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Pathak A, Marquez M, Stothard P, Chukwujindu C, Su JQ, Zhou Y, Zhou XY, Jagoe CH, Chauhan A. A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential. iScience 2024; 27:110193. [PMID: 38984199 PMCID: PMC11231605 DOI: 10.1016/j.isci.2024.110193] [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: 12/29/2023] [Revised: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Mario Marquez
- Texas Sea Grant College Program, 4115 TAMU Eller O&M 306, Texas A&M University, College Station, TX 77843, USA
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, General Services Bldg, Edmonton, AB 2-31 T6G 2H1, Canada
| | - Christian Chukwujindu
- Material & Energy Technology Department, Projects Development Institute, Emene Industrial Layout, Enugu-Nigeria 400104
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Yuan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Charles H. Jagoe
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [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: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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Wu Y, Wang H, Gao Z, Wang H, Zou H. Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes ( Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China. Animals (Basel) 2023; 14:3. [PMID: 38200734 PMCID: PMC10778468 DOI: 10.3390/ani14010003] [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: 10/28/2023] [Revised: 12/03/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).
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Affiliation(s)
- Yining Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Huan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Zhongyan Gao
- Management Bureau of Heilongjiang Zhalong National Reserve, Qiqihar 161005, China;
| | - He Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Hongfei Zou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
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4
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Liu J, Liu H, Cao G, Cui Y, Wang H, Chen X, Xu F, Li X. Microbiota Characterization of the Cow Mammary Gland Microenvironment and Its Association with Somatic Cell Count. Vet Sci 2023; 10:699. [PMID: 38133250 PMCID: PMC10747812 DOI: 10.3390/vetsci10120699] [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: 10/18/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Subclinical mastitis is a common disease that threatens the welfare and health of dairy cows and causes huge economic losses. Somatic cell count (SCC) is the most suitable indirect index used to evaluate the degree of mastitis. To explore the relationship between SCC, diversity in the microbiome, and subclinical mastitis, we performed next-generation sequencing of the 16S rRNA gene of cow's milk with different SCC ranges. The data obtained showed that the microbiota was rich and coordinated with SCC below 2 × 105. SCC above 2 × 105 showed a decrease in the diversity of microbial genera. When SCC was below 2 × 105, the phylum Actinobacteriota accounted for the most. When SCC was between 2 × 105 and 5 × 105, Firmicutes accounted for the most, and when SCC exceeded 5 × 105, Firmicutes and Proteobacteria accounted for the most. Pathogenic genera such as Streptococcus spp. were absent, while SCC above 2 × 105 showed a decrease in the diversity of microbial genera. SCC was positively correlated with the percentage of Romboutsia, Turicibacter, and Paeniclostridium and negatively correlated with the percentage of Staphylococcus, Psychrobacter, Aerococcus, and Streptococcus. Romboutsia decreased 6.19 times after the SCC exceeded 2 × 105; the SCC increased exponentially from 2 × 105 to 5 × 105 and above 1 × 106 in Psychrobacter. Analysis of the microbiota of the different SCC ranges suggests that the development of mastitis may not only be a primary infection but may also be the result of dysbiosis in the mammary gland.
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Affiliation(s)
- Jing Liu
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
| | - Huan Liu
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
| | - Guangjie Cao
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
| | - Yifang Cui
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100081, China
| | - Huanhuan Wang
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
| | - Xiaojie Chen
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
- Laboratory of Quality & Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Fei Xu
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
- Laboratory of Quality & Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xiubo Li
- National Feed Drug Reference Laboratories, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.)
- Laboratory of Quality & Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
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Wang M, Zheng H, Wang S, Luo H, Li Z, Song X, Xu H, Li P, Sun S, Wang Y, Yuan Z. Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs. Microb Pathog 2023; 185:106441. [PMID: 37944676 DOI: 10.1016/j.micpath.2023.106441] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.
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Affiliation(s)
- Meng Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shuaiwei Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Houqiang Luo
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Ziwei Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Xianzhang Song
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Hongxi Xu
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Peide Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Siyu Sun
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Yan Wang
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
| | - Zhenjie Yuan
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
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Ochoa-Sánchez M, Acuña Gomez EP, Moreno L, Moraga CA, Gaete K, Eguiarte LE, Souza V. Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns. PeerJ 2023; 11:e16290. [PMID: 37933257 PMCID: PMC10625763 DOI: 10.7717/peerj.16290] [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: 06/01/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lucila Moreno
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Claudio A. Moraga
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Katherine Gaete
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Valeria Souza
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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Kaur J, Sood U, Talwar C, Whitman WB, Lal R. Phylogenomics-based reclassifications in the genus Psychrobacter including emended descriptions of Psychrobacter pacificensis, Psychrobacter proteolyticus and Psychrobacter submarinus. Antonie Van Leeuwenhoek 2023; 116:1113-1121. [PMID: 37640969 DOI: 10.1007/s10482-023-01871-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006).
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Affiliation(s)
- Jasvinder Kaur
- Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110 049, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, 110007, India.
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007, India
- Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, New Delhi, 110019, India.
