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Research Publications (Food Safety)

This page tracks research articles published in national and international peer-reviewed journals. Recent articles are available ahead of print and searchable by Journal, Article Title, and Category. Research publications are tracked across six categories: Bacterial Pathogens, Chemical Contaminants, Natural Toxins, Parasites, Produce Safety, and Viruses. Articles produced by USDA Grant Funding Agencies (requires login) and FDA Grant Funding Agencies (requires login) are also tracked in Scopus.

Displaying 1 - 25 of 39

  1. Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome

    • FEMS Microbiology Ecology
    • The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes.

      • Bacterial pathogens
      • Vibrio
  2. Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests

    • FEMS Microbiology Ecology
    • The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China.

      • Chemical contaminants
      • Antibiotic residues
  3. Aeromonashydrophila infection in tilapia triggers changes in the microbiota composition of fish internal organs

    • FEMS Microbiology Ecology
    • Aeromonas hydrophila is a major pathogenic species that causes mass mortality in various freshwater fish species including hybrid tilapia, the main fish species in Israeli aquaculture. Our hypothesis was that A. hydrophila infection may cause changes in the microbiota composition of fish internal organs, and therefore we aimed to study the effect of A. hydrophila infection by injection or by net handling on the microbiota compositions of fish intestine, spleen, and liver.

      • Bacterial pathogens
      • Vibrio
  4. Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speci

    • FEMS Microbiology Ecology
    • Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear.

      • Chemical contaminants
      • Heavy Metals
  5. The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production

    • FEMS Microbiology Ecology
    • Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated in vitro, and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness.

      • Bacterial pathogens
      • Shigella
  6. Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns

    • FEMS Microbiology Ecology
    • Cable bacteria (CB) perform electrogenic sulfur oxidation (e-SOx) by spatially separating redox half reactions over centimetre distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new ‘agar pillar’ approach to selectively enrich and investigate CB populations.

      • Bacterial pathogens
      • Vibrio
  7. An unexpected guest: a green microalga associated with the arsenic-tolerant shrub Acacia farnesiana

    • FEMS Microbiology Ecology
    • The best-known plant endophytes include mainly fungi and bacteria, but there are also a few records of microalgae growing endophytically in vascular land plants, some of which belong to the genus Coccomyxa. In this study, we isolated a single-celled photosynthetic microorganism from the arsenic-tolerant shrub Acacia farnesiana, thus we hypothesized that it is an endophytic arsenic-tolerant microalga.

      • Chemical contaminants
      • Heavy Metals
  8. Inhibition of sulfate-reducing bacteria with formate

    • FEMS Microbiology Ecology
    • Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally.

      • Bacterial pathogens
      • Vibrio
  9. Presence of bacteria capable of PCB biotransformation in stormwater bioretention cells

    • FEMS Microbiology Ecology
    • ABSTRACT Core samples from bioretention cell media as well as surface stormwater sediment samples from seven urban areas were collected to assess the potential for biotransformation activity of polychlorinated biphenyls (PCBs). The presence of putative organohalide-respiring bacteria in these samples was studied. Based on extracted DNA, Dehalobacter, Dehalogenimonas and Dehalococcoides were detected.

      • Chemical contaminants
      • Dioxins
  10. Presence of bacteria capable of PCB biotransformation in stormwater bioretention cells

    • FEMS Microbiology Ecology
    • ABSTRACT Core samples from bioretention cell media as well as surface stormwater sediment samples from seven urban areas were collected to assess the potential for biotransformation activity of polychlorinated biphenyls (PCBs). The presence of putative organohalide-respiring bacteria in these samples was studied. Based on extracted DNA, Dehalobacter, Dehalogenimonas and Dehalococcoides were detected.

      • Chemical contaminants
  11. Plant–microbe–microbe interactions influence the faba bean nodule colonization by diverse endophytic bacteria

    • FEMS Microbiology Ecology
    • ABSTRACT Legume root nodules harbor rhizobia and other non-nodulating endophytes known as nodule-associated bacteria (NAB) whose role in the legume symbiosis is still unknown. We analysed the genetic diversity of 34 NAB isolates obtained from the root nodules of faba bean grown under various soil conditions in Egypt using 16S rRNA and concatenated sequences of three housekeeping genes.

      • Bacterial pathogens
  12. Knowledge gaps in the assessment of antimicrobial resistance in surface waters

    • FEMS Microbiology Ecology
    • ABSTRACT The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans.

  13. The dissemination of antimicrobial resistance determinants in surface water sources in Lebanon

    • FEMS Microbiology Ecology
    • ABSTRACT The prevalence of antibiotic-resistant bacteria in surface water in Lebanon is a growing concern and understanding the mechanisms of the spread of resistance determinants is essential. We aimed at studying the occurrence of resistant bacteria and determinants in surface water sources in Lebanon and understanding their mobilization and transmission. Water samples were collected from five major rivers in Lebanon.

