# Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households

Damien Ballan, Adeline Picot, Nolwenn Rolland, Clément Bovo, Claire Prévost, Emmanuel Coton, Jérôme Mounier

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## To cite this version:

Damien Ballan, Adeline Picot, Nolwenn Rolland, Clément Bovo, Claire Prévost, et al.. Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households. International Journal of Food Microbiology, 2025, 437, pp.111204. 10.1016/j.ijfoodmicro.2025.111204. hal-05075637

HAL Id: hal-05075637

https://hal.univ-brest.fr/hal-05075637v1

Submitted on 20 May 2025

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# Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households

Damien Ballan, Adeline Picot, Nolwenn Rolland, Clément Bovo, Claire Prévost, Emmanuel Coton, Jérôme Mounier*

Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France

## ARTICLE INFO

**Keywords:**

Food waste

Domestic storage

Consumer practices

Fungi

Bacteria

Microbial ecology

Citizen sciences

## ABSTRACT

Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, *Penicillium* spp. were the most common representing more than 50 % of mold isolates followed by *Botrytis* (12.4 %), *Mucor* (8.6 %) and *Cladosporium* (7.6 %) spp. *Hanseniaspora uvarum* and *Aureobasidium pullulans* were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with *Pseudomonas* spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.

## 1. Introduction

Food loss and waste are a global phenomenon leading to economic losses, ecological issues and increasing inequalities in society. They can occur at every stage of the food chain, from field to fork, involving any type of food (FAO, 2011). In industrialized countries, the highest volume of food loss and waste occurs at the consumer's level, yielding about 53 % of total food waste in Europe (Vittuari et al., 2016). Of this, fresh fruits and vegetables (FFV) represent the highest percentage of waste, estimated at approximately 40 % of total domestic waste (FAO, 2011; WRAP, 2008). Many studies focused on understanding the main drivers of food losses along the food chain (Alegbeleye et al., 2022; FAO, 2011), but few of them have been conducted at the consumer's level. Moreover, while societal and individual behaviors have been taken into consideration (Hebrok and Boks, 2017), the role and nature of microorganisms in

domestic waste remains understudied. Most household FFV waste is caused by organoleptic defects, and since FFV usually do not have an expiration date, consumers are likely to throw them away while still edible for fear of food poisoning (Neff et al., 2015). FFV spoilage is caused by plant physiological processes, such as wilting or drying, and/or by microbial growth, in particular fungi (molds and yeasts) and bacteria, even though spoilage by viruses or protozoa can also occur (Pitt and Hocking, 2009a; Snowdon, 1991). Microbial contamination of fruits and vegetables can occur at any step of the food life, from the farm to the table, and can occur at pre- and post-harvest stages (Alegbeleye et al., 2022; Balali et al., 2020; Karanth et al., 2023; Snyder and Worobo, 2018). In households, spoilage may occur because FFV are already contaminated by spoilage microorganisms able to grow under storage conditions or because of cross-contamination from other fruits or vegetables, transfer from humans or food contact surfaces. FFV are also

<footnote>* Corresponding author.
E-mail address: jerome.mounier@univ-brest.fr (J. Mounier).</footnote>
more likely to get spoiled when fragilized by shocks or skin damages, providing an entry route for infection (Hussein et al., 2020).

Fruits and vegetables are highly diverse, showing a wide susceptibility range to spoilage organisms. For instance, tissues such as bulbs or roots are more robust than fruits or leaves. Despite the fact that physicochemical parameters (mainly pH) and composition greatly vary according to FFV, all of them can be subjected to microbial spoilage. Nevertheless, most bacteria have overall poor resistance to low pH and, as such, are more likely to contaminate vegetables than fruits. For instance, enterobacteria were reported to be responsible for spoilage of tubers, leaf vegetables or fruiting vegetables (Charkowski, 2018; Lee et al., 2013; Lui et al., 2005) while *Pseudomonas* spp. were commonly associated with spoiled leaf vegetables, bulbs or cucurbits (Abd-Alla et al., 2011; Sawada et al., 2021; Snowdon, 1990) and lactic acid bacteria (LAB) with root vegetables (Lampert et al., 2017). However, these microbial spoilers are more commonly involved in fresh cut vegetables spoilage than in whole ones (Alegbeleye et al., 2022; Lampert et al., 2017). In contrast, fungi are able to resist wider ranges of physicochemical conditions and thus infect both fruits and vegetables independently (Barth et al., 2009). Filamentous fungi associated with FFV spoilage belong to various genera, the most prevalent being *Penicillium*, *Mucor*, *Aspergillus*, *Alternaria* and *Fusarium*. Given the adaptable nature of molds as well as their large diversity, FFV can be contaminated by either multiple species or more host-specific fungi. For instance, at least 20 different species in the *Penicillium* genus are able to spoil FFV (Alegbeleye et al., 2022; Karanth et al., 2023; Pitt and Hocking, 2009b; Snowdon, 1990). This genus includes species able to tolerate pH below 3 that are able to quickly spoil citrus fruits (*Penicillium digitatum* and *Penicillium italicum*). Another major *Penicillium* species involved in fruit spoilage is *Penicillium expansum* which is one of the main causes for pome fruit decay, as well as other fruit species (Pitt and Hocking, 2009b).

Yeasts are less commonly found in spoiled FFV since they dissemi-nate slower than molds. However, some species are able to colonize FFV, leading to spoilage, such as *Geotrichum candidum* on bulbs, leaf vegetables, root vegetables and citrus, or *Hanseniaspora uvarum* on different fruits (Alegbeleye et al., 2022; François et al., 2022; Pitt and Hocking, 2009c).

While the above-cited studies focused on identifying microorganisms on spoiled FFV during storage, little information is available about which FFV are more commonly subjected to microbial spoilage in a domestic environment and which organisms are responsible. Yet, such information is essential to determine control strategies to reduce FFV waste.

In this context, the aims of this study were to i) investigate which FFV are usually wasted depending on the season and storage conditions at households, and ii) identify the microorganisms associated with spoiled FFV.

# 2. Materials and methods

## 2.1. Spoiled fresh fruits and vegetables

Using a citizen science approach, FFV samples (n = 346) were collected from 49 volunteer households in the Brest area (Finistère, Brittany, France) during 2 separate periods, namely from 05/15/2021 to 07/25/2021 and from 10/10/2021 to 12/15/2021 (thereafter named "Summer" and "Autumn" periods). These samples originated from FFV that were considered « no longer edible » from the consumer's point of view. They were asked to cut portions showing signs of deterioration in a Ziplock bag and store them at -20 °C before we collected them all at the end of the period. In addition, participants were asked to answer a series of questions accompanied by a choice of answers for each FFV, including their storage place (refrigerators or room temperature), or the type of farming under which FFV were cultivated (organic or conventional). Furthermore, for data analysis purposes, FFV were separated into

different categories according to the FoodEx2 classification system (EFSA, 2015). Overall, 265 and 89 samples were retrieved from the "Summer" and "Autumn" periods, respectively, and were directly stored upon reception at -20 °C before microbiological analysis.