- PhixGen Private Limited, Gurugram, Haryana, 122001, India.
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Huang Q, Zhang H, Zhang L, Xu B. Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence. Crit Rev Food Sci Nutr 2023:1-16. [PMID: 37905560 DOI: 10.1080/10408398.2023.2272770] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.
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Affiliation(s)
- Qianli Huang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Huijuan Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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Palanisamy V, Bosilevac JM, Barkhouse DA, Velez SE, Chitlapilly Dass S. Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants. Front Cell Infect Microbiol 2023; 13:1240138. [PMID: 37743870 PMCID: PMC10515220 DOI: 10.3389/fcimb.2023.1240138] [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: 06/14/2023] [Accepted: 08/08/2023] [Indexed: 09/26/2023] Open
Abstract
Background Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments. Methods This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing. Results Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms. Conclusion This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.
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Affiliation(s)
- Vignesh Palanisamy
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Joseph M. Bosilevac
- U. S. Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Lincoln, NE, United States
| | - Darryll A. Barkhouse
- Molecular Center of Excellence, Invisible Sentinel, bioMerieux Inc., Philadelphia, PA, United States
| | - Sarah E. Velez
- Molecular Center of Excellence, Invisible Sentinel, bioMerieux Inc., Philadelphia, PA, United States
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Perry EB, Discepolo DR, Liang SY, Scott M, Williamson K, Bender KS. Biocidal effects of a wipe-down procedure using common veterinary cleansers on microbial burden within working canine exterior coats. Front Vet Sci 2023; 10:1219249. [PMID: 37565083 PMCID: PMC10411539 DOI: 10.3389/fvets.2023.1219249] [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: 05/08/2023] [Accepted: 06/19/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Recent work demonstrating reduction of aerosolized contamination via a wipe-down procedure using common veterinary antiseptics offers promise regarding health concerns associated with cross-contamination from working canines to humans. While mechanical reduction can be achieved via a wipe-down procedure, the biocidal impact on flora within the exterior coat is unknown. Methodology This study assessed the biocidal impact of antiseptics on the exterior bacterial community of the canine. Lint-free towels were saturated with 2% chlorhexidine gluconate scrub, or 7.5% povidone-iodine scrub diluted at a 1:4 ratio. Treatments were rotated across the dorsal aspect of kennel housed Foxhounds (n = 30). Sterile swabs were collected in triplicate prior to, and following wipe down, stored in Amies solution at 4°C, plated onto nutrient agar and reduction in colony forming units (CFU) was measured across both treatments. Statistical analysis utilizing PROC GLM examined effects of treatment (p ≤ 0.05). Molecular analysis of the 16S rRNA gene was completed for 3 hounds. Results Reduction in CFU was measured (p < 0.001) for both antiseptics. Qualitative molecular data indicated that both antiseptics had a biocidal effect on the dominant microbial community on the exterior coat with gram-positive, spore-forming taxa predominating post-treatment. Conclusion Effective wipe-down strategies using common veterinary cleansers should be further investigated and incorporated to safeguard working canine health and prevent cross-contamination of human personnel.
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Affiliation(s)
- Erin B. Perry
- Department of Animal Science Food and Nutrition, Southern Illinois University, Carbondale, IL, United States
| | - Dakota R. Discepolo
- Department of Animal Science Food and Nutrition, Southern Illinois University, Carbondale, IL, United States
| | - Stephen Y. Liang
- Department of Emergency Medicine and Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Maurnice Scott
- Department of Animal Science Food and Nutrition, Southern Illinois University, Carbondale, IL, United States
| | - Kyleigh Williamson
- School of Biological Sciences, Microbiology Program, Southern Illinois University, Carbondale, IL, United States
| | - Kelly S. Bender
- School of Biological Sciences, Microbiology Program, Southern Illinois University, Carbondale, IL, United States
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11
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Molina-Peñate E, Del Carmen Vargas-García M, Artola A, Sánchez A. Filling in the gaps in biowaste biorefineries: The use of the solid residue after enzymatic hydrolysis for the production of biopesticides through solid-state fermentation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:92-103. [PMID: 36871406 DOI: 10.1016/j.wasman.2023.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/31/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Alternative production processes using waste are necessary to preserve non-renewable resources and prevent scarcity of materials for future generations. Biowaste, the organic fraction of municipal solid waste, is abundant and easily available. It can be fractionated into building blocks for which fermentative processes can be designed. By using solid-state fermentation, this paper proposes a method of valorizing biowaste's residual solid fraction after enzymatic hydrolysis. In a 22 L bioreactor, two digestates from anaerobic digestion processes were evaluated as cosubstrates to modify the acidic pH of the solid residue after enzymatic hydrolysis and promote the growth of the bacterial biopesticide producer Bacillus thuringiensis. Regardless of the cosubstrate used, the final microbial populations were similar indicating microbial specialization. The final product contained 4 × 108 spores per gram of dry matter and also crystal proteins of Bacillus thuringiensis var israelensis, which have insecticidal activity against pests. This method allows for the sustainable use of all materials liberated during the enzymatic hydrolysis of biowaste, including residual solids.
