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Pandey P, Chowdhury D, Wang Y. Denaturing Gradient Gel Electrophoresis Approach for Microbial Shift Analysis in Thermophilic and Mesophilic Anaerobic Digestions. Gels 2024; 10:339. [PMID: 38786256 PMCID: PMC11120850 DOI: 10.3390/gels10050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the manure conditions, microbial community presence in manure, and their functions. Additional efforts are needed to understand the GHG emissions from manure and develop control strategies to minimize the biological GHG emissions from manure. To study the microbial shift during anaerobic processes responsible for GHG emission, we conducted a series of manure anaerobic digestion experiments, and these experiments were conducted in lab-scale reactors operated under various temperature conditions (28 °C, 36 °C, 44 °C, and 52 °C). We examined the third variable region (V3) of the 16S rRNA gene fingerprints of bacterial presence in anaerobic environment by PCR amplification and DGGE separation. Results showed that bacterial community was affected by the temperature conditions and anaerobic incubation time of manure. The microbial community structure of the original manure changed over time during anaerobic processes, and the community composition changed substantially with the temperature of the anaerobic process. At Day 0, the sequence similarity confirmed that most of the bacteria were similar (>95%) to Acinetobacter sp. (strain: ATCC 31012), a Gram-negative bacteria, regardless of temperature conditions. At day 7, the sequence similarity of DNA fragments of reactors (28 °C) was similar to Acinetobacter sp.; however, the DNA fragments of effluent of reactors at 44 °C and 52 °C were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 97%) and Tepidimicrobium ferriphilum (strain: DSM 16624) (similarity: 100%), respectively. At day 60, the analysis showed that DNA fragments of effluent of 28 °C reactor were similar to Galbibacter mesophilus (strain: NBRC 10162) (similarity: 87%), and DNA fragments of effluent of 36 °C reactors were similar to Syntrophomonas curvata (strain: GB8-1) (similarity: 91%). In reactors with a relatively higher temperature, the DNA fragments of effluent of 44 °C reactor were similar to Dielma fastidiosa (strain: JC13) (similarity: 86%), and the DNA fragments of effluent of 52 °C reactor were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 99%). To authors' knowledge, this is one of the few studies where DGGE-based approach is utilized to study and compare microbial shifts under mesophilic and thermophilic anaerobic digestions of manure simultaneously. While there were challenges in identifying the bands during gradient gel electrophoresis, the joint use of DGGE and sequencing tool can be potentially useful for illustrating and comparing the change in microbial community structure under complex anaerobic processes and functionality of microbes for understanding the consequential GHG emissions from manure.
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Affiliation(s)
- Pramod Pandey
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
| | - Dhrubajyoti Chowdhury
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
- Department of Life Sciences, School of Science, Gandhi Institute of Technology and Management, Rushikonda, Visakhapatnam 530045, Andhra Pradesh, India
| | - Yi Wang
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
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Shetty BD, Pandey PK, Mai K. Microbial diversity in dairy manure environment under liquid-solid separation systems. ENVIRONMENTAL TECHNOLOGY 2024:1-17. [PMID: 38310325 DOI: 10.1080/09593330.2024.2309481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.
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Affiliation(s)
- B Dharmaveer Shetty
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Pramod K Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Kelly Mai
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Mechanisms of Disease and Translational Research, School of Medical Science, University of New South Wales, Sydney, Australia
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Mortezaei Y, Williams MR, Demirer GN. The fate of antibiotic resistance genes during anaerobic digestion of sewage sludge with ultrasonic pretreatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5513-5525. [PMID: 38127236 DOI: 10.1007/s11356-023-31558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
This study investigated the effect of ultrasonic (US) pretreatment at three different contact times (30, 45, and 60 min) with a power of 240 W and frequency of 40 kHz on the fate of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and enteric pathogens during anaerobic digestion (AD) of sludge. By using real time-qPCR, three MGEs (int1, int2, and tnpA) and seven ARGs (sul1, sul2, tetW, tetA, tetO, ermF, and aac(6')-lb) were quantified that have serious human health impacts and represent the most widely used antibiotics (tetracycline, sulfonamide, macrolide, and aminoglycoside). Results indicated that US pretreatment under different contact times improved the removal of ARGs and MGEs. Compared to 30 and 45 min of US pretreatment, 60 min of US pretreatment resulted in a higher reduction of ARGs with total ARG reduction of 41.70 ± 1.13%. Furthermore, the relative abundance of ARGs and MGEs after US pretreatment was reduced more effectively in anaerobic reactors than in a control AD without US pretreatment. The total ARGs and MGEs removal efficiency of control AD was 44.07 ± 0.72% and 63.69 ± 1.43%, and if US pretreatment at different times were applied, the total ARGs and MGEs removal efficiency of the whole pretreatment AD process improved to 59.71 ± 2.76-68.54 ± 1.58% and 69.82 ± 2.15-76.84 ± 0.22%. The highest removal of total ARGs (68.54 ± 1.58%) and MGEs (76.84 ± 0.22%) was achieved after AD with US pretreatment at 45 min. However, US pretreatment and AD with US pretreatment were not effective in inactivation of enteric pathogens (total coliforms and E. coli), suggesting that posttreatment is needed prior to land application of sludge to reduce the level of enteric pathogens. There was no detection of the studied ARGs and MGEs in the enteric pathogens after US pretreatment in subsequent AD. According to this study, long contact times of US pretreatment can mitigate ARGs and MGEs in AD processes, offering valuable insight into improving environmental safety and sustainable waste management. Additionally, the study highlights the need to investigate posttreatment techniques for reducing enteric pathogens in AD effluent, a crucial consideration for agricultural use and environmental protection.