## 2.2. Microbiological analysis

Spoiled samples were plated directly with a loop when fungal mycelium was visible on the fragment surface on M2Lev (20 g/L malt extract, 3 g/L yeast extract, 15 g/L, 5 mg/L penicillin G (Sigma-Aldrich, Dormstat, Germany), 5 mg/L streptomycin (Sigma-Aldrich, Dormstat, Germany) medium. For samples which did not show any visible mycelium, a fragment of about 1 to 2 g was placed into a 50-ml tube filled with 10 mL of saline solution (9 g/L NaCl), before being vortexed at high speed for 10 s. The obtained suspension was then directly plated on both M2Lev and Plate Count Agar (PCA, Difco, Saint-Ferreol, France) supplemented with 11 mg/L amphotericin B (Sigma-Aldrich, Dormstat, Germany) in order to retrieve any fungal or bacterial contaminant, respectively.

After incubation at 30 °C for 2–3 days and 25 °C for 3–7 days for PCA and M2Lev, respectively, dominant morphotypes were then selected and purified on the same media without antibiotic supplementation and incubated as described above. Purified isolates were then stored in a 20 % (v/v) glycerol solution and kept at -80 °C until further use.

## 2.3. Isolate identification

### 2.3.1. MALDI-ToF identification

#### 2.3.1.1. Sample preparation for mold isolates.
Isolates were first identified using a Matrix Assisted Laser Desorption Ionization – Time of Flight mass spectrometry (MALDI-ToF) method (VITEK MS system (bioMérieux, Marcy l'Etoile, France), following the manufacturer's instructions. Biomass of mold isolates cultivated for 2 to 8 days on potato dextrose agar (PDA, Difco, Saint-Ferreol, France) was collected on a ~ 1-cm² surface using a sterile cotton swab moisturized with API Suspension Medium (bioMérieux, Marcy l'Etoile, France). The collected biomass was transferred into a microtube containing 900 µL of 70 % ethanol and then vortexed for approximately 5 s and centrifuged at 14,000 xg for 2 min. The supernatant was discarded and the pellet was resuspended in 40 µL of 70 % formic acid (Sigma-Aldrich, St. Quentin Fallavier, France), before vortexing for 5 s. Forty µL of acetonitrile were then added, followed by a centrifugation at 14,000 xg for 5 min. One µL of the obtained supernatant was deposited on the acquisition chip in duplicate. Once the spot was dry, 1 µL of α-cyano-hydroxycinnamic acid matrix solution (CHCA; bioMérieux, Marcy l'Etoile, France) was deposited on the spot and allowed to dry.

#### 2.3.1.2. Sample preparation for bacteria and yeast isolates.
For bacteria, a quarter of a colony was collected with a sterile loop from PCA incubated for 24 to 48 h, deposited on the acquisition chip and covered with 1 µL of CHCA solution following the manufacturer's instructions. Yeast were cultivated on PDA for 24 to 48 h and treated the same as bacteria except that 1 µL of 70 % formic acid was first deposited and allowed to dry on the spot before adding the CHCA solution. Fresh cells of *Escherichia coli* ATCC 8739 were used for the run calibration.

#### 2.3.1.3. MALDI-ToF MS analysis.
Fungal (mold and yeast) and bacterial spectra were finally acquired in linear positive extraction mode in a mass range from 2000 to 20,000 Da using the "Auto-Quality" option using the VITEK MS system (bioMérieux, Marcy l'Etoile, France) equipped with the Launchpad version 2.9.5.6 acquisition software as described previously (Rolland et al., 2024). Each spectrum was generated by the accumulation of 500 laser shots, 100 profiles being acquired from each spot with five shots per profile. Calibration was externally
made using fresh cells of *Escherichia coli* ATCC 8739. Two quality control
strains, *Aspergillus brasiliensis* ATCC 16404 for molds and *Candida glab-
rata* MYA-3950 for yeasts, were also included for each reagent kit and on
each day of spectra acquisition. The Launchpad acquisition software
automatically processed raw spectra through smoothing and peak
detection procedures and assignments were obtained for each isolate
using the IVO V3.4 spectral database.

2.3.2. Assignment confirmation using DNA sequencing

Once MALDI-ToF assignments were obtained, spectra of isolates
from the same genus were compared to build clusters based on their
similarities using SARAMIS software (bioMérieux, Marcy l'Etoile,
France) as described by Penland et al. (2020). A threshold of 65 %
similarity was applied for bacteria and of 50 % for fungi (Lindgren et al.,
2018). One isolate from each cluster (n = 130) was then selected and
fresh biomass was collected for DNA extraction.

2.3.2.1. DNA extraction. DNA from the 130 selected isolates was extracted using the Fast DNA Spin Kit (MP Biomedicals, Solon, USA) following the manufacturer's instructions. DNA quantification was performed using a NanoDrop1000 spectrophotometer (Thermo-Scientific, Wilmington, USA).

2.3.2.2. **PCR and sequencing.** In order to confirm the MALDI-ToF assignment, and to identify isolates without an assignment from the MALDI-ToF database, the extracted DNAs were amplified using primers corresponding to their presumptive genus. Seven primers pairs allowing to precisely identify up to the species main groups of organisms found on spoiled FFV were selected. PCR conditions were the same as those cited in the original article describing their first use. For fungal isolates, partial β- tubulin gene (Bt2A: 5'-GGTAAC-CAAATCGGTGCTGCTTTC-3', Bt2B: 5'-ACCCTCAGTGTAGTGACCCTTGGC-3', Glass and Donaldson, 1995) was sequenced for Penicillium spp. and Aspergillus spp. isolates, partial actin gene (ACT-512F 5'-ATGTCAAGGCCGGTTTCGC-3', ACT-783R 5'-TACGAGTCCTTCTGGCCCAT-3' Carbone and Kohn, 1999) for Cladosporium spp., partial elongation factor alpha-1 (EF1-f 5'-ATGGGTAAGGAGCAAGACTCA-3', EF1-r TGGAGATACCAGCCTCGAAC-3' O'Donnell et al., 1998) for Fusarium spp. while the internal transcribed spacer (ITS) region (ITS4 5'-TCCTCCGCTTATTGATATGC-3', ITS5 5'-GGAAGTAAAAGTCGTAACAAGG-3' White et al., 1990) was used for all other mold isolates. The D1-D2 domain of the 26S rRNA gene (NL1 5'-GCA-TATCAATAAGCGGAGGAAAAG-3', NL4 5'-GGTCCGTGTTTCAAGACGG-3' Kurtzman and Robnett, 1998) was sequenced for yeast isolates. Concerning bacteria, partial B-protein subunit of DNA gyrase gene (Gyr B) (gyr-320 5'-TAARTTYGAYGAYAACTCYTAYAAAGT-3', gyr-1260 5'-CMCCYTCCACCARGTAMAGTTC-3' Dauga, 2002) sequencing was used for Enterobacterales isolates, rpoB (LAPS 5'-TGGCCGAGAACAGTTCCGCGT-3', LAPS27 5'-CGGCTTCGTCCAGCTTGTCAG-3' Ait Tayeb et al., 2005) for Pseudomonas spp. and partial 16S rRNA gene (16S-f 5'-CCGAATTCGTCGACAACAGAGTTTGATCCTGGCTCAG-3', 16S-r 5'-CCCGGGATCCAAGCTTACGCTACCTTGTTACGACTT-3' Weisburg et al., 1991) for other bacterial isolates. PCR amplification was controlled by performing an electrophoresis on a 1 % agarose gel.

