{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T12:45:06Z","timestamp":1763729106487,"version":"3.45.0"},"reference-count":113,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T00:00:00Z","timestamp":1738800000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T00:00:00Z","timestamp":1738800000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Rio Grande do Sul - FAPERGS and Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico \u2013 CNPq."}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s11030-025-11116-7","type":"journal-article","created":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T12:52:12Z","timestamp":1738846332000},"page":"5995-6013","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Metagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese"],"prefix":"10.1007","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7256-265X","authenticated-orcid":false,"given":"Wemerson","family":"de Castro Oliveira","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7334-4707","authenticated-orcid":false,"given":"Pedro Henrique","family":"Marques","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3730-2515","authenticated-orcid":false,"given":"Magnolia Martins","family":"Erhardt","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8813-8850","authenticated-orcid":false,"given":"Andrei Giacchetto","family":"Felice","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9660-0816","authenticated-orcid":false,"given":"Caio Luigi Antunes Moura","family":"Trist\u00e3o","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1067-1882","authenticated-orcid":false,"given":"Flavia Figueira","family":"Aburjaile","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6767-6596","authenticated-orcid":false,"given":"Maria Beatriz Prior Pinto","family":"Oliveira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6610-5567","authenticated-orcid":false,"given":"Neila Silvia Pereira","family":"dos Santos Richards","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,2,6]]},"reference":[{"key":"11116_CR1","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1016\/j.ijfoodmicro.2009.10.014","volume":"139","author":"RV Tauxe","year":"2010","unstructured":"Tauxe RV, Doyle MP, Kuchenm\u00fcller T et al (2010) Evolving public health approaches to the global challenge of foodborne infections. Int J Food Microbiol 139:S16\u2013S28. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2009.10.014","journal-title":"Int J Food Microbiol"},{"key":"11116_CR2","unstructured":"Machado TF (2013) Pat\u00f3genos emergentes em alimentos. Embrapa Agroind\u00fastria Tropical 19"},{"key":"11116_CR3","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.3390\/microorganisms8091405","volume":"8","author":"MT Rahman","year":"2020","unstructured":"Rahman MT, Sobur MA, Islam MS et al (2020) Zoonotic diseases: etiology, impact, and control. Microorganisms 8:1405. https:\/\/doi.org\/10.3390\/microorganisms8091405","journal-title":"Microorganisms"},{"key":"11116_CR4","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1007\/s42770-020-00416-9","volume":"52","author":"AC Camargo","year":"2021","unstructured":"Camargo AC, de Ara\u00fajo JPA, Fusieger A et al (2021) Microbiological quality and safety of Brazilian artisanal cheeses. Braz J Microbiol 52:393\u2013409. https:\/\/doi.org\/10.1007\/s42770-020-00416-9","journal-title":"Braz J Microbiol"},{"key":"11116_CR5","doi-asserted-by":"publisher","first-page":"105612","DOI":"10.1016\/j.idairyj.2023.105612","volume":"140","author":"R-O del Carmen","year":"2023","unstructured":"del Carmen R-O, Campos-M\u00fazquiz LG, Charles-Rodriguez AV et al (2023) Biological control of pathogens in artisanal cheeses. Int Dairy J 140:105612","journal-title":"Int Dairy J"},{"key":"11116_CR6","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.666922","author":"APA Pineda","year":"2021","unstructured":"Pineda APA, Campos GZ, Pimentel-Filho NJ et al (2021) Brazilian artisanal cheeses: diversity, microbiological safety, and challenges for the sector. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2021.666922","journal-title":"Front Microbiol"},{"key":"11116_CR7","doi-asserted-by":"publisher","first-page":"111265","DOI":"10.1016\/j.foodres.2022.111265","volume":"157","author":"CI Kothe","year":"2022","unstructured":"Kothe CI, Mohellibi N, Renault P (2022) Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics. Food Res Int 157:111265. https:\/\/doi.org\/10.1016\/j.foodres.2022.111265","journal-title":"Food Res Int"},{"key":"11116_CR8","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.ijfoodmicro.2014.02.019","volume":"177","author":"M-C Montel","year":"2014","unstructured":"Montel M-C, Buchin S, Mallet A et al (2014) Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol 177:136\u2013154. