Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens

Margot, H.; Stephan, Roger; Tasara, Taurai

doi:10.1186/s40168-016-0193-y

Cited by 8 publications

(8 citation statements)

References 30 publications

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“…In both samples, the dominant phylum of uncultured samples (before cultivation, 0 h) was Proteobacteria (sample A 91.9% and sample B 97%), followed by Firmicutes (sample A 7.9% and sample B 2.6%), while Bacteroidetes were more or less frequent (in both samples under 0.5%). This corresponds partly to the findings of Margot et al [ 26 ], who analyzed the uncultured bacteriome of mungo bean sprouts by 16S rRNA sequencing. Margot et al also found Proteobacteria as the most prevalent phylum (90.4%), but Firmicutes (0.6%) were exceeded by Bacteroidetes (8.8%) [ 26 ].…”

Section: Resultssupporting

confidence: 88%

“…They are known from previous analyses (data not shown) to contain quite high loads of microorganisms and also due their high potential for microbial contamination (a difficult journey from farm to consumer). As they are high in raw consumption (preservation of all nutrients), they can serve as an excellent foyer for ARB into the human gastrointestinal microbiome, and their consumption can lead to food poisoning [ 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

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Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts

2021

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The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed Gammaproteobacteria (Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae) and then Firmicutes (Streptococcaceae). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (gyrA, gyrB, parC, parD) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant.

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Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts

2021

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“…In most cases, a conserved segment of a hypervariable region of the 16S rDNA gene is used. In recent years, the field of metagenomics has flourished and published studies now include insights into the microbiomes of cilantro [ 1 ], spinach [ 2 ], bean sprouts [ 3 ], kimchi [ 4 ], kefir [ 5 ], meat [ 6 ], wine [ 7 ], and cheese [ 8 – 13 ]. The composition of the native microbiota in these food products may help determine property characteristics contributed to by microorganisms such as flavor, texture, color, aroma, shelf-life, and spoilage.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing

et al. 2018

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BackgroundThe microbiome of cheese is diverse, even within a variety. The metagenomics of cheese is dependent on a vast array of biotic and abiotic factors. Biotic factors include the population of microbiota and their resulting cellular metabolism. Abiotic factors, including the pH, water activity, fat, salt, and moisture content of the cheese matrix, as well as environmental conditions (temperature, humidity, and location of aging), influence the biotic factors. This study assessed the metagenomics of commercial Gouda cheese prepared using pasteurized or unpasteurized cow milk or pasteurized goat milk via 16S rDNA sequencing.ResultsResults were analyzed and compared based on milk pasteurization and source, spatial variability (core, outer, and under the rind), and length of aging (2–4 up to 12–18 months). The dominant organisms in the Gouda cheeses, based on percentage of sequence reads identified at the family or genus levels, were Bacillaceae, Lactococcus, Lactobacillus, Streptococcus, and Staphylococcus. More genus- or family-level (e.g. Bacillaceae) identifications were observed in the Gouda cheeses prepared with unpasteurized cow milk (120) compared with those prepared with pasteurized cow milk (92). When assessing influence of spatial variability on the metagenomics of the cheese, more pronounced differences in bacterial genera were observed in the samples taken under the rind; Brachybacterium, Pseudoalteromonas, Yersinia, Klebsiella, and Weissella were only detected in these samples. Lastly, the aging length of the cheese greatly influenced the number of organisms observed. Twenty-seven additional genus-level identifications were observed in Gouda cheese aged for 12–18 months compared with cheese only aged 2–4 months.ConclusionsCollectively, the results of this study are important in determining the typical microbiota associated with Gouda cheese and how the microbiome plays a role in safety and quality.

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“…The results show the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes phyla on broccoli florets, as seen on other fresh vegetables (10,11,30). Such bacterial diversity of the broccoli phyllosphere is greater than that predicted by culture-based analysis, which detects only a few bacterial species (31), and suggests that the majority of phyllosphere bacteria on broccoli florets are novel.…”

Section: Discussionmentioning

confidence: 78%

Geographic and Host-Associated Variations in Bacterial Communities on the Floret Surfaces of Field-Grown Broccoli

Kim

Bae

Park

2018

Appl Environ Microbiol

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Fresh vegetables harbor diverse bacterial populations on their surfaces. However, information on this microbiota is limited to a few types of fresh vegetables, and little is known about how it varies with geography and host condition. Here, we analyzed bacterial communities on the floret surfaces of 66 field-grown broccoli collected from 22 farms in four farming regions of Jeju Island, South Korea, using 454 pyrosequencing of 16S rRNA amplicons, and we determined their relationships to farming region and host-associated factors. Geographic variations in bacterial community composition and diversity were observed among farming regions, which partly reflected their relative humidity and insolation. The most abundant phyla were , followed by, , and; core operational taxonomic units (OTUs) assigned to ,, ,, and contributed to the community differences. Bacterial community composition differed between immature and mature samples, with mature samples harboring higher bacterial diversity. In comparison with communities on other types of fresh vegetables and fruits, bacterial communities on broccoli florets were unique but more similar to those of ground vegetables than to those of tree fruits/vegetables. This study presents novel data on the variability of floret-associated bacterial populations of field-grown broccoli relative to environmental and host-associated factors. Fresh vegetables harbor diverse and complex bacterial populations on their surfaces. These indigenous bacteria may play a role in human and crop health; however, the diversity and variability of bacterial communities on fresh vegetables require further study. A popular crop of leafy vegetables, broccoli, is of great agricultural and industrial importance. This study provides a detailed description of the bacterial community composition and diversity on the surfaces of broccoli florets. The variability of bacterial communities is associated with the geographic location of farming sites and is affected by host growth and health. The bacterial communities specific to broccoli were identified and showed greater similarity to those found on ground vegetables than to those found on tree fruits/vegetables. This study presents novel data on the impact of environmental and host-associated conditions on the variability of floret-associated bacterial populations present on field-grown broccoli.

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Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens

Cited by 8 publications

References 30 publications

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts

Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing

Geographic and Host-Associated Variations in Bacterial Communities on the Floret Surfaces of Field-Grown Broccoli

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