All successfully amplified DNA fragments were sequenced at Euro-
fins Genomics (Edersberg, Germany). Sequences were assembled into
contigs using the Geneious Prime 2024.0.5 software (www.geneious.
com) and were compared to the GenBank database using the "Basic
Local Alignment Search Tool" (BLAST) (http://www.ncbi.nlm.nih.
gov/BLAST).

Ambiguous assignments were verified using phylogenetic analysis
with type strain sequences retrieved from GenBank using tools available
on www.phylogeny.fr (Dereeper et al., 2008), using the MUSCLE algo-
rithm to perform multiple alignment, Gblocks for curation, PhyML for
the construction of phylogenetic tree and TreeDyn to visualize

phylogenetic tree. Sequences have been deposited in Genbank (acces-
sion numbers: PQ453748-PQ453779, PQ462741-PQ462745,
PQ594429-PQ594434, PQ594435-PQ594450, PQ568103-PQ568108,
PQ444165-PQ444173, PQ454080-PQ454118).

2.4. Statistical analysis

Significant differences between frequencies of spoiled FFV or of
microorganisms depending on the FFV nature were established using
Chi2 tests of independence, combined with pairwise comparisons to
establish statistically different groups using Rstudio Version 2022.07.2
+ 576 base "chiq.test" followed by a pairwise post hoc comparison using
the "chisq.posthoc.test" package. Plots were generated using Rstudio,
using the "ggplot2" and "dplyr" packages.

2.5. Meta-analysis of observed microbial diversity

The diversity of spoilage microorganisms identified to the species
level and observed at least twice on the sampled products in the present
study was compared to the diversity reported in the scientific literature
on pre- and post-harvest stages of the food chain. For this purpose, a
database was built by assembling FFV microbial spoilers described in
literature reviews by Alegbeleye et al. (2022), Pitt and Hocking (2009a,
2009b, 2009c, 2009d) and Snowdon (1990, 1991) as well as various
recent research articles (Abo-Elyoursr and Abdel-Rahim, 2015; Chandra
Mohana et al., 2022; Duduk et al., 2021; Dugan et al., 2017; Elbanna
et al., 2014; Fan et al., 2016; Hoang et al., 2023; Janave and Sharma,
2008; Kazerooni et al., 2021; Louw and Korsten, 2014; Maghsoodi et al.,
2025; Mrvová et al., 2024; Smith et al., 1979; Tomar et al., 2022;
Vetrova et al., 2024; Zhao et al., 2021). Using the created database and
the UpSet R package (Conway et al., 2017), an UpSet plot was generated
to visualize the number of microbial taxa uniquely collected from a
single FFV category or shared across multiple categories. In total, eight
FFV categories were selected (namely stone fruits, root vegetables, pome
fruits, miscellaneous fruits, fruiting vegetables, citrus, bulb vegetables
and berries), each of which divided into the household level or the
earlier stages (pre- and/or post-harvest).

3. Results

3.1. *Typology of wasted FFV*

Among the 346 FFV samples, 193 corresponded to fruits, of which 146 were collected during the “Summer” period and 47 during the “Autumn” one. The 153 remaining samples were vegetables, with 114 and 39 collected during the “Summer” and “Autumn” periods, respectively (Fig. 1).

During the “Autumn” period, most discarded fruits were pome or
citrus fruits (38 and 36 %, respectively), while stone fruits accounted for
about half (45 %) of total collected samples during the “Summer” period
while none were collected during the “Autumn (Fig. 1A). The percentage
of “small fruits and berries” and “miscellaneous and exotic fruits” was
similar between the two seasons.

Concerning vegetables (Fig. 1B), the most wasted ones corresponded to fruit vegetables during both studied periods (47 % and 37 % during the “Summer” and “Autumn” periods, respectively), followed by root vegetables (14 % and 18 %, respectively), leaf vegetables (8 % and 18 %), and bulb vegetables (12 % and 8 %). Stem vegetables, brassica vegetables, tubers and cultivated fungi represented less samples in both periods (about 10 % or less).

While 37 % of spoiled FFV corresponded to conventional products,
39 % were organic, the remaining 24 % had no information about their
production methods. Discarded FFV were significantly more stored at
room temperature than in the fridge (73 % and 27 %, respectively, Chi2
P value = 2.2 × 10⁻²², difference between obtained and predicted values
of number of spoiled FFV = + 80).
<figure><img src="image_5.png" /><figcaption>Fig. 1. Distribution (%) of spoiled fresh fruits (A) and vegetables (B) collected during the 2 different periods.</figcaption></figure>

## 3.2. Isolated microorganisms

Overall, 194 filamentous fungi, 146 bacteria and 34 yeasts were isolated from 264 samples, representing respectively 52 %, 39 % and 9 % of isolated microorganisms (Table 1). Ninety samples (25 %) did not show significant microbial growth. Filamentous fungi, yeasts and bacteria were not evenly distributed between the different Foodex FFV categories (Table 1). Indeed, filamentous fungi were the most prevalent on bulb vegetables, citrus fruits, fruit vegetables and stone fruits as compared to bacteria and yeasts. In contrast, bacteria were only more prevalent on leaf vegetables, while yeasts remained the least prevalent group of organisms whatever the FFV category.

<table><caption>**Table 1**
Distribution of isolated microorganisms on spoiled FFV based on Foodex categories.</caption><thead><tr><th rowspan="2"></th><th colspan="3">Number (N) and frequency (%)</th></tr><tr><th>Molds</th><th>Bacteria</th><th>Yeasts</th></tr></thead><tbody><tr><td>Berries and small fruits<br>(N = 21)</td><td>11<br>52.4 %</td><td>5<br>23.8 %</td><td>5<br>23.8 %</td></tr><tr><td>Brassica vegetables<br>(N = 5)</td><td>2<br>40.0 %</td><td>3<br>60.0 %</td><td>0<br>0 %</td></tr><tr><td>Bulb vegetables<br>(N = 21)</td><td>21<br>100 %</td><td>0<br>0 %</td><td>0<br>0 %</td></tr><tr><td>Citrus fruits<br>(N = 26)</td><td>20<br>76.9 %</td><td>5<br>19.2 %</td><td>1<br>3.9 %</td></tr><tr><td>Cultivated mushrooms<br>(N = 7)</td><td>2<br>28.6 %</td><td>5<br>71.4 %</td><td>0<br>0 %</td></tr><tr><td>Fruiting vegetables<br>(N = 60)</td><td>39<br>65.0 %</td><td>16<br>26.7 %</td><td>5<br>8.3 %</td></tr><tr><td>Leaf vegetables<br>(N = 10)</td><td>1<br>10 %</td><td>8<br>80 %</td><td>1<br>10 %</td></tr><tr><td>Miscellaneous fruits<br>(N = 21)</td><td>7<br>33.3 %</td><td>11<br>52.4 %</td><td>3<br>14.3 %</td></tr><tr><td>Pome fruits<br>(N = 37)</td><td>21<br>56.8 %</td><td>15<br>40.5 %</td><td>1<br>2.7 %</td></tr><tr><td>Root vegetables<br>(N = 36)</td><td>18<br>50.0 %</td><td>15<br>41.7 %</td><td>3<br>8.3 %</td></tr><tr><td>Stem vegetables<br>(N = 11)</td><td>3<br>27.4 %</td><td>7<br>63.5 %</td><td>1<br>9.1 %</td></tr><tr><td>Stone fruits<br>(N = 65)</td><td>43<br>66.2 %</td><td>9<br>13.8 %</td><td>13<br>20.0 %</td></tr><tr><td>Tubers<br>(N = 10)</td><td>5<br>50.0 %</td><td>5<br>50.0 %</td><td>0<br>0 %</td></tr></tbody><tfoot><tr><td>Total</td><td>193</td><td>104</td><td>33</td></tr></tfoot></table>