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Affiliation(s)
- Yasna Mortezaei
- Earth and Ecosystem Science, Central Michigan University, Mount Pleasant, MI, USA
| | - Maggie R Williams
- School of Engineering and Technology, Central Michigan University, Mount Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Goksel N Demirer
- School of Engineering and Technology, Central Michigan University, Mount Pleasant, MI, USA.
- Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.
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Jauregi L, González A, Garbisu C, Epelde L. Organic amendment treatments for antimicrobial resistance and mobile element genes risk reduction in soil-crop systems. Sci Rep 2023; 13:863. [PMID: 36650207 PMCID: PMC9845208 DOI: 10.1038/s41598-023-27840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Agricultural fertilization with organic amendments of animal origin often leads to antibiotic resistance dissemination. In this study, we evaluated the effect of different treatments (anaerobic digestion, biochar application, ozonation, zerovalent iron nanoparticle application, and spent mushroom substrate addition) on the resistome in dairy cow manure-derived amendments (slurry, manure, and compost). Anaerobic digestion and biochar application resulted in the highest reduction in antibiotic resistance gene (ARG) and mobile genetic element (MGE) gene abundance. These two treatments were applied to cow manure compost, which was then used to fertilize the soil for lettuce growth. After crop harvest, ARG and MGE gene absolute and relative abundances in the soil and lettuce samples were determined by droplet digital PCR and high-throughput qPCR, respectively. Prokaryotic diversity in cow manure-amended soils was determined using 16S rRNA metabarcoding. Compared to untreated compost, anaerobic digestion led to a 38% and 83% reduction in sul2 and intl1 absolute abundances in the soil, respectively, while biochar led to a 60% reduction in intl1 absolute abundance. No differences in lettuce gene abundances were observed among treatments. We conclude that amendment treatments can minimize the risk of antibiotic resistance in agroecosystems.
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Affiliation(s)
- Leire Jauregi
- NEIKER - Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain.
| | - Aitor González
- NEIKER - Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Carlos Garbisu
- NEIKER - Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Lur Epelde
- NEIKER - Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
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Burch TR, Firnstahl AD, Spencer SK, Larson RA, Borchardt MA. Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:352-363. [PMID: 35388483 DOI: 10.1002/jeq2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion has been suggested as an intervention to attenuate antibiotic resistance genes (ARGs) in livestock manure but supporting data have typically been collected at laboratory scale. Few studies have quantified ARG fate during full-scale digestion of livestock manure. We sampled untreated manure and digestate from seven full-scale mesophilic dairy manure digesters to assess ARG fate through each system. Samples were collected biweekly from December through August (i.e., winter, spring, and summer; n = 235 total) and analyzed by quantitative polymerase chain reaction for intI1, erm(B), sul1, tet(A), and tet(W). Concentrations of intI1, sul1, and tet(A) decreased during anaerobic digestion, but their removal was less extensive than expected based on previous laboratory studies. Removal for intI1 during anaerobic digestion equaled 0.28 ± 0.03 log10 units (mean ± SE), equivalent to only 48% removal and notable given intI1's role in horizontal gene transfer and multiple resistance. Furthermore, tet(W) concentrations were unchanged during anaerobic digestion (p > 0.05), and erm(B) concentrations increased by 0.52 ± 0.03 log10 units (3.3-fold), which is important given erythromycin's status as a critically important antibiotic for human medicine. Seasonal log10 changes in intI1, sul1, and tet(A) concentrations were ≥50% of corresponding log10 removals by anaerobic digestion, and variation in ARG and intI1 concentrations among digesters was quantitatively comparable to anaerobic digestion effects. These results suggest that mesophilic anaerobic digestion may be limited as an intervention for ARGs in livestock manure and emphasize the need for multiple farm-level interventions to attenuate antibiotic resistance.