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2014.02.019","journal-title":"Int J Food Microbiol"},{"key":"11116_CR9","doi-asserted-by":"publisher","first-page":"101785","DOI":"10.1016\/j.cimid.2022.101785","volume":"84","author":"BB Arag\u00e3o","year":"2022","unstructured":"Arag\u00e3o BB, Trajano SC, de Oliveira RP et al (2022) Occurrence of emerging multiresistant pathogens in the production chain of artisanal goat coalho cheese in Brazil. Comp Immunol Microbiol Infect Dis 84:101785. https:\/\/doi.org\/10.1016\/j.cimid.2022.101785","journal-title":"Comp Immunol Microbiol Infect Dis"},{"key":"11116_CR10","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/s43016-020-0129-3","volume":"1","author":"AM Walsh","year":"2020","unstructured":"Walsh AM, Macori G, Kilcawley KN, Cotter PD (2020) Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nat Food 1:500\u2013510. https:\/\/doi.org\/10.1038\/s43016-020-0129-3","journal-title":"Nat Food"},{"key":"11116_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41572-018-0005-8","volume":"4","author":"C Baker-Austin","year":"2018","unstructured":"Baker-Austin C, Oliver JD, Alam M et al (2018) Vibrio spp. infections. Nat Rev Dis Primer 4:1\u201319. https:\/\/doi.org\/10.1038\/s41572-018-0005-8","journal-title":"Nat Rev Dis Primer"},{"key":"11116_CR12","doi-asserted-by":"publisher","first-page":"129","DOI":"10.3390\/microorganisms8010129","volume":"8","author":"A Fern\u00e1ndez-Bravo","year":"2020","unstructured":"Fern\u00e1ndez-Bravo A, Figueras MJ (2020) An update on the genus aeromonas: taxonomy, epidemiology, and pathogenicity. Microorganisms 8:129","journal-title":"Microorganisms"},{"key":"11116_CR13","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.1016\/S0140-6736(17)30559-7","volume":"390","author":"JD Clemens","year":"2017","unstructured":"Clemens JD, Nair GB, Ahmed T et al (2017) Cholera. Lancet Lond Engl 390:1539\u20131549. https:\/\/doi.org\/10.1016\/S0140-6736(17)30559-7","journal-title":"Lancet Lond Engl"},{"key":"11116_CR14","doi-asserted-by":"publisher","DOI":"10.12788\/cutis.0183","author":"KM Coerdt","year":"2021","unstructured":"Coerdt KM, Khachemoune A (2021) Vibrio vulnificus: review of mild to life-threatening skin infections. Cutis. https:\/\/doi.org\/10.12788\/cutis.0183","journal-title":"Cutis"},{"key":"11116_CR15","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1111\/jam.13246","volume":"121","author":"SM Raszl","year":"2016","unstructured":"Raszl SM, Froelich BA, Vieira CRW et al (2016) Vibrio parahaemolyticus and Vibrio vulnificus in South America: water, seafood and human infections. J Appl Microbiol 121:1201\u20131222. https:\/\/doi.org\/10.1111\/jam.13246","journal-title":"J Appl Microbiol"},{"key":"11116_CR16","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.tim.2016.09.008","volume":"25","author":"C Baker-Austin","year":"2017","unstructured":"Baker-Austin C, Trinanes J, Gonzalez-Escalona N, Martinez-Urtaza J (2017) Non-cholera vibrios: the microbial barometer of climate change. Trends Microbiol 25:76\u201384","journal-title":"Trends Microbiol"},{"key":"11116_CR17","doi-asserted-by":"publisher","first-page":"e005111","DOI":"10.1099\/jmmcr.0.005111","volume":"4","author":"M Ballal","year":"2017","unstructured":"Ballal M, Shetty V, Bangera SR et al (2017) Vibrio furnissii, an emerging pathogen causing acute gastroenteritis: a case report. JMM Case Rep 4:e005111. https:\/\/doi.org\/10.1099\/jmmcr.0.005111","journal-title":"JMM Case Rep"},{"key":"11116_CR18","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00091","author":"T Ramamurthy","year":"2014","unstructured":"Ramamurthy T, Chowdhury G, Pazhani G, Shinoda S (2014) Vibrio fluvialis: an emerging human pathogen. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2014.00091","journal-title":"Front Microbiol"},{"key":"11116_CR19","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.micpath.2019.02.036","volume":"130","author":"RBG Pessoa","year":"2019","unstructured":"Pessoa RBG, de Oliveira WF, Marques DSC et al (2019) The genus aeromonas: a general approach. Microb Pathog 130:81\u201394. https:\/\/doi.org\/10.1016\/j.micpath.2019.02.036","journal-title":"Microb Pathog"},{"key":"11116_CR20","doi-asserted-by":"publisher","first-page":"3893","DOI":"10.1038\/s41598-023-28247-2","volume":"13","author":"EJ Archer","year":"2023","unstructured":"Archer EJ, Baker-Austin C, Osborn TJ et al (2023) Climate warming and increasing Vibrio vulnificus infections in North America. Sci Rep 13:3893. https:\/\/doi.org\/10.1038\/s41598-023-28247-2","journal-title":"Sci