<figure><img src="image_6.png" /></figure>

## 3.3. Microbial diversity in spoiled fruits and vegetables

### 3.3.1. Mold diversity

Among the 194 molds retrieved from spoiled FFV, 183 isolates belonging to 15 genera and 42 different species from the Ascomycota (88.6 %) and Mucoromycota (9.7 %) phyla were identified, the remaining isolates (n = 11) being unidentified due to “no identification” results using MALDI-ToF analysis and PCR/sequencing failure. More than half of identified filamentous fungi (55 %) belonged to Penicillium, distributed among 17 different species. Other genera were fairly abundant and represented most of the remaining molds identified, among which Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %). Among the 21 most commonly isolated organisms, molds represented 16 species (Table 2, Fig. 2). The most prevalent species were P. expansum (n = 26 isolates), B. cinerea (n = 14), P. crustosum (n = 12), P. olsonii (n = 12) and P. italicum (n = 12) (Table 2 and Fig. 2). In addition, some of these species were found on a large array of FFV. For instance, of the 13 Foodex FFV categories, P. expansum was isolated across 9 categories, P. crustosum on 6 categories and C. cladosporioides complex on 5 categories (Table 2 and Fig. 2). Other prevalent species were isolated from a narrower range of FFV. For instance, all 6 P. digitatum isolates were collected from citrus fruits and all 8 Botrytis pelargonii isolates came from either small fruits and berries, or fruit vegetables. A few rarer genera (n = 5) were only represented by one species isolate, namely Acrostalagmus luteoalbus, found on starchy roots and tubers, Dothiora viticola, on berries and small fruits, Didymella glomerata, on pome fruits, Plectosphaerella niemeijerarum, on starchy roots and tubers, and Talaromyces germanicus, on bulb vegetables (Table 2).

### 3.3.2. Yeast diversity

About two thirds of isolated yeasts were collected from fruits (68 %), while some vegetable Foodex categories (brassica vegetables, bulb vegetables, cultivated mushrooms and starchy roots and tubers) did not harbor any yeast isolates (Table 3). Among the 31 identified isolates, 24 isolates belonged to the Ascomycota phylum and 7 to the Basidiomycota phylum. Thirteen different genera were identified, among which 8 were only isolated once (Candida helenica, Debaryomyces hansenii, Exophiala dermatitidis, Metschnikowia pulcherrima, Meyerozyma guilliermondii, Filobasidium sp., Holtermaniella takashimae, Papilliotrema flavescens). Overall, 15 different species were identified and two species accounted for about half of the yeast isolated from spoiled FFV, namely H. uvarum (n = 9 isolates) and Aureobasidium pullulans (n = 7), the former was isolated from small fruits and berries, stone fruits and fruiting vegetables while the latter was only found on stone fruits (Table 3 and Fig. 2).
<table><caption>**Table 2**

Diversity of spoilage-associated filamentous fungi on FFV at consumer's level.</caption><thead><tr><th rowspan="3">Closest phylogenetic affiliation</th><th colspan="5">Isolation source</th><th colspan="8">Vegetables</th><th rowspan="3">Total</th><th rowspan="3">Frequency (%)</th></tr><tr><th colspan="5">Fruits</th><th colspan="8">Vegetables</th></tr><tr><th>Berries and small fruits</th><th>Citrus fruits</th><th>Misc. fruits<fnref n="1" /></th><th>Pome fruits</th><th>Stone fruits</th><th>Brassica veg.</th><th>Bulb veg.</th><th>Cultivated mushrooms</th><th>Fruiting veg.</th><th>Leaf veg.</th><th>Root veg.</th><th>Starchy roots & tubers</th><th>Stem veg.</th><th>Other</th></tr></thead><tbody><tr><td>Ascomycota</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Acrostalagmus</td><td>luteoalbus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Alternaria</td><td>alternata</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>sp.</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Aspergillus</td><td>creber</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Botryotinia</td><td>niger complex</td><td>-</td><td>-</td><td>2</td><td>-</td><td>1</td><td>-</td><td>2</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>5</td><td>2.6</td></tr><tr><td>Botrytis</td><td>ranunculi</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>2</td><td>1.0</td></tr><tr><td></td><td>cinerea</td><td>2</td><td>-</td><td>-</td><td>-</td><td>6</td><td>-</td><td>1</td><td>-</td><td>5</td><td>-</td><td>-</td><td>-</td><td>-</td><td>14</td><td>7.2</td></tr><tr><td></td><td>pelargonii</td><td>3</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>5</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>9</td><td>4.6</td></tr><tr><td></td><td>sp.</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Cladosporium</td><td>cladosporioides complex</td><td>1</td><td>-</td><td>-</td><td>-</td><td>5</td><td>1</td><td>-</td><td>2</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>10</td><td>5.2</td></tr><tr><td></td><td>ramonetellum</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Dothiora</td><td>snafimbriatum</td><td>-</td><td>2</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>3</td><td>1.5</td></tr><tr><td>Fusarium</td><td>viticola</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>3</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>annulatum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>3</td><td>1.5</td></tr><tr><td></td><td>sambucinum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>2</td><td>-</td><td>-</td><td>2</td><td>1.0</td></tr><tr><td></td><td>solani complex</td><td>-</td><td>-</td><td>-</td><td>1</td><td>1</td><td>-</td><td>-</td><td>1</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>4</td><td>2.1</td></tr><tr><td>Penicillium</td><td>allii</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>4</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>5</td><td>2.6</td></tr><tr><td></td><td>aurantiogriseum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>2</td><td>1.0</td></tr><tr><td></td><td>bialowiezense</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>brevicompactum</td><td>3</td><td>-</td><td>-</td><td>-</td><td>2</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>6</td><td>3.1</td></tr><tr><td></td><td>citrinum</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>crustosum</td><td>-</td><td>1</td><td>-</td><td>2</td><td>2</td><td>-</td><td>1</td><td>-</td><td>3</td><td>-</td><td>3</td><td>-</td><td>-</td><td>12</td><td>6.2</td></tr><tr><td></td><td>digitatum</td><td>-</td><td>6</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>6</td><td>3.1</td></tr><tr><td></td><td>expansum</td><td>-</td><td>1</td><td>2</td><td>11</td><td>6</td><td>-</td><td>1</td><td>1</td><td>1</td><td>-</td><td>2</td><td>1</td><td>-</td><td>26</td><td>13.4</td></tr><tr><td></td><td>glabrum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>5</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>6</td><td>3.1</td></tr><tr><td></td><td>italicum</td><td>-</td><td>9</td><td>-</td><td>2</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>12</td><td>6.2</td></tr><tr><td></td><td>olsonii</td><td>-</td><td>-</td><td>-</td><td>-</td><td>2</td><td>-</td><td>-</td><td>-</td><td>10</td><td>-</td><td>-</td><td>-</td><td>-</td><td>12</td><td>6.2</td></tr><tr><td></td><td>onobense</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>paneum</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>polonicum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>raistrickii</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>solitum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>sp.</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Didymella</td><td>glomerata</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Plectosphaerella</td><td>niemeijarum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Talaromyces</td><td>germanicus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td>Trichoderma</td><td>harzianum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>6</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>8</td><td>4.1</td></tr><tr><td>Mucoromycota</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Mucor</td><td>brunneogriseus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>4</td><td>-</td><td>1</td><td>-</td><td>1</td><td>-</td><td>6</td><td>3.1</td></tr><tr><td></td><td>circinelloides complex</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>4</td><td>2.1</td></tr><tr><td></td><td>hiemalis</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>0.5</td></tr><tr><td></td><td>sp.</td><td>-</td><td>-</td><td>1</td><td>1</td><td>2</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>5</td><td>2.6</td></tr><tr><td>Rhizopus</td><td>stolonifer</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>2</td><td>1.0</td></tr><tr><td></td><td>Unidentified fungi</td><td>-</td><td>-</td><td>1</td><td>-</td><td>5</td><td>1</td><td>1</td><td>1</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>11</td><td>5.7</td></tr><tr><td></td><td>Total</td><td>11</td><td>20</td><td>7</td><td>21</td><td>43</td><td>2</td><td>21</td><td>2</td><td>39</td><td>1</td><td>18</td><td>5</td><td>3</td><td>194</td><td></td></tr><tr><td></td><td>Frequency (%)</td><td>5.7</td><td>10.3</td><td>3.6</td><td>10.8</td><td>22.2</td><td>1.0</td><td>10.8</td><td>1.0</td><td>20.1</td><td>0.5</td><td>9.3</td><td>2.6</td><td>1.5</td><td>100</td><td></td></tr></tbody></table>

