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Gu G, Ding Q, Redding M, Yang Y, O'Brien R, Gu T, Zhang B, Zhou B, Micallef SA, Luo Y, Fonseca JM, Nou X. Differential microbiota shift on whole romaine lettuce subjected to source or forward processing and on fresh-cut products during cold storage. Int J Food Microbiol 2024; 416:110665. [PMID: 38457887 DOI: 10.1016/j.ijfoodmicro.2024.110665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Romaine lettuce in the U.S. is primarily grown in California or Arizona and either processed near the growing regions (source processing) or transported long distance for processing in facilities serving distant markets (forward processing). Recurring outbreaks of Escherichia coli O157:H7 implicating romaine lettuce in recent years, which sometimes exhibited patterns of case clustering in Northeast and Midwest, have raised industry concerns over the potential impact of forward processing on romaine lettuce food safety and quality. In this study, freshly harvested romaine lettuce from a commercial field destined for both forward and source processing channels was tracked from farm to processing facility in two separate trials. Whole-head romaine lettuce and packaged fresh-cut products were collected from both forward and source facilities for microbiological and product quality analyses. High-throughput amplicon sequencing targeting16S rRNA gene was performed to describe shifts in lettuce microbiota. Total aerobic bacteria and coliform counts on whole-head lettuce and on fresh-cut lettuce at different storage times were significantly (p < 0.05) higher for those from the forward processing facility than those from the source processing facility. Microbiota on whole-head lettuce and on fresh-cut lettuce showed differential shifting after lettuce being subjected to source or forward processing, and after product storage. Consistent with the length of pre-processing delays between harvest and processing, the lettuce quality scores of source-processed romaine lettuce, especially at late stages of 2-week storage, was significantly higher than of forward-processed product (p < 0.05).
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Affiliation(s)
- Ganyu Gu
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Qiao Ding
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, United States of America
| | - Marina Redding
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Yishan Yang
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Regina O'Brien
- Food Quality Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Tingting Gu
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, United States of America
| | - Boce Zhang
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, United States of America
| | - Bin Zhou
- Food Quality Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, United States of America; Centre for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, United States of America
| | - Yaguang Luo
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, United States of America; Food Quality Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Jorge M Fonseca
- Food Quality Laboratory, USDA ARS, Beltsville, MD 20705, United States of America
| | - Xiangwu Nou
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, United States of America.
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Wang B, Chen C, Xiao YM, Chen KY, Wang J, Zhao S, Liu N, Li JN, Zhou GY. Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions. Microbiol Res 2024; 280:127603. [PMID: 38199002 DOI: 10.1016/j.micres.2024.127603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Rhizosphere microorganisms play a vital role in enhancing plant health, productivity, and the accumulation of secondary metabolites. Currently, there is a limited understanding of the ecological processes that control the assembly of community. To address the role of microbial interactions in assembly and for functioning of the rhizosphere soil microbiota, we collected rhizosphere soil samples from Anisodus tanguticus on the Tibetan Plateau spanning 1500 kilometers, and sequenced the bacteria, fungi, archaea, and protist communities. We observed a significant but weak distance-decay relationship in the microbial communities of rhizosphere soil. Our comprehensive analysis of spatial, abiotic, and biotic factors showed that trophic relationships between protists and bacteria and fungi predominantly influenced the alpha and beta diversity of bacterial, fungal, and protistan communities, while abiotic factors had a greater impact on archaeal communities, including soil pH, available phosphorus, total phosphorus and mean annual temperature. Importantly, microbial interactions had a more significant influence on Anisodus tanguticus physiological and ecological functions compared to individual microorganisms. Network analyses revealed that bacteria occupy a central position of the co-occurrence network and play a crucial role of connector within this community. The addition of protists increased the stability of bacterial, fungal, and archaeal networks. Overall, our findings indicate that trophic relationships play an important role in assembly and for functioning of the rhizosphere soil microbiota. Bacterial communities serve as a crucial link between different kingdoms of microorganisms in the rhizosphere community. These findings help us to fully harness the beneficial functions of rhizosphere microorganisms for plants and achieve sustainable use of biological resources.
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Affiliation(s)
- Bo Wang
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Chen
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yuan-Ming Xiao
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China
| | - Kai-Yang Chen
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Wang
- Qinghai University, Xining 810016, China
| | - Shuo Zhao
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Liu
- Qinghai University, Xining 810016, China
| | - Jia-Nan Li
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Ying Zhou
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining 810008, China.