Rep"},{"key":"11116_CR21","doi-asserted-by":"publisher","first-page":"2002041","DOI":"10.2807\/1560-7917.ES.2021.26.41.2002041","volume":"26","author":"TT Brehm","year":"2021","unstructured":"Brehm TT, Berneking L, Martins MS et al (2021) Heatwave-associated Vibrio infections in Germany, 2018 and 2019. Eurosurveillance 26:2002041. https:\/\/doi.org\/10.2807\/1560-7917.ES.2021.26.41.2002041","journal-title":"Eurosurveillance"},{"key":"11116_CR22","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.3201\/eid2806.212451","volume":"28","author":"N Benamrouche","year":"2022","unstructured":"Benamrouche N, Belkader C, Njamkepo E et al (2022) Outbreak of imported seventh pandemic Vibrio cholerae O1 El tor, Algeria, 2018. Emerg Infect Dis 28:1241","journal-title":"Emerg Infect Dis"},{"key":"11116_CR23","first-page":"224","volume":"16","author":"T Tsheten","year":"2016","unstructured":"Tsheten T, Tshering D, Gyem K et al (2016) An Outbreak of aeromonas hydrophila food poisoning in Deptsang Village, Samdrup Jongkhar, Bhutan, 2016. J Res Health Sci 16:224\u2013227","journal-title":"J Res Health Sci"},{"key":"11116_CR24","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2023.1235837","author":"A Bogomazova","year":"2023","unstructured":"Bogomazova A, Krylova E, Soltynskaya I et al (2023) In silico analysis to develop PCR assays for identification of bacterial pathogens in animals: what can we improve? Front Vet Sci. https:\/\/doi.org\/10.3389\/fvets.2023.1235837","journal-title":"Front Vet Sci"},{"key":"11116_CR25","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1128\/CMR.17.4.840-862.2004","volume":"17","author":"JE Clarridge","year":"2004","unstructured":"Clarridge JE (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840\u2013862. https:\/\/doi.org\/10.1128\/CMR.17.4.840-862.2004","journal-title":"Clin Microbiol Rev"},{"key":"11116_CR26","doi-asserted-by":"publisher","first-page":"2081","DOI":"10.1093\/bioinformatics\/btab059","volume":"37","author":"B Haubold","year":"2021","unstructured":"Haubold B, Kl\u00f6tzl F, Hellberg L et al (2021) Fur: find unique genomic regions for diagnostic PCR. Bioinformatics 37:2081\u20132087. https:\/\/doi.org\/10.1093\/bioinformatics\/btab059","journal-title":"Bioinformatics"},{"key":"11116_CR27","doi-asserted-by":"publisher","first-page":"8183","DOI":"10.1128\/AEM.02601-15","volume":"81","author":"SR Leonard","year":"2015","unstructured":"Leonard SR, Mammel MK, Lacher DW, Elkins CA (2015) Application of metagenomic sequencing to food safety: detection of shiga toxin-producing Escherichia coli on fresh bagged spinach. Appl Environ Microbiol 81:8183\u20138191. https:\/\/doi.org\/10.1128\/AEM.02601-15","journal-title":"Appl Environ Microbiol"},{"key":"11116_CR28","doi-asserted-by":"publisher","first-page":"e263363","DOI":"10.1590\/1519-6984.263363","volume":"84","author":"BT Mohammed","year":"2022","unstructured":"Mohammed BT (2022) Identification and bioinformatic analysis of invA gene of Salmonella in free range chicken. Braz J Biol 84:e263363. https:\/\/doi.org\/10.1590\/1519-6984.263363","journal-title":"Braz J Biol"},{"key":"11116_CR29","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nmeth.2066","volume":"9","author":"N Segata","year":"2012","unstructured":"Segata N, Waldron L, Ballarini A et al (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9:811\u2013814. https:\/\/doi.org\/10.1038\/nmeth.2066","journal-title":"Nat Methods"},{"key":"11116_CR30","doi-asserted-by":"publisher","first-page":"41","DOI":"10.3390\/fermentation9010041","volume":"9","author":"MM Erhardt","year":"2023","unstructured":"Erhardt MM, de Castro Oliveira W, Fr\u00f6der H et al (2023) Lactic bacteria in artisanal cheese: characterization through metagenomics. Fermentation 9:41. https:\/\/doi.org\/10.3390\/fermentation9010041","journal-title":"Fermentation"},{"key":"11116_CR31","doi-asserted-by":"publisher","first-page":"3705","DOI":"10.1111\/1462-2920.16022","volume":"24","author":"I Keenum","year":"2022","unstructured":"Keenum I, Wind L, Ray P et al (2022) Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis. Environ Microbiol 24:3705\u20133721. https:\/\/doi.org\/10.1111\/1462-2920.16022","journal-title":"Environ Microbiol"},{"key":"11116_CR32","doi-asserted-by":"publisher","first-page":"108559","DOI":"10.1016\/j.foodcont.2021.108559","volume":"132","author":"SH Moon","year":"2022","unstructured":"Moon SH, Udaondo Z, Abram KZ et al (2022) Isolation of AmpC- and extended spectrum \u03b2-lactamase-producing enterobacterales from fresh vegetables in the United States. Food Control 132:108559. https:\/\/doi.org\/10.1016\/j.foodcont.2021.108559","journal-title":"Food