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Affiliation(s)
- Esther Molina-Peñate
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Aeris Tecnologías Ambientales S.L, Carrer Santa Rosa, 38, local, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - María Del Carmen Vargas-García
- Microbiology Unit, Department of Biology and Geology, University of Almeria, International Excellence Campus of the Sea (CEI·MAR), Crta. Sacramento s/n, La Cañada de San Urbano, 04120 Almería, Spain
| | - Adriana Artola
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Antoni Sánchez
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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12
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Fackelmann G, Pham CK, Rodríguez Y, Mallory ML, Provencher JF, Baak JE, Sommer S. Current levels of microplastic pollution impact wild seabird gut microbiomes. Nat Ecol Evol 2023; 7:698-706. [PMID: 36973353 PMCID: PMC10172112 DOI: 10.1038/s41559-023-02013-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/14/2023] [Indexed: 03/29/2023]
Abstract
Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways. A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. Here, we investigated if microplastics are associated with changes in proventricular and cloacal microbiomes in two seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters. The amount of microplastics in the gut was significantly correlated with gut microbial diversity and composition: microplastics were associated with decreases in commensal microbiota and increases in (zoonotic) pathogens and antibiotic-resistant and plastic-degrading microbes. These results illustrate that environmentally relevant microplastic concentrations and mixtures are associated with changes in gut microbiomes in wild seabirds.
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Affiliation(s)
- Gloria Fackelmann
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany.
| | - Christopher K Pham
- Institute of Marine Sciences - Okeanos, University of the Azores, Horta, Portugal
| | - Yasmina Rodríguez
- Institute of Marine Sciences - Okeanos, University of the Azores, Horta, Portugal
| | - Mark L Mallory
- Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Jennifer F Provencher
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Julia E Baak
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany.
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13
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Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities. mSystems 2023; 8:e0070122. [PMID: 36622155 PMCID: PMC9948695 DOI: 10.1128/msystems.00701-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.
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14
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Gao L, Zhang Z, Xing Z, Li Q, Kong N, Wang L, Song L. The variation of intestinal autochthonous bacteria in cultured tiger pufferfish Takifugu rubripes. Front Cell Infect Microbiol 2022; 12:1062512. [PMID: 36583108 PMCID: PMC9792791 DOI: 10.3389/fcimb.2022.1062512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Intestinal autochthonous bacteria play important roles in the maintenance of the physiological homeostasis of animals, especially contributing to the host immune system. In the present study, the variation of autochthonous bacterial community in the intestinal tract of 2-7 months-old tiger pufferfish Takifugu rubripes and bacterial communities in the seawater of recirculating aquaculture system (RAS) and the following offshore sea cage aquaculture system (OSCS) were analyzed during the aquaculture period from May to October 2021. Proteobacteria was found to be the most dominant phyla in both intestinal and seawater bacterial communities, which accounted for 68.82% and 65.65% of the total bacterial abundance, respectively. Arcobacter was the most core bacterial taxon in the intestinal bacterial community, with the most dominant abundance (42.89%) at the genus level and dominant positions in co-occurrence relationships with other bacterial taxa (node-betweenness value of 150). Enterococcaceae was specifically enriched in the intestinal bacterial community of pufferfishes from RAS, while Vibrionaceae was enriched in the intestinal bacterial community from OSCS. The F-values of beta diversity analysis between intestinal and seawater bacterial communities generally increased from May (6.69) to October (32.32), indicating the increasing differences between the intestinal and seawater bacterial communities along with the aquaculture process. Four bacterial taxa of Weissella sp., Akkermansia muciniphila, Dietzia sp. and Psychrobacter pacificensis had significant correlations with immune response parameters, and they were suggested to be the indicators for immune status and pathological process of pufferfish. The knowledge about the specific core bacteria, potentially pathogenic bacteria and the change of bacterial community in the intestinal tract of cultured pufferfish is of great scientific significance and will contribute to the understanding of intestinal bacterial homeostasis and biosecurity practice in pufferfish aquaculture.
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Affiliation(s)
- Lei Gao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Ziyang Zhang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Zhen Xing
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Qingsong Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Ning Kong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China,Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China,Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,*Correspondence: Linsheng Song,
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15
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Hofer U. Leaving your polar bear host behind. Nat Rev Microbiol 2021; 19:344. [PMID: 33883722 DOI: 10.1038/s41579-021-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Jarvis KG, Hsu CK, Pettengill JB, Ihrie J, Karathia H, Hasan NA, Grim CJ. Microbiome Population Dynamics of Cold-Smoked Sockeye Salmon during Refrigerated Storage and after Culture Enrichment. J Food Prot 2021; 85:238-253. [PMID: 34614175 DOI: 10.4315/jfp-21-228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/05/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food. HIGHLIGHTS
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Affiliation(s)
- Karen G Jarvis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
| | - Chiun-Kang Hsu
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20742
| | - John Ihrie
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20742
| | - Hiren Karathia
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
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