<footnote n="1">¹, veg.: vegetables; misc., miscellaneous.</footnote>
<figure><img src="image_7.png" /><figcaption>Fig. 2. Most commonly isolated microorganisms on spoiled fresh fruits and vegetables.</figcaption></figure>

### 3.3.3. Bacterial diversity

Bacterial isolates were distributed among each of the Foodex categories (prevalence ranging from 2.8 to 15.0 %), except for bulb vegetables for which no bacteria were retrieved. Bacterial isolates showed the highest diversity of all identified organisms (49 species for 96 identified isolates), but the vast majority of them were only found once (70 %). Those were distributed among 4 phyla, 5 classes and belonged to 28 different genera. The most frequently isolated species included *Curtobacterium* sp. (n = 11 isolates), *Pseudomonas fluorescens* (n = 9) and *Microbacterium phyllosphaerae* (n = 7) (Table 4 and Fig. 2).

### 3.3.4. Meta-analysis of observed microbial diversity

Microbial diversity associated with eight defined FFV categories in households was compared to that of spoilage organisms described in the literature (Fig. 3, Tables S1 and S2). Among the 42 identified species (for which at least 2 isolates were obtained in the present study), 21 species, including 15 bacterial and 6 fungal species, were unique to one or more FFV categories sampled at the household level. This result indicated that, based on the constructed literature database, these species are not usually considered as spoilers of these same FFV categories at earlier food-chain stages (i.e. pre- et post-harvest stages). Unique bacterial species corresponded to both Gram-positive (*Bacillus cereus* group, *Curtobacterium herbarum*, *Kocuria salsicia*, *Leuconostoc citreum*, *Leuconostoc mesenteroides*, *M. phyllosphearae*, *Staphylococcus sciuri*, *Staphylococcus succinus*) and Gram-negative species (*Enterobacter hormaechei*, *Klebsiella michiganensis*, *Pantoea agglomerans*, *P. fluorescens*, *Rhodococcus erythropolis*, *Stenotrophomonas maltophilia*, *Stenotrophomonas rhizophilia*) while fungal species corresponded to *A. pullulans*, *H. uvarum* and *Rhodotorula mucilaginosa* for yeasts, and *Botryotinia ranunculi*, *Cladosporium snafimbriatum* and *Mucor brunneogriseus* for molds (Tables S1 and S2). As expected, species such as *B. cinerea* and *P. expansum* which are largely reported in the literature to spoil various FFV categories at pre- and/or post-harvest stages were also retrieved from the same FFV categories at the household level. More interestingly, the former was also isolated from spoiled bulbs and roots, and the latter from bulb vegetables which have not been systematically reported as FFV categories spoiled by these

two organisms. A few other common spoilage species isolated from the present study were also collected on unusual FFV; for example, this was the case for *M. circinelloides* and *P. italicum* isolated from spoiled pome fruits and root vegetables, respectively.