Control"},{"key":"11116_CR33","doi-asserted-by":"publisher","first-page":"e09089","DOI":"10.1016\/j.heliyon.2022.e09089","volume":"8","author":"O Onalenna","year":"2022","unstructured":"Onalenna O, Rahube TO (2022) Assessing bacterial diversity and antibiotic resistance dynamics in wastewater effluent-irrigated soil and vegetables in a microcosm setting. Heliyon 8:e09089. https:\/\/doi.org\/10.1016\/j.heliyon.2022.e09089","journal-title":"Heliyon"},{"key":"11116_CR34","doi-asserted-by":"publisher","first-page":"397","DOI":"10.3390\/fermentation10080397","volume":"10","author":"MAP Pedroso","year":"2024","unstructured":"Pedroso MAP, de Castro Oliveira W, Felice AG et al (2024) Pathogenic and harmful bacteria in dairy technology: genomic characterization and its correlation with physicochemical parameters of sheep\u2019s cheese sold in Southern Brazil. Fermentation 10:397. https:\/\/doi.org\/10.3390\/fermentation10080397","journal-title":"Fermentation"},{"key":"11116_CR35","doi-asserted-by":"publisher","first-page":"96","DOI":"10.3168\/jds.2022-22449","volume":"106","author":"G Secchi","year":"2023","unstructured":"Secchi G, Amalfitano N, Carafa I et al (2023) Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing. J Dairy Sci 106:96\u2013116. https:\/\/doi.org\/10.3168\/jds.2022-22449","journal-title":"J Dairy Sci"},{"key":"11116_CR36","doi-asserted-by":"publisher","first-page":"112202","DOI":"10.1016\/j.foodres.2022.112202","volume":"162","author":"V Valentino","year":"2022","unstructured":"Valentino V, Sequino G, Cobo-D\u00edaz JF et al (2022) Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities. Food Res Int 162:112202. https:\/\/doi.org\/10.1016\/j.foodres.2022.112202","journal-title":"Food Res Int"},{"key":"11116_CR37","doi-asserted-by":"publisher","first-page":"111190","DOI":"10.1016\/j.foodres.2022.111190","volume":"157","author":"M Yasir","year":"2022","unstructured":"Yasir M, Al-Zahrani IA, Bibi F et al (2022) New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria. Food Res Int 157:111190. https:\/\/doi.org\/10.1016\/j.foodres.2022.111190","journal-title":"Food Res Int"},{"key":"11116_CR38","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.824644","author":"Y Yu","year":"2022","unstructured":"Yu Y, Li L, Xu Y et al (2022) Metagenomics reveals the microbial community responsible for producing biogenic amines during mustard [Brassica juncea (L.)] fermentation. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2022.824644","journal-title":"Front Microbiol"},{"key":"11116_CR39","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1111\/1471-0307.12944","volume":"76","author":"MNZ Yurt","year":"2023","unstructured":"Yurt MNZ, Ersoy Omeroglu E, Tasbasi BB et al (2023) Bacterial and fungal microbiota of mould-ripened cheese produced in Konya. Int J Dairy Technol 76:627\u2013637. https:\/\/doi.org\/10.1111\/1471-0307.12944","journal-title":"Int J Dairy Technol"},{"key":"11116_CR40","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1111\/j.1574-6976.2008.00136.x","volume":"33","author":"M Juhas","year":"2009","unstructured":"Juhas M, van der Meer JR, Gaillard M et al (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33:376\u2013393. https:\/\/doi.org\/10.1111\/j.1574-6976.2008.00136.x","journal-title":"FEMS Microbiol Rev"},{"key":"11116_CR41","doi-asserted-by":"publisher","first-page":"e162","DOI":"10.1016\/S2666-5247(21)00354-2","volume":"3","author":"R Nepal","year":"2022","unstructured":"Nepal R, Houtak G, Wormald P-J et al (2022) Prophage: a crucial catalyst in infectious disease modulation. Lancet Microbe 3:e162\u2013e163. https:\/\/doi.org\/10.1016\/S2666-5247(21)00354-2","journal-title":"Lancet Microbe"},{"key":"11116_CR42","doi-asserted-by":"publisher","first-page":"435","DOI":"10.3389\/fmicb.2014.00435","volume":"5","author":"TM Lux","year":"2014","unstructured":"Lux TM, Lee R, Love J (2014) Genome-wide phylogenetic analysis of the pathogenic potential of Vibrio furnissii. Front Microbiol 5:435. https:\/\/doi.org\/10.3389\/fmicb.2014.00435","journal-title":"Front Microbiol"},{"key":"11116_CR43","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/s43141-022-00411-7","volume":"20","author":"MR Lemes","year":"2022","unstructured":"Lemes MR, Rodrigues TCV, Jaiswal AK et al (2022) In silico designing of a recombinant multi-epitope antigen for leprosy diagnosis. J Genet Eng Biotechnol 20:128. https:\/\/doi.org\/10.1186\/s43141-022-00411-7","journal-title":"J Genet Eng Biotechnol"},{"key":"11116_CR44","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1002\/ddr.20413","volume":"72","author":"D Barh","year":"2011","unstructured":"Barh D, Tiwari S, Jain