      • Bacterial pathogens
  14. The interactions of bacteriophage Ace and Shiga toxin-producing Escherichia coli during biocontrol

    • FEMS Microbiology Ecology
    • ABSTRACT Strictly lytic phages are considered powerful tools for biocontrol of foodborne pathogens. Safety issues needed to be addressed for the biocontrol of Shiga toxin-producing Escherichia coli (STEC) include: lysogenic conversion, Shiga toxin production through phage induction, and emergence/proliferation of bacteriophage insensitive mutants (BIMs).

      • Bacterial pathogens
  15. Editorial to the Thematic Topic “Towards a more sustainable agriculture through managing soil microbiomes”

    • FEMS Microbiology Ecology
    • Consistent with the concept of ecosystem sustainability—defined as ‘the ability of an ecosystem to maintain its potential for self-regulation in the long term’ (Bender, Wagg and van der Heijden 2016)—sustainable agricultural production aims to meet future food, feed and fibre demands with the given natural resources and without adverse environmental impact or greater land consumption.

  16. Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

    • FEMS Microbiology Ecology
    • ABSTRACT Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils.

  17. Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer

    • FEMS Microbiology Ecology
    • ABSTRACT The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3–V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences.

      • Seasonal Produce
      • Produce Safety
  18. In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions

    • FEMS Microbiology Ecology
    • ABSTRACT Douglas Channel and the adjacent Hecate Strait (British Columbia, Canada) are part of a proposed route to ship diluted bitumen (dilbit). This study presents how two types of dilbit naturally degrade in this environment by using an in situ microcosm design based on dilbit-coated beads. We show that dilbit-associated n-alkanes were microbially biodegraded with estimated half-lives of 57–69 days.

      • Chemical contaminants
  19. Limited carbon sources prevent sulfate remediation in circumneutral abandoned mine drainage

    • FEMS Microbiology Ecology
    • ABSTRACT Passive remediation systems (PRS) use both biotic and abiotic processes to precipitate contaminants from abandoned mine drainage (AMD) so that the contaminants do not spread into local watersheds. PRS are efficient at removing heavy metals but sulfate remediation frequently does not occur. To understand the reasons for the lack of sulfate remediation, we studied four PRS that treat circumneutral AMD and one raw mine drainage discharge.

  20. Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling

    • FEMS Microbiology Ecology
    • ABSTRACT One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant.

  21. Salinity increases growth and pathogenicity of water mold to cause mortality and early hatching in Rana sylvatica embryos

    • FEMS Microbiology Ecology
    • ABSTRACT Amphibian embryos often suffer increased mortality and altered hatching when exposed to road deicing salt runoff or pathogens such as water molds. However, the combined effects of such contaminants on embryos remain understudied.

  22. Matrix inhibition by Salmonella excludes uropathogenic E. coli from biofilm

    • FEMS Microbiology Ecology
    • ABSTRACT Biofilm is a predominant lifestyle of bacteria that comprises of cells as collectives enmeshed in a polymeric matrix. Biofilm formation is vital for bacterial species as it provides access to nutrients and protects the cells from environmental stresses. Here we show that interference in biofilm matrix production is a strategy by the competing bacterial species to reduce the ability of the other species to colonize a surface.

      • Salmonella
      • Shigella
      • Bacterial pathogens
  23. Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability

    • FEMS Microbiology Ecology
    • The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures.

  24. From the roots to the stem: unveiling pear root colonization and infection pathways by Erwinia amylovora

    • FEMS Microbiology Ecology
    • ABSTRACT Fire blight caused by Erwinia amylovora affects pome fruit worldwide, generating serious economic losses. Despite the abundant literature on E. amylovora infection mechanisms of aerial plant organs, root infection routes remain virtually unexplored. Assessing these infection pathways is necessary for a full understanding of the pathogen's ecology. Using the pathosystem Pyrus communis–E.

  25. Distribution of phenotypic and genotypic antimicrobial resistance and virulence genes in Vibrio parahaemolyticus isolated from cultivated oysters and estuarine water

    • FEMS Microbiology Ecology
    • ABSTRACT A total of 594 Vibrio parahaemolyticus isolates from cultivated oysters (n = 361) and estuarine water (n = 233) were examined for antimicrobial resistance (AMR) phenotype and genotype and virulence genes. Four hundred forty isolates (74.1%) exhibited resistance to at least one antimicrobial agent and 13.5% of the isolates were multidrug-resistant strains. Most of the V.

      • Vibrio
      • Bacterial pathogens