, Klebsiella, Mycobacterium, Salmonella and Legionella. This is the first work in which FLA microbiome isolated from organic products has been characterized, underscoring the significance of understanding FLA's role as carriers of pathogenic bacteria in the context of organic food safety.

Keywords: amoeba-resistant bacteria; free-living amoebae; microbiome; organic vegetables.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Relative abundance (%) of bacterial phyla (A) and classes (B) identified as part of the FLA microbiome isolated from fresh organic produce.
Figure 2
Figure 2
Heatmap of the relative abundance (%) of the most abundant bacterial genera (>2% in at least one type of sample) identified as part of the FLA microbiome isolated from fresh organic produce.
Figure 3
Figure 3
Microbial diversity analysis. (A) Rarefaction curve. (B) Faith’s Phylogenetic Diversity index. (C) Two-dimensional principal coordinate analysis (PCoA) plots based on unweighted UniFrac distance matrices. (D) Two-dimensional principal coordinate analysis (PCoA) plots based on weighted UniFrac distance matrices.
See this image and copyright information in PMC

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