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Jeong S, Kim I, Kim BE, Jeong MI, Oh KK, Cho GS, Franz CMAP. Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment. Microorganisms 2023; 11:1241. [PMID: 37317216 DOI: 10.3390/microorganisms11051241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 06/16/2023] Open
Abstract
The consumption of fresh produce and fruits has increased over the last few years as a result of increasing consumer awareness of healthy lifestyles. Several studies have shown that fresh produces and fruits could be potential sources of human pathogens and antibiotic-resistant bacteria. In this study, 248 strains were isolated from lettuce and surrounding soil samples, and 202 single isolates selected by the random amplified polymorphic DNA (RAPD) fingerprinting method were further characterized. From 202 strains, 184 (91.2%) could be identified based on 16S rRNA gene sequencing, while 18 isolates (8.9%) could not be unequivocally identified. A total of 133 (69.3%) and 105 (54.7%) strains showed a resistance phenotype to ampicillin and cefoxitin, respectively, while resistance to gentamicin, tobramycin, ciprofloxacin, and tetracycline occurred only at low incidences. A closer investigation of selected strains by whole genome sequencing showed that seven of the fifteen sequenced strains did not possess any genes related to acquired antibiotic resistance. In addition, only one strain possessed potentially transferable antibiotic resistance genes together with plasmid-related sequences. Therefore, this study indicates that there is a low possibility of transferring antibiotic resistance by potential pathogenic enterobacteria via fresh produce in Korea. However, with regards to public health and consumer safety, fresh produce should nevertheless be continuously monitored to detect the occurrence of foodborne pathogens and to hinder the transfer of antibiotic resistance genes potentially present in these bacteria.
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Affiliation(s)
- Sunyoung Jeong
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
- College of Life Sciences and Biotechnology, Korea University, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ile Kim
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
- Department of Life Science, Handong Global University, 558 Handong-ro, Buk-gu, Pohang 37554, Republic of Korea
| | - Bo-Eun Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, 166 Nongsaengmyeong-ro, Iseo-myeon, Wanju 55365, Republic of Korea
| | - Myeong-In Jeong
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, 166 Nongsaengmyeong-ro, Iseo-myeon, Wanju 55365, Republic of Korea
| | - Kwang-Kyo Oh
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, 166 Nongsaengmyeong-ro, Iseo-myeon, Wanju 55365, Republic of Korea
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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Li X, Gao Y, Han Y, Zhang R, Wang C, Wu X. Microbial communities and metabolite profiles during the fermentation of Chinese Dongbei suancai with Chinese baijiu as supplementary material. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:3521-3530. [PMID: 36799142 DOI: 10.1002/jsfa.12510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In industrial production of suancai, baijiu is commonly used to inhibit the spoilage bacteria and enhance the flavor. However, the effects of baijiu on the microbial diversity and metabolic pathways of suancai are rarely reported in the literature. This study aimed to explore the microbial community, its predicted functional roles, and the metabolites formed during fermentation of Chinese Dongbei suancai fermented using a mixed starter with Chinese baijiu as supplementary material. RESULTS Results showed that Lactobacillus, Enterobacter, and Leuconostoc were the major bacterial genera in the Dongbei suancai fermented by adding baijiu. Linear discriminant analysis effect size indicated that Leuconostoc was the major biomarker in the early stage of fermentation, whereas Lactococcus, Weissella, and Lactobacillus plantarum were biomarkers in the middle and later stages of fermentation. A total of 638 metabolites were detected in suancai fermented by adding baijiu. However, the principal component analysis showed that baijiu significantly affected the metabolites of suancai in the early and later stages of fermentation. Furthermore, 58, 22, and 26 significantly differential metabolites (P < 0.01) were found on day 0, day 2, and day 30 of fermentation respectively. Moreover, Lactobacillus, Lactococcus, and Enterobacter had positive correlations with amino acids, nucleotides, organic acids, alcohols, and esters. Functional analysis implied that carbohydrate, amino acid, energy, and nucleotide metabolism were the major determinants of the characteristics of suancai fermented with baijiu as supplementary material. CONCLUSION Baijiu changed the metabolites of inoculated fermented Dongbei suancai. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiao Li
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Ya Gao
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanqiu Han
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Rui Zhang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Chen Wang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xingzhuang Wu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
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