## 4. Discussion

Using a participatory science approach, this study provides, for the first time, a comprehensive insight into the typology of FFV that are wasted at the consumer's level and the microorganisms associated with spoiled FFV. Logically, according to the considered period, either "Summer" or "Autumn", collected spoiled FFV changed both in terms of nature and abundance. These differences in composition can be easily explained by the seasonality of fruits and vegetables, which impact the nature of FFV consumed. For instance, stone fruits are mainly represented by peaches, nectarines, apricots and cherries, which are sold only during spring and summer in Western Europe, while apples are harvested in late summer and citrus during autumn and winter, and distributed throughout the year (CTIFL, 2023a; libertyprim, 2017). These differences in abundance must also be put in perspective with the French purchase (or consumption) volume. For instance, French people consume roughly 25 kg of citrus fruits per year per inhabitant, 16 kg of apples per year per inhabitant, while they only consume 5 kg of onions per year per inhabitant (CTIFL, 2024a, 2024b; libertyprim, 2017). More interestingly, our data showed a notable difference between the number of FFV collected during the summer and autumn campaigns (260 samples vs. 86, respectively). This may be explained by different factors, primarily by the nature of the FFV usually consumed during each period themselves, with more fragile and sensitive products being available and consumed in summer such as stone fruits or berries, while autumn vegetables such as onions or pumpkins tend to be more robust overall, and usually present a longer shelf life. Besides, French people were reported to buy less (~-15%) FFV during cold seasons than during spring and summer (FranceAgriMer, 2021), thus logically leading to a lower number of spoiled FFV. Finally, since this study relied on citizen participation, we cannot exclude that some volunteers collected less
<table><caption>Table 3
Diversity of spoilage-associated yeasts on fresh fruits and vegetables at consumer's level.</caption><thead><tr><th rowspan="2">Closest phylogenetic affiliation</th><th colspan="2">Isolation source</th><th colspan="8">Vegetables</th></tr><tr><th>Fruits</th><th>Citrus fruits (n = 1)</th><th>Miscellaneous fruits (n = 3)</th><th>Pome fruits</th><th>Berries and small fruits (n = 5)</th><th>Stone fruits (n = 11)</th><th>Fruiting vegetables (n = 3)</th><th>Leaf vegetables (n = 1)</th><th>Root vegetables (n = 2)</th><th>Stem vegetables (n = 1)</th><th>Other</th><th>Total</th><th>Frequency (%)</th></tr></thead><tbody><tr><td rowspan="10">Phylum Ascomycota</td><td rowspan="10">Genus Aureobasidium</td><td>Species pullulans</td><td>-</td><td>-</td><td>-</td><td>-</td><td>7</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>7</td><td>20.6</td></tr><tr><td>sp. hellenica</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Candida</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Debaryomyces</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>hansenii</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>dermatitidis</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Geotrichum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>1</td><td>-</td><td>-</td><td>-</td><td>2</td><td>5.9</td></tr><tr><td>candidum</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>9</td><td>26.5</td></tr><tr><td>avarum</td><td>-</td><td>1</td><td>-</td><td>-</td><td>3</td><td>4</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>pulcherrima</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td rowspan="10">Basidiomycota</td><td>Metschnikowia</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Meyerozyma</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Filobasidium</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Hollermanniella</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Papiliontea</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>2.9</td></tr><tr><td>Rhodotorula</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>2</td><td>5.9</td></tr><tr><td>mucilaginosa</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>2</td><td>5.9</td></tr><tr><td>Unidentified yeast</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Total</td><td>1</td><td>3</td><td>1</td><td>5</td><td>13</td><td>5</td><td>1</td><td>1</td><td>3</td><td>1</td><td>1</td><td>3</td><td>8.8</td></tr><tr><td>Frequency (%)</td><td>2.9</td><td>8.8</td><td>2.9</td><td>14.7</td><td>38.2</td><td>14.7</td><td>2.9</td><td>8.8</td><td>2.9</td><td>2.9</td><td>1</td><td>34</td><td>100</td></tr></tbody></table>

samples during the second period due to a loss of commitment, as already described in past studies (Hansen and Bonney, 2022).

Another striking result from our dataset was that three quarters of collected samples were stored at room temperature, in link with the fact that refrigeration reduces the spoilage risk but might be underused by consumers. This corroborates studies such as that of the Waste and Resources Action Programme (WRAP, 2008) which focused mainly on the physiological impact on the product, while our study underlines microbiological spoilage led by such practices as well. Porat et al. (2018) noted that poor home-storage management was one of the main factors involved in household food waste for FFV, alongside poor planification and over-purchasing. As advised by the French Interprofessional Technical Center for Fruit and Vegetables (CTIFL), almost every frequently consumed FFV in France have an optimal storage temperature between 4 and 10 °C and therefore should be stored in domestic fridges, with a few exceptions for fruits such as tomatoes, whose aromas can be negatively impacted by low temperatures, or bananas which are sensible to cold injuries (CTIFL, 2023b). The production method is also known to influence the spoilage risk. In our case, among the collected spoiled samples for which this information was available, 49 % were organic while 51 % originated from conventional agriculture. However, these results must be related to the purchase volume to determine whether production method significantly impacts spoilage. Based on a study conducted by the French observatory of organic French agriculture in 2021, organic FFV only represent a small portion of FFV market share in France (8.6 % for fruits and 7.7 % for vegetables) (Renault et al., 2022). According to this result, conventionally-grown FFV would be less likely wasted, potentially because pesticide treatments might enhance resistance to microorganisms for FFV, although actual purchase volume of volunteer households would be necessary to validate this assumption. Another noticeable information from this study is that 25 % of the samples studied showed no microbial growth, and therefore, were likely spoiled because of physiological spoilage such as drying or wilting indicating that microbial spoilage is the main cause of FFV waste at households, while physiological decay is less prevalent.

To the best of our knowledge, this is the first time that organisms associated with spoiled FFV at consumer's level are studied in depth, making it difficult to find comparisons with our data outside of experiments focusing on early stages of the food chains (i.e. pre- or post-harvest) or on fresh cut FFV at home. Most of the 264 samples led to the isolation of filamentous fungi (52 %), closely followed by bacteria (39 %) while yeasts were scarcer (9 %). Physico-chemical parameters of FFV such as high $a_w$, rich nutrient content, or moderate pH make those matrices prone to microbial contamination and colonization. It is worth noticing that fruits usually show lower pH values than most vegetables. For instance, pH of apples is around ~3.5 or lemons around 2.3, while that of pepper and lettuce are usually of 5.1 and 6.0, respectively (Bridges and Mattice, 1939). As the pH goes up towards neutrality, bacteria presence becomes more likely (Pitt and Hocking, 2009d). In this study, based on FFV pH reported by Bridges and Mattice (1939), we found that bacteria were significantly more prevalent on FFV with pH between [5.10–6.5], compared to pH classes [2.30–3.69] and [3.70–5.09] (Chi2 *P* = 0.008, difference between obtained and predicted value = +13 with the [2.30–3.69] category and Chi2 *P* = 0.0014, difference between obtained and predicted value = +11 with the [3.70–5.09] category respectively), thus in line with their known pH preference. In contrast, fungal prevalence was not significantly impacted by pH range, again in line with their large pH range preference. It is worth mentioning that more fruits than vegetables were provided by the participant households in this study, which may explain why we observed a higher mold prevalence.

Among filamentous fungi associated with spoiled FFV, the Penicillium genus accounted for more than half of the identified mold isolates, with 16 different species. Penicillium is frequently reported as one of the most prevalent and diverse genera when it comes to post-harvest losses, as the different species can tolerate wide pH ranges, produce large amounts of
<caption>Table 4</caption>

Diversity of spoilage-associated bacteria on fresh fruits and vegetables at consumer's level.

