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Cai W, Fei L, Zhang D, Ni H, Peng B, Zhao X, Zhang Q, Tang F, Zhang Y, Shan C. Impact of ultra-high-pressure treatment on microbial community composition and flavor quality of jujube juice: Insights from high-throughput sequencing technology, intelligent bionic sensory system, and metabolomics approach. Food Res Int 2024; 191:114688. [PMID: 39059944 DOI: 10.1016/j.foodres.2024.114688] [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: 03/03/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
Ultra-high-pressure (UHP1) technology for cold pasteurization is a viable alternative to traditional heat sterilization for preserving food nutrients and flavor compounds during fruit juice processing. In this study, cutting-edge techniques, including high-throughput sequencing technology, intelligent bionic sensory systems, and metabolomics, were used to examine the impact of UHP treatment on microbial community composition, odor, and taste quality of jujube juice. The UHP treatment demonstrated its effect by inducing a reddish-yellow color in the jujube juice, thereby enhancing its brightness, overall color, and stability. The most significant enhancement was observed at 330 MPa. The microorganisms responsible for spoilage and deterioration of jujube juice during storage were categorized into three clusters: bacterial clusters at 0-330 MPa, 360-450 MPa, and 480-630 Mpa. The results showed no distinct distribution patterns for fungi based on the pressure strength. The dominant bacterial genera were Lactobacillus, Nocardia, Achromobacter, Enterobacter, Pseudomonas, Mesorhizobium, and Rhodococcus, whereas the dominant fungal genera were yeast and mold. Notably, Lactobacillus, Achromobacter, Enterobacter, and Pseudomonas were responsible for the significant differences between the 360 MPa to 450 MPa and 480 MPa to 630 MPa clusters in terms of bacterial spoilage, whereas Torulaspora, Lodderomyces, Wickerhamomyces, and Fusarium were the primary fungal spoilage genera. UHP treatment exerted no significant impact on the taste of jujube juice but influenced its sourness. Treatment at 330 MPa had the most pronounced effect on the presence of aromatic compounds and other odorants, which were substantially increased. Further analysis revealed the prevalence of organic acids, such as malic acid, succinic acid, and tartaric acid, in jujube juice and demonstrated a consistent relationship between changes in organic acids and sourness. In addition, nine distinct odorants with VIP values greater than 1 were identified in the jujube juice. Among these, methyl acetate and methyl caproate exhibited substantial increases following the UHP treatment at 330 MPa.
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Affiliation(s)
- Wenchao Cai
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Liyue Fei
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Dongsheng Zhang
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Office of the Party Committee of Xinjiang Production and Construction Corps, Urumqi, Xinjiang 830000, China
| | - Hui Ni
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Bo Peng
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Xinxin Zhao
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Qin Zhang
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Fengxian Tang
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Yan Zhang
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China.
| | - Chunhui Shan
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory of Processing and Quality and Safety Control of Specialty Agricultural Products (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China; Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science, Shihezi University, Shihezi, Xinjiang 832000, China.
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Kessler SE, Tsangaras K, Rasoloharijaona S, Radespiel U, Greenwood AD. Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression. Virus Evol 2022; 9:veac117. [PMID: 36632481 PMCID: PMC9825726 DOI: 10.1093/ve/veac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Madagascar's flora and fauna have evolved in relative isolation since the island split from the African and Indian continents. When the last common ancestors of lemurs left Africa between 40 and 70 million years ago, they carried a subset of the viral diversity of the mainland population within them, which continued to evolve throughout the lemur radiation. Relative to other primate radiations, we know very little about the past or present viral diversity of lemurs, particularly mouse lemurs. Using high-throughput sequencing, we identified two gammaretroviruses and three betaretroviruses in the genomes of four species of wild mouse lemurs. The two gammaretroviruses and two betaretroviruses have not previously been described. One betaretrovirus was previously identified. All identified viruses are present in both Lorisiformes and Lemuriformes but absent from haplorrhine primates. The estimated ages of these viruses are consistent with the estimated divergence dates of the host lineages, suggesting they colonized the lemur genome after the Haplorrhine-Strepsirrhine split, but before the Lorisiformes-Lemuriformes split and before the colonization of Madagascar. The viral phylogenies connect multiple lineages of retroviruses from non-lemur and non-Madagascar-native species, suggesting substantial cross-species transmission occurred deep in the primate clade prior to its geographic dispersal. These phylogenies provide novel insights into known retroviral clades. They suggest that the origin of gammaretroviruses in rodents or bats may be premature and that the Jaagsiekte sheep virus clade may be older and more broadly distributed among mammals than previously thought.
