16S rRNA metagenomic profiling of red amaranth grown organically with different composts and soils

In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about pathogens in organic produces. This study was designed to understand the effect of different composts and soils on the status of the microbiome present in organically grown leafy vegetables. 16S rRNA metagenomic profiling of the leaves was done, and data were analyzed. It was found that by adding composts, the OTU of the microbiome in the organic produce was higher than in the conventional produce. The beneficial genera identified across the samples included plant growth promoters (Achromobacter, Paenibacillus, Pseudomonas, Sphingobacterium) and probiotics (Lactobacillus), which were higher in the organic produce. Some pathogenic genera, viz., plant pathogenic bacteria (Cellvibrio, Georgenia) and human pathogenic bacteria (Corynebacterium, Acinetobacter, Streptococcus, Streptomyces) were also found but with relatively low counts in the organic produce. Thus, the present study highlights that organic produce has lesser pathogen contamination than the conventional produce. KEY POINTS: • 16S rRNA metagenomics profiling done for organic red amaranth cultivar • Microbial richness varied with respect to the soil and compost type used • The ratio of beneficial to pathogenic genera improves with the addition of compost.

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

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.

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

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.

Salmonella and other Enterobacteriaceae in conventional and organic vegetables grown in Brazilian farms

This study aimed to assess the microbiological profile of conventional and organic vegetables grown in Brazilian farms through the detection of Salmonella and other Enterobacteriaceae. A total of 200 samples (100 conventional and 100 organic), including leafy greens, spices/herbs, and other unusual vegetables, were submitted to the enumeration of Enterobacteriaceae by plating on VRBG agar. Moreover, colonies of Enterobacteriaceae were randomly selected and submitted to identification by MALDI-TOF MS. Samples were also tested for Salmonella, using culture-based and PCR-based enrichment methods. The mean counts of Enterobacteriaceae in conventional and organic vegetables were 5.1 ± 1.5 and 5.4 ± 1.4 log CFU/g, respectively (P > 0.05). A total of 18 genera (including 38 species) of Enterobacteriaceae were identified, and the most frequent ones found in samples from both farming systems were Enterobacter (76%) and Pantoea (68%). Salmonella was identified in 17 samples (8.5%): nine (4.5%) in conventional and eight (4.0%) in organic vegetables. These results indicate that the farming system had no impact on the Enterobacteriaceae populations and rates of Salmonella and revealed unsatisfactory microbiological safety of some samples, mainly due to the presence of Salmonella. These findings highlight the need for control measures during vegetable production, regardless of the farming system, to reduce microbial contamination and the risks of foodborne illnesses.

A worldwide review of illness outbreaks involving mixed salads/dressings and factors influencing product safety and shelf life

The trends toward healthy living, vegetarianism, and busy schedules have increased salad popularity. Salads are usually consumed raw without any thermal treatment, and therefore, without proper care they can become major vehicles for foodborne illness outbreaks. This review examines the microbial quality of 'dressed' salads which contain two or more vegetables/fruits and salad dressings. The possible sources of ingredient contamination, recorded illnesses/outbreaks, and overall microbial quality observed worldwide, besides the antimicrobial treatments available are discussed in detail. Noroviruses were most frequently implicated in outbreaks. Salad dressings usually play a positive role in influencing microbial quality. However, this depends on several factors like the type of contaminating microorganism, storage temperature, dressing pH and ingredients, plus the type of salad vegetable. Very limited literature exists on antimicrobial treatments that can be used successfully with salad dressings and 'dressed' salads. The challenge with antimicrobial treatments is to find ones sufficiently broad in spectrum, compatible with produce flavour which can be applied at competitive cost. It is evident that renewed emphasis on prevention of produce contamination at the producer, processor, wholesale and retail levels plus enhanced hygiene vigilance at foodservice will have a major impact on reducing the risk of foodborne illnesses from salads.