<table><thead><tr><th rowspan="2">Closest phylogenetic affiliation</th><th rowspan="2">Genus</th><th rowspan="2">Species</th><th colspan="10">Isolation source</th><th rowspan="2">Frequency (%)</th></tr><tr><th colspan="3">Fruits</th><th colspan="6">Vegetables</th><th rowspan="2">Other</th><th rowspan="2">Total</th></tr><tr><th>Phylum / Class</th><th>Genus</th><th>Species</th><th>Berries and small fr.<sup>1</sup></th><th>Citrus fr.</th><th>Misc. fr.</th><th>Pome fr.</th><th>Stone fr.</th><th>Brassica veg.</th><th>Bulb veg.</th><th>Cultivated mushrooms</th><th>Fruiting veg.</th><th>Leaf veg.</th><th>Root veg.</th><th>Starchy roots & tubers</th><th>Stem veg.</th></tr></thead><tbody><tr><td rowspan="12">Actinomycetota<br>Actinomycetes</td><td>Curtobacterium</td><td>herbarum</td><td>—</td><td>1</td><td>—</td><td>2</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>4</td><td>3.7</td></tr><tr><td>Frigoribacterium</td><td>sp.</td><td>—</td><td>1</td><td>1</td><td>2</td><td>—</td><td>—</td><td>—</td><td>1</td><td>2</td><td>—</td><td>2</td><td>—</td><td>1</td><td>1</td><td>11</td><td>10.3</td></tr><tr><td>Frondihabitans</td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Kocuria</td><td>peucedani</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Leifsonia</td><td>salsicia</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>3</td><td>2.8</td></tr><tr><td>Microbacterium</td><td>phylosphaerae</td><td>1</td><td>—</td><td>—</td><td>—</td><td>2</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>1</td><td>1</td><td>7</td><td>6.5</td></tr><tr><td>proteolyticum<br>testaceum</td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Pseudoclavibacter</td><td>terrae</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Rhodococcus</td><td>erythropolis</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Sanguibacter</td><td>inulinus</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>3</td><td>2.8</td></tr><tr><td>Bacillota<br>Bacilli</td><td>Bacillus</td><td>altitudinis</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>cereus group</td><td>1</td><td>—</td><td>—</td><td>—</td><td>1</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>—</td><td>—</td><td>5</td><td>4.7</td></tr><tr><td></td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Carnobacterium<br>Exiguobacterium</td><td>maltaromaticum</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Leuconostoc</td><td>citreum</td><td>—</td><td>1</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>mesenteroides</td><td>—</td><td>1</td><td>—</td><td>1</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>2.8</td></tr><tr><td></td><td>pseudomesenteroides</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Staphylococcus</td><td>sciuri</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>succinus</td><td>—</td><td>2</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>3</td><td>2.8</td></tr><tr><td></td><td>xylosus</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td>Bacteroidota<br>Cytophagia<br>Pseudomononadota<br>Alphaproteobacteria</td><td>Wautersiella</td><td>enshiensis</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Agrobacterium</td><td>sp.</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Gluconobacter</td><td>kondonii</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>thailandicus</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Acinetobacter</td><td>calcoaceticus</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Enterobacter</td><td>hormaechei</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Erwinia</td><td>rhapontici</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>sp.</td><td>—</td><td>—</td><td>—</td><td>2</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>Ewingella</td><td>americana</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Klebsiella</td><td>michiganensis</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>variicola</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Moraxella</td><td>osloensis</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Pantoea</td><td>agglomerans</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>1</td><td>1</td><td>—</td><td>—</td><td>—</td><td>3</td><td>2.8</td></tr><tr><td></td><td>dispersa</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Pseudomonas</td><td>fluorescens</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>—</td><td>2</td><td>3</td><td>2</td><td>—</td><td>—</td><td>9</td><td>8.4</td></tr><tr><td></td><td>sp.</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>Rahnella</td><td>aquatilis</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>Serratia</td><td>liquefaciens</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>marcescens</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Stenotrophomonas</td><td>maltophilia</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>rhizophila</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>2</td><td>1.9</td></tr><tr><td></td><td>Unidentified</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>1</td><td>0.9</td></tr><tr><td></td><td>Enterobacterales</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td></tr><tr><td></td><td>Unidentified bacteria</td><td>—</td><td>—</td><td>1</td><td>2</td><td>—</td><td>—</td><td>—</td><td>1</td><td>—</td><td>—</td><td>—</td><td>3</td><td>1</td><td>—</td><td>—</td><td>10</td><td>9.3</td></tr><tr><td></td><td>Total</td><td>—</td><td>5</td><td>5</td><td>11</td><td>15</td><td>9</td><td>3</td><td>0</td><td>5</td><td>16</td><td>8</td><td>15</td><td>5</td><td>7</td><td>3</td><td>107</td><td>100</td></tr><tr><td></td><td>Frequency (%)</td><td>4.7</td><td>4.7</td><td>10.3</td><td>14.0</td><td>8.4</td><td>2.8</td><td>0.0</td><td>4.7</td><td>15.0</td><td>7.5</td><td>14.0</td><td>4.7</td><td>6.5</td><td>2.8</td><td>—</td><td>—</td><td>100</td></tr></tbody></table>

<footnote n="1">¹, fr.: fruits; veg.: vegetables; misc., miscellaneous.</footnote>
<figure><img src="image_8.png" /><figcaption>**Fig. 3.** UpSet plot of the shared diversity of spoilage organisms on different categories of fresh fruit and vegetables collected in households in the present study (green dots) compared to pre- and post-harvest steps of the food chain (black dots). Intersection size indicates the number of microbial species uniquely collected from a single FFV category or shared across multiple categories while set size indicates the total number of spoilage species across categories. Only species observed at least twice on the sampled products in the present study were compared to those reported in the scientific literature on pre- and post-harvest stages of the food chain.</figcaption></figure>

airborne conidia and produce a range of enzymes deteriorating fruit and vegetable tissues (Pitt and Hocking, 2009d; Prusky et al., 2004). *P. expansum* was by far the most commonly isolated organism in this study, with 26 isolates, while the second highest organism (*Botrytis cinerea* complex) was found 14 times. The former species has been widely reported as the major threat of pome fruits, a serious threat to stone fruits, and occasionally on other plant products, such as root vegetables, fruit vegetables or bulb vegetables (Duduk et al., 2017; Pitt and Hocking, 2009b; Snowdon, 1990, 1991; Zhang et al., 2007), which is corroborated by our results. Our results also showed other *Penicillium* species commonly described as post-harvest pathogens such as *P. italicum* and *P. digitatum* on citrus fruits, or *P. glabrum* on bulb vegetables, which corresponds to their preferred hosts as shown by the scientific literature (Pitt and Hocking, 2009b; Snowdon, 1990, 1991). It is worth noticing that some species, such as *P. crustosum* or *P. olsonii* which were here respectively isolated from a large FFV array and from fruiting vegetables, are usually marginally described as spoilage organisms. It would be interesting to study their FFV spoilage potential, as these 2 species are also commonly reported in indoor air (Samson et al., 2019).

Other important genera identified in this study included organisms from taxa widely described as post-harvest pathogens, notably *Botrytis*, *Mucor*, *Cladosporium*, *Fusarium* and *Aspergillus* spp. (Amorim et al., 2008; Dwivedi et al., 2024; Mondani et al., 2021; Perrone et al., 2007; Smith

et al., 1979). On the other hand, some filamentous fungi that were least commonly found, sometimes corresponded to species never described on French products. For instance, *A. luteoalbus* has only been described to this date on potatoes from Russia (Chudinova et al., 2022) but was isolated for the first time on spoiled potatoes from France in the present study. In the same type of product, we retrieved an isolate of *P. niumeijerarum*, which has been firstly isolated from soil in the Netherlands in 2017 (Crous et al., 2017). Finally, one isolate related to the *Mucor* genus, isolated from a cherry sample, showed no satisfying assignment after ITS sequencing (96.34 % identity for the best hit, *Mucor lusitanicus*), suggesting that it might correspond to a new species. In this context, a more in-depth taxonomic approach using a multigene approach or genome sequencing would be of interest. Finally, it is worth mentioning that several of the mold species identified in the present study, e.g., *P. expansum*, *P. brevicompactum* or *A. alternata*, are known mycotoxin producers (Pitt and Hocking, 2009a, 2009b, 2009c, 2009d). Further investigations are required to evaluate the safety risk associated with mycotoxin exposure if healthy parts of moldy FFV are consumed to reduce food waste.