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Affiliation(s)
| | - Kyriakos Tsangaras
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin 10315, Germany,Department of Life and Health Sciences, University of Nicosia, 46 Makedonitissas Avenue, CY-2417, P.O. Box 24005, Nicosia, CY-1700, Cyprus
| | - Solofonirina Rasoloharijaona
- Faculty of Science, Technology and Environment, University of Mahajanga, 5 Georges V Street - Building KAKAL Mahajanga Be - Po. Box 652 , Mahajanga 401, Madagascar
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Buenteweg 17, Hannover 30559, Germany
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Gillingham MAF, Montero BK, Wihelm K, Grudzus K, Sommer S, Santos PSC. A novel workflow to improve genotyping of multigene families in wildlife species: An experimental set-up with a known model system. Mol Ecol Resour 2020; 21:982-998. [PMID: 33113273 DOI: 10.1111/1755-0998.13290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022]
Abstract
Genotyping complex multigene families in novel systems is particularly challenging. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most genotyping pipelines have been validated in nonmodel systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and genotype complexity (i.e. number of alleles per genotype) within a PCR remains poorly described. Here, we investigated the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well-defined 'optimal' primers, we simulated a nonmodel species situation by designing 'cross-species' primers based on sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA; https://gitlab.com/psc_santos/ACACIA), and compared its performance with another, previously published pipeline (AmpliSAS). Allele calling accuracy was higher when using ACACIA (98.5% versus 97% and 77.8% versus 75% for the 'optimal' and 'cross-species' data sets, respectively). Systematic allele dropout of three alleles owing to primer mismatch in the 'cross-species' data set explained high allele calling repeatability (100% when using ACACIA) despite low accuracy, demonstrating that repeatability can be misleading when evaluating genotyping workflows. Genotype complexity was positively associated with nonchimeric artefacts, chimeric artefacts (nonlinearly by levelling when amplifying more than 4-6 alleles) and allele amplification bias. Our study exemplifies and demonstrates pitfalls researchers should avoid to reliably genotype complex multigene families.
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Affiliation(s)
- Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany
| | - B Karina Montero
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany.,Zoological Institute, Animal Ecology and Conservation, Biocenter Grindel, Universität Hamburg, Hamburg,, Germany
| | - Kerstin Wihelm
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany
| | - Kara Grudzus
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany
| | - Pablo S C Santos
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm Universität, Ulm, Germany
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Kling KJ, Yaeger K, Wright PC. Trends in forest fragment research in Madagascar: Documented responses by lemurs and other taxa. Am J Primatol 2020; 82:e23092. [PMID: 31960516 DOI: 10.1002/ajp.23092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/02/2019] [Accepted: 12/20/2019] [Indexed: 11/05/2022]
Abstract
The rise in research investigating fragmentation and its impact on primates and other taxa reflects the growing presence of fragmented landscapes themselves. Although numerous studies report the negative effects of fragmentation on biodiversity, it is difficult to generalize responses to fragmentation for specific taxonomic groups, such as non-human primates, when studies have not employed a definitive concept of fragmentation or fragments themselves. Madagascar's high degree of fragmentation, wealth of endemic taxa, and extensive history of ecological research provide the opportunity to compare fragmentation studies across similar contexts. We conducted a literature search of peer-reviewed articles on fragmentation in Madagascar to characterize its trends. A total of 70 articles, 46 of which concentrated on lemurs, tested the impacts of fragmentation on Malagasy taxa, while additional sources conducted research in one or more fragments without testing its effects (n = 112 total, 79 on lemurs). Studies on lemurs most frequently tested fragmentation's impacts on genetics and biodiversity metrics (n = 16 and 15 studies, respectively), although health, modeling, behavioral, and cross-disciplinary techniques were also reported. Responses to fragmentation were reported for 49 lemur species, with most studies concentrated in eastern Madagascar (87%). Although there was variation in the metrics reported in studies testing the effects of fragmentation on Malagasy species, the most common measures were fragment area, isolation, or comparison to a control site. Landscape-scale approaches and examination of fragmentation per se were rarely employed. Characterizing trends of fragmentation research in Madagascar emphasizes the challenges of documenting fragmentation's effects while highlighting the benefits of research within fragmented landscapes, particularly when combined with consideration for how the matrix within human-modified landscapes may impact primate populations.
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Affiliation(s)
- Katherine J Kling
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York
| | - Kimberley Yaeger
- Department of Anthropology, Stony Brook University, Stony Brook, New York
| | - Patricia C Wright
- Department of Anthropology, Stony Brook University, Stony Brook, New York.,Institute for the Conservation of Tropical Environments, Stony Brook University, Stony Brook, New York
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