Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing

Kim, Seo Young; Ban, Ga-Hee; Hong, Ye Won; Jang, Min Ji

doi:10.1016/j.foodres.2021.110896

Cited by 5 publications

(4 citation statements)

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“…Most importantly, when combined with the enumeration results, these results indicate that the microbiota profiling method we adapted (i.e., V3-V4 amplicon sequencing) is an unsuitable method to predict and/or assess the pathogen contamination status of raw oysters. In contrast to the previous studies [12,13,15,23], no correlation was observed between the presence of foodborne pathogen (V. parahaemolyticus) and the relative abundance of potentially hazardous genus (Vibrio) (Figs. 2B and 5).…”

Section: Discussioncontrasting

confidence: 99%

“…In this study, the lowest-rank taxa we could assign was the genus Vibrio , and no specific OTU was matched to V. parahaemolyticus (data not shown). Similarly, the previous studies failed to assign any specific foodborne pathogens from their short amplicon sequencing-based metabarcoding analyses [ 12 , 13 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

“…These claims were based on the observed expansion of certain bacterial family and/or genus in relative abundance. For example, Kim et al [23] demonstrated that the relative abundance of family Enterobacteriaceae, which includes major foodborne pathogens such as Escherichia spp. and Shigella spp., was significantly increased during the seed soaking step of alfalfa sprout production and, consequently, suggested the addition of further interventions during this step.…”

Section: Discussionmentioning

confidence: 99%

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Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

Kim

2023

J. Microbiol. Biotechnol.

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16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen ( Vibrio parahaemolyticus ) contamination and/or V. parahaemolyticus -specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

Kim

2023

J. Microbiol. Biotechnol.

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“…Some fungi and bacteria can colonize the internal tissues of a germinating seedling as endophytic symbionts [9], but many more grow on the root surface, consuming the carbon-and nitrogen-rich chemicals that rapidly growing plant roots normally exude [10]. These external rhizosphere colonists include a broad diversity of bacteria and fungi [11,12]; some have close affinities to plants as hosts, while others grow casually in the rhizosphere as saprotrophic commensals taking advantage of abundant resources. Sprouts grown for food inevitably develop a rich community of rhizosphere microorganisms; this can become problematic when the microbiome includes human pathogens such as Salmonella spp., toxin-producing Escherichia coli or Aspergillus spp., or plant pathogenic microbes that damage the sprouts.…”

Section: Introductionmentioning

confidence: 99%

Seed Disinfestation Practices to Control Seed-Borne Fungi and Bacteria in Home Production of Sprouts

Gilbert

Diaz

Bregoff

2023

Foods

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Concern over microbial contamination limits the adoption of home production of sprouts as a nutritious and sustainable food. Simple, accessible approaches to seed disinfection could support safe home seed sprouting. Here, we quantify bacterial and fungal contamination of seeds of 14 plant cultivars sold for home sprout production and test a range of chemical and physical methods for seed disinfestation appropriate for home use. Most seeds are contaminated with a variety of bacteria and fungi, and those microbes are usually limited to the seed surface. Heat treatments are not effective for seed disinfection because the high temperatures needed to effectively reduce microbial contamination also reduce seed germination. Two chlorine-based chemical disinfectants—dilute household bleach (0.6% sodium hypochlorite) and freshly generated hypochlorous acid (800 ppm chlorine)—were the most effective disinfection agents tested (up to a 5-log reduction in bacteria) that also did not harm seed germination.

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Application of Metagenomics in Dry Fish Microbial Quality Assessment

Krinal,

Jhanvi,

Laishram

et al. 2024

Dry Fish: A Global Perspective on Nutritional Security and Economic Sustainability

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Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing

Cited by 5 publications

References 53 publications

Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

Seed Disinfestation Practices to Control Seed-Borne Fungi and Bacteria in Home Production of Sprouts

Application of Metagenomics in Dry Fish Microbial Quality Assessment

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