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Implementing Sequencing Analysis to Uncover Spoilage and Food Safety Concerns Linked to the Microbiota of Food Processing Environments and Onions.
Implementing Sequencing Analysis to Uncover Spoilage and Food Safety Concerns Linked to the Microbiota of Food Processing Environments and Onions.
상세정보
- 자료유형
- 학위논문(국외)
- 기본표목-개인명
- 표제와 책임표시사항
- Implementing Sequencing Analysis to Uncover Spoilage and Food Safety Concerns Linked to the Microbiota of Food Processing Environments and Onions.
- 발행, 배포, 간사 사항
- 발행, 배포, 간사 사항
- 형태사항
- 241 p.
- 일반주기
- Source: Dissertations Abstracts International, Volume: 87-07, Section: B.
- 일반주기
- Includes supplementary digital materials.
- 일반주기
- Advisor: Snyder, Abigail.
- 학위논문주기
- Thesis (Ph.D.)--Cornell University, 2025.
- 요약 등 주기
- 요약Food processing environments and fresh produce harbor spoilage and pathogenic microbes that can affect food quality and safety. Assessing the distribution of microbes on food processing environment surfaces and fresh produce is essential for identifying food safety and quality concerns and for developing strategies to address these concerns. Conventionally, microbial assessments were conducted using culture-based methods to detect pathogens and enumerate indicator organisms. Advances in sequencing technologies have introduced new approaches for assessing microbes in processing environments and food products. For instance, amplicon sequencing has been widely used to analyze microbial community structures in food processing environments. However, multiple challenges exist in applying amplicon sequencing to characterize microbial communities in food production environments. This collection of work aims to address these challenges.In Chapter 1, we addressed the challenge of determining the harborage sites of spoilage organisms and pathogens using unstructured metadata. We analyzed 1,498 free-text swab site descriptions to identify common issues and language structures. We identified five information facets represented in these swab site descriptions and observed that 99.6% of these descriptions depicted only a single information facet about the swab site. To address problems associated with free-text swab site descriptions, we developed a metadata schema to standardize the structure and term usage of swab site descriptions. This schema was integrated into the One Health Enteric Package available at NCBI. Insufficient cell collection from processing environment surfaces and low DNA extraction yields can also pose challenges for characterizing microbial communities. Hence, in Chapter 2, we assessed the impact of cell recovery and DNA extraction protocols on the relative abundance estimates of microorganisms on artificially inoculated surfaces. We found that existing protocols for cell recovery and DNA extraction distorted the relative abundance of microorganisms on surfaces, indicating a need to improve current methods to enhance accuracy. In Chapter 3, we collected environmental samples from dairy facilities and conducted analyses using both amplicon sequencing and culturing methods to study microbial communities in dairy processing environments. The goal of these analyses was to understand the distribution of hygiene indicator genera (i.e., Gram-negative, Enterobacteriaceae, Spore-former, and Gram-positive genera) in dairy processing environments. These distributions provided insights into strategies for applying amplicon sequencing and culturing method to determine microbial harborage. In Chapter 4, we further applied amplicon sequencingx to study the impact of plant pathogens on the growth dynamics of Salmonella in onions. We found that plant pathogens can cause onion tissue decay and support Salmonella growth.
- 주제명부출표목-일반주제명
- 주제명부출표목-일반주제명
- 주제명부출표목-일반주제명
- 비통제 색인어
- 비통제 색인어
- 비통제 색인어
- 비통제 색인어
- 비통제 색인어
- 비통제 색인어
- 부출표목-단체명
- 기본자료저록
- Dissertations Abstracts International. 87-07B.
- 전자적 위치 및 접속
- 원문정보보기
MARC
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■1001 ▼aFeng, Jingzhang.
■24510▼aImplementing Sequencing Analysis to Uncover Spoilage and Food Safety Concerns Linked to the Microbiota of Food Processing Environments and Onions.
■260 ▼a[S.l.]▼bCornell University. ▼c2025
■260 1▼aAnn Arbor▼bProQuest Dissertations & Theses▼c2025
■300 ▼a241 p.
■500 ▼aSource: Dissertations Abstracts International, Volume: 87-07, Section: B.
■500 ▼aIncludes supplementary digital materials.
■500 ▼aAdvisor: Snyder, Abigail.
■5021 ▼aThesis (Ph.D.)--Cornell University, 2025.
■520 ▼aFood processing environments and fresh produce harbor spoilage and pathogenic microbes that can affect food quality and safety. Assessing the distribution of microbes on food processing environment surfaces and fresh produce is essential for identifying food safety and quality concerns and for developing strategies to address these concerns. Conventionally, microbial assessments were conducted using culture-based methods to detect pathogens and enumerate indicator organisms. Advances in sequencing technologies have introduced new approaches for assessing microbes in processing environments and food products. For instance, amplicon sequencing has been widely used to analyze microbial community structures in food processing environments. However, multiple challenges exist in applying amplicon sequencing to characterize microbial communities in food production environments. This collection of work aims to address these challenges.In Chapter 1, we addressed the challenge of determining the harborage sites of spoilage organisms and pathogens using unstructured metadata. We analyzed 1,498 free-text swab site descriptions to identify common issues and language structures. We identified five information facets represented in these swab site descriptions and observed that 99.6% of these descriptions depicted only a single information facet about the swab site. To address problems associated with free-text swab site descriptions, we developed a metadata schema to standardize the structure and term usage of swab site descriptions. This schema was integrated into the One Health Enteric Package available at NCBI. Insufficient cell collection from processing environment surfaces and low DNA extraction yields can also pose challenges for characterizing microbial communities. Hence, in Chapter 2, we assessed the impact of cell recovery and DNA extraction protocols on the relative abundance estimates of microorganisms on artificially inoculated surfaces. We found that existing protocols for cell recovery and DNA extraction distorted the relative abundance of microorganisms on surfaces, indicating a need to improve current methods to enhance accuracy. In Chapter 3, we collected environmental samples from dairy facilities and conducted analyses using both amplicon sequencing and culturing methods to study microbial communities in dairy processing environments. The goal of these analyses was to understand the distribution of hygiene indicator genera (i.e., Gram-negative, Enterobacteriaceae, Spore-former, and Gram-positive genera) in dairy processing environments. These distributions provided insights into strategies for applying amplicon sequencing and culturing method to determine microbial harborage. In Chapter 4, we further applied amplicon sequencingx to study the impact of plant pathogens on the growth dynamics of Salmonella in onions. We found that plant pathogens can cause onion tissue decay and support Salmonella growth.
■590 ▼aSchool code: 0058.
■650 4▼aFood science.
■650 4▼aMicrobiology.
■650 4▼aGenetics.
■653 ▼aAmplicon sequencing
■653 ▼aDNA
■653 ▼aMetadata
■653 ▼aOntology
■653 ▼aPathogen
■653 ▼aSpoilage
■690 ▼a0359
■690 ▼a0410
■690 ▼a0369
■71020▼aCornell University▼bFood Science and Technology.
■7730 ▼tDissertations Abstracts International▼g87-07B.
■790 ▼a0058
■791 ▼aPh.D.
■792 ▼a2025
■793 ▼aEnglish
■85640▼uhttp://www.riss.kr/pdu/ddodLink.do?id=T17360179▼nKERIS▼z이 자료의 원문은 한국교육학술정보원에서 제공합니다.