The lower number of isolated yeasts is not surprising as few studies about FFV reported them as threats on post-harvest steps of the food chain, and they are rather characterized as spoilage organisms of processed products, notably on fresh cut vegetables or non-carbonated fruit
juices (Krisch et al., 2016). However, two species were predominant, *A. pullulans* and *H. uvarum*. The former has been described as a common organism of FFV surfaces (cabbage, strawberries, grapes and citrus) (Pitt and Hocking, 2009a, 2009b, 2009c, 2009d), both in fields and retail, but rarely as a cause of spoilage, and all of the isolates in the present study came from stone fruits. On the other hand, certain studies underlined the positive impact of *A. pullulans* as a biological control agent, making it unclear if those isolates were primary actors of the spoilage process (Di Francesco et al., 2020; Schena et al., 2003). The latter, which is also commonly found on healthy FFV, but can also lead to undesirable fermentation or sporadic spoilage, notably on berries or stone fruits, which were the most frequent sources of isolation in our study (Pitt and Hocking, 2009c). Other species already described as sporadic spoilage organisms such as *G. candidum* or *D. hansenii* were also isolated in our study, but they also belong to the natural microbiota of a wide range of FFV, so it is unclear whether they actively contributed to spoilage.

As for bacteria, they showed a wider diversity, including 28 different genera and 49 species, mostly found once or twice. The most frequently isolated bacteria were *Curtobacterium* sp., *M. phyllosphaerae*, *B. cereus sensu lato* and *P. fluorescens sensu lato*. *Curtobacterium* sp. and *M. phyllosphaerae* are usually described as belonging to soil or phyllosphere microbiota, and their spoilage potential is yet to be determined. On the other hand, *B. cereus* and *P. fluorescens sensu lato* have been widely described as either food spoilers or plant pathogenic organisms (Ehling-Schulz et al., 2019; Liao, 1987; Sawada et al., 2021; Scales et al., 2014). In the present study, these species were retrieved from spoiled fruit vegetables, leaf vegetables, root vegetables as well as cultivated mushrooms. *Bacillus* spp. have been reported as responsible for degradation of vegetables, fresh or canned (onions, arrowhead or potato) (Balali et al., 2020; Hwang et al., 2012; Wang et al., 2017; Zhong et al., 2015), and were found on root vegetables, brassica as well as fruits in our study. Other bacterial groups such as LAB or enterobacteria have been sporadically isolated and are known for their opportunistic spoilage potential on plant products (Gillis et al., 2014; Khalifa, 2022; Lampert et al., 2017; Pérombelon, 2002). As bacterial isolates were only obtained by dilution plating from the spoiled portion of FFV samples, it is unclear if those isolates are directly responsible for the observed spoilage, or if they acted as opportunistic organisms for instance. Some other isolates belonged to groups usually affiliated with natural soil or rhizosphere microbiota, and unrelated to FFV spoilage, such as *Wautersiella enshiensis* on a banana or *Frondihabitans peucedani* (Lee, 2010; Yuan et al., 2023). Concerning the latter, it is worth mentioning that higher relative abundances of *Frondihabitans* sp. were found in diseased apples as compared to healthy ones in a recent study by Wassermann et al. (2019) while the one specimen isolated in this study have also been retrieved from an apple, stored at room temperature at household.

Our meta-analysis approach allowed pinpointing taxa that are common FFV contaminants since they are able to produce spoilage both at pre and/or post-harvest, and at the consumer's level. They corresponded to *Penicillium*, *Botrytis* or *Pseudomonas*. Interestingly, we also found taxa that were uniquely found at the household's level. Among them, a few household-associated taxa were most likely commensal bacteria, (e.g. *C. herbarum* or *S. rhizophilia*) rather than having a direct impact on spoilage, as previously explained. Interestingly, some species, largely described as FFV spoilers, were isolated from unusual spoiled matrices (e.g. *P. italicum*, *P. expansum*, *M. circinelloides* on pome fruits). This raises important questions on how these species end up contaminating unusual products. Since products stored in households are usually kept alongside other FFV, it is possible that cross contamination from other products or contaminated storage surfaces occur, while such cross-contamination events are less likely to occur in earlier stages before the retail stage where FFV of different groups do not usually share the same environment. Moreover, some fungal species we identified have rarely, if ever, been reported to be associated with FFV spoilage although the fungal genera they belong to are well-known FFV spoiler (e.g. *P. brevicompactum*, *M. brunneogriseus* or *C. snafimbriatum*). This might

suggest that some rarer species can contribute to FFV spoilage, at least in households but also potentially in previous steps of the food chain. Alternatively, products stored at home are often kept in suboptimal conditions (unsuitable temperature mainly) and can therefore be fragrized. We cannot exclude that this can lead to spoilage caused by unusual organisms, acting as opportunistic spoilers.

## 5. Conclusion

This study reports for the first time the microbial diversity associated with spoiled FFV at the consumer's level, revealing the prevalence of various microbial groups, in particular molds including *Penicillium* spp. and *Botrytis* spp. The microbial diversity associated with FFV spoilage at home partially differed from that of the organisms typically identified as post-harvest spoilers. This suggests that determinants of contamination at the household level cannot be entirely inferred from earlier stages and should be considered a crucial area of study. In a societal and environmental context in which food waste is a major concern, our results will help understand which organisms are a major threat towards fresh products at the household level, although obviously both the diversity and prevalence may change according to geographic location. Our results also provide insights into possible means to help reduce premature spoilage. A better usage of FFV refrigeration and a better cleaning routine of the storage compartments to ensure that lower amounts of organisms are in contact with food might lead to a significant increase in shelf life of products for consumers, and thus, reduce food waste.

### CRediT authorship contribution statement

**Damien Ballan:** Writing – review & editing, Writing – original draft, Visualization, Investigation, Formal analysis, Data curation. **Adeline Picot:** Writing – review & editing, Supervision, Methodology, Funding acquisition, Conceptualization. **Nolwenn Rolland:** Investigation. **Clément Bovo:** Investigation. **Claire Prévost:** Investigation. **Emma-nuel Coton:** Writing – review & editing, Funding acquisition, Conceptualization. **Jérôme Mounier:** Writing – review & editing, Supervision, Project administration, Methodology, Funding acquisition, Conceptualization.

### Funding

This work was funded by the French National Research Agency (ANR) in the framework of the FOODREST project (ANR-20-CE21-0006) and benefited from equipments funded by the French Contrat de Plan Etat-Région CPER BIOALTERNATIVE (2021-2027).

### Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

### Acknowledgements

The authors are grateful to the households that participated in this study as well as to Charlotte Veron, Dr. Morgane Innocent, Pr. Bertrand Urien, Dr. Annick Tamaro, Pr. Marine Le Gall-Ely and Pr. Patrick Gabriel from the Laboratoire d' Economie et de Gestion de l'Ouest (Univ. Brest), who contributed to the setting of this participatory science study.

## Appendix A. Supplementary data

Supplementary data to this article can be found online at https://doi.org/10.1016/j.ijfoodmicro.2025.111204.
# Data availability

Data will be made available on request.

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