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Affiliation(s)
- Tucker R Burch
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Aaron D Firnstahl
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- USGS, Upper Midwest Water Science Center, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Susan K Spencer
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Rebecca A Larson
- Dep. of Biological Systems Engineering, Univ. of Wisconsin-Madison, 232C Agricultural Engineering Building, 460 Henry Mall, Madison, WI, 53706, USA
| | - Mark A Borchardt
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
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Damtie MM, Lee J, Shin J, Shin SG, Son H, Wang J, Kim YM. Identification of factors affecting removal of antibiotic resistance genes in full-scale anaerobic digesters treating organic solid wastes. BIORESOURCE TECHNOLOGY 2022; 351:126929. [PMID: 35247556 DOI: 10.1016/j.biortech.2022.126929] [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: 01/02/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Efficiencies of removing antibiotic resistance genes (ARGs) and intI1 were explored using eight full-scale anaerobic digesters. The digesters demonstrated different characteristics on the basis of substrate types (food waste, manure or sludge); configuration (single or two-stage); temperature (psychrophilic, mesophilic or thermophilic); hydraulic retention time (HRT) (9.7-44 days); and operation mode (continuous stirred tank reactor or plug flow reactor). Digesters' configuration or operating parameters showed a greater effect on abundance of ARGs than the type of input substrate. Redundancy analysis (RDA) accounted for 85.2% of the total variances and digesters with the same configuration and operational conditions showed similar performance for removal of ARGs. The highest efficiencies of removing ARGs (99.99%) were observed in two-stage thermophilic digesters with relatively long HRTs (32 days). The lowest removal efficiency (97.93%) was observed in single-stage mesophilic with relatively short HRTs (9.7 days), likely due to vertical and horizontal gene transfer.
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Affiliation(s)
- Mekdimu Mezemir Damtie
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jangwoo Lee
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Heejong Son
- Busan Water Quality Institute, Busan 50804, Republic of Korea
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taiwan 271018, China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
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Clarification of the Dynamic Autothermal Thermophilic Aerobic Digestion Process Using Metagenomic Analysis. Microbiol Spectr 2022; 10:e0056122. [PMID: 35348372 PMCID: PMC9045309 DOI: 10.1128/spectrum.00561-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study details a unique process of autothermal thermophilic aerobic digestion (ATAD) of human excreta useful in producing nitrogen-rich and pathogen-free organic fertilizer. The process was divided into initial, middle, and final phases, based on changes in temperature, dissolved oxygen (DO), and bacterial community structure. The aim of this study was to determine bacterial factors that would affect liquid fertilizer production in the process, using shotgun metagenomic analysis of each phase. Although the abundances of all 28 gene categories include 4 categories in SEED subsystems level 1 were similar to those in another type of wastewater treatment system, the abundances of 4 gene categories changed remarkably. Among them, a decrease in the abundance of the phage-related gene category and the presence of antibacterial substances in secondary metabolism may explain the change in bacterial community structure from the material to the initial phase. Increases in the abundances of two gene categories, phage-related and secondary metabolism, coincided with a decrease in alpha diversity from the material to the initial phase. A potential increase in the abundance of genes in the category of sporulation from the middle to the final phase was correlated with deterioration of growth conditions and stabilization processes. In addition, prompt consumption of short-chain fatty acids in the initial phase and unusually stable ammonia accumulation throughout the process could be explained by the presence/absence of related metabolic genes. In conclusion, the relationships between bacterial function and unique characteristics of ATAD were revealed; our findings support the enhancement of liquid fertilizer production from wastewater. IMPORTANCE Metagenome analysis was performed to determine the microbial dynamics of the unique autothermal thermophilic aerobic digestion process of human excreta, which includes initial, middle, and final phases. In this study, we revealed the details of functional genes related to physicochemical and bacterial characteristics in the ATAD process. Four gene categories showed increases and decreases during the digestion process. In addition, the unusual stable accumulation of ammonia and prompt consumption of short-chain fatty acids were explained by the absence or presence of related metabolic genes. In addition to revealing the relationships between bacteria and physicochemical properties, the results of this research may support improving wastewater management systems worldwide by using the ATAD process in liquid fertilizer production systems.
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Liu Y, Gao P, Wu Y, Wang X, Lu X, Liu C, Li N, Sun J, Xiao J, Jesus SG. The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing. Front Nutr 2022; 8:800932. [PMID: 34977133 PMCID: PMC8717741 DOI: 10.3389/fnut.2021.800932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/02/2021] [Indexed: 02/05/2023] Open
Abstract
Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.
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Affiliation(s)
- Yanxia Liu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Peng Gao
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Yuhao Wu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Xiaorui Wang
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Xiaoming Lu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Chao Liu
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningyang Li
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Taian, China
| | - Jinyue Sun
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianbo Xiao
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Universidade de Vigo, Ourense, Spain
| | - Simal-Gandara Jesus
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Universidade de Vigo, Ourense, Spain
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