N et al (2011) In silico subtractive genomics for target identification in human bacterial pathogens. Drug Dev Res 72:162\u2013177. https:\/\/doi.org\/10.1002\/ddr.20413","journal-title":"Drug Dev Res"},{"key":"11116_CR45","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/978-1-4939-1115-8_3","volume-title":"Immunoinformatics","author":"N Tomar","year":"2014","unstructured":"Tomar N, De RK (2014) Immunoinformatics: a brief review. In: De RK, Tomar N (eds) Immunoinformatics. Springer, New York, NY, pp 23\u201355"},{"key":"11116_CR46","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","volume":"6","author":"JG Caporaso","year":"2012","unstructured":"Caporaso JG, Lauber CL, Walters WA et al (2012) Ultra-high-throughput microbial community analysis on the illumina HiSeq and MiSeq platforms. ISME J 6:1621\u20131624. https:\/\/doi.org\/10.1038\/ismej.2012.8","journal-title":"ISME J"},{"key":"11116_CR47","doi-asserted-by":"publisher","first-page":"e7401","DOI":"10.1371\/journal.pone.0007401","volume":"4","author":"Y Wang","year":"2009","unstructured":"Wang Y, Qian P-Y (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS ONE 4:e7401. https:\/\/doi.org\/10.1371\/journal.pone.0007401","journal-title":"PLoS ONE"},{"key":"11116_CR48","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. https:\/\/doi.org\/10.1186\/s13059-019-1832-y","journal-title":"Genome Biol"},{"key":"11116_CR49","doi-asserted-by":"publisher","first-page":"W20","DOI":"10.1093\/nar\/gkh435","volume":"32","author":"S McGinnis","year":"2004","unstructured":"McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32:W20\u2013W25. https:\/\/doi.org\/10.1093\/nar\/gkh435","journal-title":"Nucleic Acids Res"},{"key":"11116_CR50","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1002\/pmic.200800195","volume":"9","author":"A Barinov","year":"2009","unstructured":"Barinov A, Loux V, Hammani A et al (2009) Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other gram-positive bacteria. Proteomics 9:61\u201373. https:\/\/doi.org\/10.1002\/pmic.200800195","journal-title":"Proteomics"},{"key":"11116_CR51","doi-asserted-by":"publisher","first-page":"W671","DOI":"10.1093\/nar\/gkab279","volume":"49","author":"E Ong","year":"2021","unstructured":"Ong E, Cooke MF, Huffman A et al (2021) Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res 49:W671\u2013W678. https:\/\/doi.org\/10.1093\/nar\/gkab279","journal-title":"Nucleic Acids Res"},{"key":"11116_CR52","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-8-4","volume":"8","author":"IA Doytchinova","year":"2007","unstructured":"Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform 8:4. https:\/\/doi.org\/10.1186\/1471-2105-8-4","journal-title":"BMC Bioinform"},{"key":"11116_CR53","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1002\/prot.21078","volume":"65","author":"S Saha","year":"2006","unstructured":"Saha S, Raghava GPS (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins Struct Funct Bioinforma 65:40\u201348. https:\/\/doi.org\/10.1002\/prot.21078","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"11116_CR54","doi-asserted-by":"publisher","first-page":"W502","DOI":"10.1093\/nar\/gkz452","volume":"47","author":"SK Dhanda","year":"2019","unstructured":"Dhanda SK, Mahajan S, Paul S et al (2019) IEDB-AR: immune epitope database\u2014analysis resource in 2019. Nucleic Acids Res 47:W502\u2013W506. https:\/\/doi.org\/10.1093\/nar\/gkz452","journal-title":"Nucleic Acids Res"},{"key":"11116_CR55","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","volume":"19","author":"M Mirdita","year":"2022","unstructured":"Mirdita M, Sch\u00fctze K, Moriwaki Y et al (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679\u2013682. https:\/\/doi.org\/10.1038\/s41592-022-01488-1","journal-title":"Nat Methods"},{"key":"11116_CR56","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1007\/BF00228148","volume":"8","author":"RA Laskowski","year":"1996","unstructured":"Laskowski RA, Rullmann JAC, MacArthur MW et al (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477\u2013486. https:\/\/doi.org\/10.1007\/BF00228148","journal-title":"J Biomol NMR"},{"key":"11116_CR57","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1002\/pro.5560020916","volume":"2","author":"C Colovos","year":"1993","unstructured":"Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci Publ Protein Soc 2:1511\u20131519. https:\/\/doi.org\/10.1002\/pro.5560020916","journal-title":"Protein Sci Publ Protein Soc"},{"key":"11116_CR58","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1016\/s0076-6879(97)77022-8","volume":"277","author":"D Eisenberg","year":"1997","unstructured":"Eisenberg