Short Communication: Low Prevalence of Clinically Important Antibiotic-Resistant Strains among Non-Pathogenic Genera of the Tribe Klebsielleae

Hafnia sp. and Serratia sp. belong to the Tribe Klebsielleae; although they are not considered pathogenic bacteria, there are many documented cases of diseases caused by these microorganisms. The aim of this study was to determine the antibiotic resistance profiles of strains belonging to the genus Hafnia and Serratia isolated from fish and shrimps. Phenotypic antibiotic resistance was determined using the semi-automatic Vitek 2 system (bioMérieux, Marcy-l’Étoile, France), while the presence of the extended-spectrum beta-lactamase, AmpC beta-lactamases, Klebsiella pneumoniae carbapenemases and Metallo-β-Lactamase producing strains were determined using the MIC Test Strip (Liofilchem, Roseto degli Abbruzzi, Italy). As a result of the conducted research, it was observed that a vast number of Hafnia sp. strains were resistant to cefalexin (84.61%), while Serratia sp. Strains to cefuroxime (79.41%) and nitrofurantoin (85.29%). In addition, it was observed that of all strains, only one had an ability to produce enzymes typical for β-lactamase-producing Enterobacterales. Although the strains of Hafnia sp. and Serratia sp. isolated from fish and shrimp are not characterized by frequent resistance to antibiotics, taking into account the constantly growing number of antibiotic-resistant strains, this may be a problem in the future, mainly due to gene transfer through mobile genetic elements and the acquisition of resistance expressed phenotypically through contact with stress factors. Therefore, studies monitoring the antibiotic resistance profile of these species should be carried out on a regular basis.

Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

Consumer Preference, Quality, and Safety of Organic and Conventional Fresh Fruits, Vegetables, and Cereals

Growing and purchasing demand for organic fresh produce is increasing rapidly. Consumers are aware of health, environmental safety, pesticide harmfulness, nutrients, bioactive compounds, and safe food. Many research works are available on organic and conventional fresh produce. As organic fresh produce growing and purchasing demand is increasing, it has become necessary to review the recent trends in quality, safety, and consumer preferences of organic and conventional fresh food products. A few reports have been compiled on organic and conventional fresh produce. Researchers have started working on organic and conventional fresh produce with the help of modern technology to improve nutritional and functional quality, safety, and consumer preferences. Nutritional and functional quality, safety, and consumer preferences depend on cultivation techniques, treatment, crop cultivar, and appearance of products. Therefore, it is necessary to compile the literature on organic and conventional fresh produce based on quality, safety, and consumer preferences.

Sources of food contamination in a closed hydroponic system

This study investigated potential contamination sources in a commercial, closed hydroponic system. Water, substrate and lettuce (Lactuca sativa) samples were evaluated for microbiological indicator populations, including aerobic plate count (APC), coliform bacteria (CB) and yeast and mould (YM). Listeria spp. detection via cultural enrichment and agglutination was negative for all samples. Peat moss substrate (postharvest) had the highest counts for APC (6·8 log CFU per g), CB (4·5 log MPN per g) and YM (5·1 and 4·8 log CFU per g respectively). Roots embedded in plugs demonstrated counts for all populations nearly as high as the substrate. Among water samples, a seedling water reservoir housing germinated plants yielded the highest count for APC (5·1 log CFU per g) and CB (2·4 log MPN per g) likely due to the large numbers of plugs and their close proximity in the reservoir. Harvested lettuce leaves demonstrated higher APC (4·1 log CFU per g) than preharvest leaves (1·7 log CFU per g) due to the transfer of microbes from the root ball. These data suggest that substrates are a significant potential source of contamination in hydroponic systems and likely facilitate microbial transfer to harvested leaves. There is, therefore, the need to further investigate mitigation of potential contamination events. SIGNIFICANCE AND IMPACT OF THE STUDY: Hydroponic production is known to provide safe, clean produce. This study, however, suggests that the hydroponic substrate (peat moss plug) is a possible source of contamination in the hydroponic system. This finding is important as most harvested hydroponic lettuces are packaged and sold with substrate and root ball intact. This implies a high probability of microbial transfer from the root ball to edible harvested lettuce leaves.