D, L\u00fcthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396\u2013404. https:\/\/doi.org\/10.1016\/s0076-6879(97)77022-8","journal-title":"Methods Enzymol"},{"key":"11116_CR59","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1186\/1471-2105-9-514","volume":"9","author":"J Ponomarenko","year":"2008","unstructured":"Ponomarenko J, Bui H-H, Li W et al (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform 9:514. https:\/\/doi.org\/10.1186\/1471-2105-9-514","journal-title":"BMC Bioinform"},{"key":"11116_CR60","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I et al (2021) eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38:5825\u20135829. https:\/\/doi.org\/10.1093\/molbev\/msab293","journal-title":"Mol Biol Evol"},{"key":"11116_CR61","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","volume":"44","author":"D Arndt","year":"2016","unstructured":"Arndt D, Grant JR, Marcu A et al (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16\u2013W21. https:\/\/doi.org\/10.1093\/nar\/gkw387","journal-title":"Nucleic Acids Res"},{"key":"11116_CR62","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.jbiotec.2015.09.008","volume":"232","author":"SC Soares","year":"2016","unstructured":"Soares SC, Geyik H, Ramos RTJ et al (2016) GIPSy: Genomic island prediction software. J Biotechnol 232:2\u201311. https:\/\/doi.org\/10.1016\/j.jbiotec.2015.09.008","journal-title":"J Biotechnol"},{"key":"11116_CR63","doi-asserted-by":"publisher","first-page":"4394","DOI":"10.1111\/1462-2920.15128","volume":"22","author":"J Hoff","year":"2020","unstructured":"Hoff J, Daniel B, Stukenberg D et al (2020) Vibrio natriegens: an ultrafast-growing marine bacterium as emerging synthetic biology chassis. Environ Microbiol 22:4394\u20134408. https:\/\/doi.org\/10.1111\/1462-2920.15128","journal-title":"Environ Microbiol"},{"key":"11116_CR64","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","volume":"12","author":"N-F Alikhan","year":"2011","unstructured":"Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. https:\/\/doi.org\/10.1186\/1471-2164-12-402","journal-title":"BMC Genomics"},{"key":"11116_CR65","doi-asserted-by":"publisher","first-page":"4118","DOI":"10.1093\/bioinformatics\/bty496","volume":"34","author":"B Taboada","year":"2018","unstructured":"Taboada B, Estrada K, Ciria R, Merino E (2018) Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 34:4118\u20134120. https:\/\/doi.org\/10.1093\/bioinformatics\/bty496","journal-title":"Bioinformatics"},{"key":"11116_CR66","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00230","author":"DF Nieuwenhuijse","year":"2017","unstructured":"Nieuwenhuijse DF, Koopmans MPG (2017) Metagenomic sequencing for surveillance of food- and waterborne viral diseases. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2017.00230","journal-title":"Front Microbiol"},{"key":"11116_CR67","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1186\/1471-2180-13-274","volume":"13","author":"CR Jackson","year":"2013","unstructured":"Jackson CR, Randolph KC, Osborn SL, Tyler HL (2013) Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol 13:274. https:\/\/doi.org\/10.1186\/1471-2180-13-274","journal-title":"BMC Microbiol"},{"key":"11116_CR68","doi-asserted-by":"publisher","first-page":"e59310","DOI":"10.1371\/journal.pone.0059310","volume":"8","author":"JW Leff","year":"2013","unstructured":"Leff JW, Fierer N (2013) Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS ONE 8:e59310. https:\/\/doi.org\/10.1371\/journal.pone.0059310","journal-title":"PLoS ONE"},{"key":"11116_CR69","doi-asserted-by":"publisher","first-page":"2264","DOI":"10.1128\/AEM.02157-10","volume":"77","author":"JY Jung","year":"2011","unstructured":"Jung JY, Lee SH, Kim JM et al (2011) Metagenomic analysis of Kimchi, a traditional Korean fermented food. Appl Environ Microbiol 77:2264\u20132274. https:\/\/doi.org\/10.1128\/AEM.02157-10","journal-title":"Appl Environ Microbiol"},{"key":"11116_CR70","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.868383","author":"P Kharnaior","year":"2022","unstructured":"Kharnaior P, Tamang JP (2022) Metagenomic-metabolomic mining of Kinema, a naturally fermented soybean food of the Eastern Himalayas. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2022.868383","journal-title":"Front Microbiol"},{"key":"11116_CR71","doi-asserted-by":"publisher","first-page":"109450","DOI":"10.1016\/j.lwt.2020.109450","volume":"129","author":"M Xie","year":"2020","unstructured":"Xie M, An F, Zhao Y et al (2020) Metagenomic analysis of bacterial community structure and functions during the fermentation of da-jiang, a Chinese traditional fermented food. LWT 129:109450. https:\/\/doi.org\/10.1016\/j.lwt.2020.109450","journal-title":"LWT"},{"key":"11116_CR72","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01805","author":"J Gr\u00fctzke","year":"2019","unstructured":"Gr\u00fctzke J, Malorny B, Hammerl JA et al (2019) Fishing in the soup\u2014pathogen detection in food safety using metabarcoding and metagenomic sequencing. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2019.01805","journal-title":"Front Microbiol"},{"key":"11116_CR73","doi-asserted-by":"publisher","first-page":"2480","DOI":"10.3390\/foods12132480","volume":"12","author":"A Bester","year":"2023","unstructured":"Bester A, O\u2019Brien M, Cotter PD et al (2023) Shotgun metagenomic sequencing revealed the prebiotic potential of a fruit juice drink with fermentable fibres in healthy humans. Foods 12:2480. https:\/\/doi.org\/10.3390\/foods12132480","journal-title":"Foods"},{"key":"11116_CR74","doi-asserted-by":"publisher","first-page":"213","DOI":"10.21548\/42-2-4724","volume":"42","author":"S Ghosh","year":"2021","unstructured":"Ghosh S, Divol B, Setati ME (2021) A shotgun metagenomic sequencing exploration of cabernet sauvignon grape must reveals yeast hydrolytic enzymes. South Afr J Enol Vitic. 42:213\u2013223. https:\/\/doi.org\/10.21548\/42-2-4724","journal-title":"South Afr J Enol Vitic."},{"key":"11116_CR75","doi-asserted-by":"publisher","first-page":"249","DOI":"10.3390\/foods11030249","volume":"11","author":"A De Cesare","year":"2022","unstructured":"De Cesare A, Oliveri C, Lucchi A et al (2022) Pilot study on poultry meat from antibiotic free and conventional farms: can metagenomics detect any difference? Foods 11:249. https:\/\/doi.org\/10.3390\/foods11030249","journal-title":"Foods"},{"key":"11116_CR76","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.ijfoodmicro.2012.04.016","volume":"157","author":"TT Nieminen","year":"2012","unstructured":"Nieminen TT, Koskinen K, Laine P et al (2012) Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics. Int J Food Microbiol 157:142\u2013149. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2012.04.016","journal-title":"Int J Food Microbiol"},{"key":"11116_CR77","doi-asserted-by":"publisher","first-page":"100918","DOI":"10.1016\/j.cofs.2022.100918","volume":"48","author":"D Van der Veken","year":"2022","unstructured":"Van der Veken D, Leroy F (2022) Prospects for the applicability of coagulase-negative cocci in fermented-meat products using omics approaches. Curr Opin Food Sci 48:100918. https:\/\/doi.org\/10.1016\/j.cofs.2022.100918","journal-title":"Curr Opin Food Sci"},{"key":"11116_CR78","doi-asserted-by":"publisher","first-page":"2052","DOI":"10.3390\/microorganisms11082052","volume":"11","author":"HM Mohamed","year":"2023","unstructured":"Mohamed HM, Barzideh Z, Siddiqi M, LaPointe G (2023) Taxonomy, sequence variance and functional profiling of the microbial community of long-ripened cheddar cheese using shotgun metagenomics. Microorganisms 11:2052. https:\/\/doi.org\/10.3390\/microorganisms11082052","journal-title":"Microorganisms"},{"key":"11116_CR79","doi-asserted-by":"publisher","first-page":"e13334","DOI":"10.1016\/j.heliyon.2023.e13334","volume":"9","author":"M R\u00fcstemo\u011flu","year":"2023","unstructured":"R\u00fcstemo\u011flu M, Erkan ME, Cengiz G, Hajyzadeh M (2023) Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential. Heliyon 9:e13334. https:\/\/doi.org\/10.1016\/j.heliyon.2023.e13334","journal-title":"Heliyon"},{"key":"11116_CR80","doi-asserted-by":"publisher","first-page":"e23220530","DOI":"10.1590\/1678-4324-2023220530","volume":"66","author":"JA Str\u00f6her","year":"2023","unstructured":"Str\u00f6her JA, Sant\u2019Anna V, de Castro Oliveira W, Padilha RL (2023) The effect of temperature on physicochemical and microbiological aspects of serrano artisanal cheese ripening. Braz Arch Biol Technol 66:e23220530. https:\/\/doi.org\/10.1590\/1678-4324-2023220530","journal-title":"Braz Arch Biol Technol"},{"key":"11116_CR81","doi-asserted-by":"publisher","first-page":"990","DOI":"10.3390\/foods12050990","volume":"12","author":"MC Coelho","year":"2023","unstructured":"Coelho MC, Malcata FX, Silva CCG (2023) Distinct bacterial communities in S\u00e3o Jorge cheese with protected designation of origin (PDO). Foods 12:990. https:\/\/doi.org\/10.3390\/foods12050990","journal-title":"Foods"},{"key":"11116_CR82","doi-asserted-by":"publisher","first-page":"1735","DOI":"10.3390\/microorganisms11071735","volume":"11","author":"K Korena","year":"2023","unstructured":"Korena K, Krzyzankova M, Florianova M et al (2023) Microbial succession in the cheese ripening process\u2014competition of the starter cultures and the microbiota of the cheese plant environment. Microorganisms 11:1735. https:\/\/doi.org\/10.3390\/microorganisms11071735","journal-title":"Microorganisms"},{"key":"11116_CR83","doi-asserted-by":"publisher","first-page":"001","DOI":"10.4103\/0974-2727.176234","volume":"8","author":"P Batra","year":"2016","unstructured":"Batra P, Mathur P, Misra MC (2016) Aeromonas spp.: an emerging nosocomial pathogen. J Lab Physicians 8:001\u2013004. https:\/\/doi.org\/10.4103\/0974-2727.176234","journal-title":"J Lab Physicians"},{"key":"11116_CR84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00248-009-9596-7","volume":"59","author":"T Vesth","year":"2010","unstructured":"Vesth T, Wassenaar TM, Hallin PF et al (2010) On the origins of a vibrio species. Microb Ecol 59:1\u201313. https:\/\/doi.org\/10.1007\/s00248-009-9596-7","journal-title":"Microb Ecol"},{"key":"11116_CR85","doi-asserted-by":"publisher","first-page":"103653","DOI":"10.1016\/j.sjbs.2023.103653","volume":"30","author":"HN Altayb","year":"2023","unstructured":"Altayb HN, Badri RM, Chaieb K, Moglad E (2023) Detection and characterization of the most common foodborne pathogens by using multiplex PCR procedure. Saudi J Biol Sci 30:103653. https:\/\/doi.org\/10.1016\/j.sjbs.2023.103653","journal-title":"Saudi J Biol Sci"},{"key":"11116_CR86","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.1099\/ijs.0.016493-0","volume":"60","author":"A Bleicher","year":"2010","unstructured":"Bleicher A, Neuhaus K, Scherer S (2010) Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses. Int J Syst Evol Microbiol 60:1745\u20131749. https:\/\/doi.org\/10.1099\/ijs.0.016493-0","journal-title":"Int J Syst Evol Microbiol"},{"key":"11116_CR87","doi-asserted-by":"publisher","first-page":"6046","DOI":"10.3168\/jds.2014-8225","volume":"97","author":"V Delcenserie","year":"2014","unstructured":"Delcenserie V, Taminiau B, Delhalle L et al (2014) Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis. J Dairy Sci 97:6046\u20136056. https:\/\/doi.org\/10.3168\/jds.2014-8225","journal-title":"J Dairy Sci"},{"key":"11116_CR88","doi-asserted-by":"publisher","first-page":"5717","DOI":"10.1128\/AEM.00918-12","volume":"78","author":"L Quigley","year":"2012","unstructured":"Quigley L, O\u2019Sullivan O, Beresford TP et al (2012) High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol 78:5717\u20135723. https:\/\/doi.org\/10.1128\/AEM.00918-12","journal-title":"Appl Environ Microbiol"},{"key":"11116_CR89","doi-asserted-by":"publisher","first-page":"2377","DOI":"10.3390\/microorganisms9112377","volume":"9","author":"P Papadakis","year":"2021","unstructured":"Papadakis P, Konteles S, Batrinou A et al (2021) Characterization of bacterial microbiota of P.D.O. Feta cheese by 16S metagenomic analysis. Microorganisms 9:2377. https:\/\/doi.org\/10.3390\/microorganisms9112377","journal-title":"Microorganisms"},{"key":"11116_CR90","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1590\/S0102-09352002000300017","volume":"54","author":"CCC Bulh\u00f5es","year":"2002","unstructured":"Bulh\u00f5es CCC, Rossi J\u00fanior OD (2002) Occurrence of the genus Aeromonas in minas frescal cheese. Arq Bras Med Veterin\u00e1ria E Zootec 54:320\u2013324. https:\/\/doi.org\/10.1590\/S0102-09352002000300017","journal-title":"Arq Bras Med Veterin\u00e1ria E Zootec"},{"key":"11116_CR91","first-page":"1","volume":"28","author":"BA Effat","year":"2000","unstructured":"Effat BA, Hosny IM, Dabiza NM (2000) Occurrence of Aeromonas hydrophila and its growth in Egyptian soft cheese. Egypt J Dairy Sci 28:1\u201312","journal-title":"Egypt J Dairy Sci"},{"key":"11116_CR92","doi-asserted-by":"publisher","first-page":"184","DOI":"10.21608\/avmj.1998.183207","volume":"39.2","author":"E El-Prince","year":"1998","unstructured":"El-Prince E (1998) Incidence and characterization of aeromonas species in Domiati and Kareish cheese sold in Assiut province. Assiut Vet Med J 39.2:184\u2013193. https:\/\/doi.org\/10.21608\/avmj.1998.183207","journal-title":"Assiut Vet Med J"},{"key":"11116_CR93","doi-asserted-by":"publisher","first-page":"463","DOI":"10.4315\/0362-028X-62.5.463","volume":"62","author":"DS Melas","year":"1999","unstructured":"Melas DS, Papageorgiou DK, Mantis AI (1999) Enumeration and confirmation of Aeromonas hydrophila, Aeromonas caviae, and Aeromonas sobria Isolated from raw milk and other milk products in Northern Greece. J Food Prot 62:463\u2013466. https:\/\/doi.org\/10.4315\/0362-028X-62.5.463","journal-title":"J Food Prot"},{"key":"11116_CR94","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.idairyj.2016.07.011","volume":"63","author":"ABMB Tahoun","year":"2016","unstructured":"Tahoun ABMB, Ahmed HA, Abou Elez RMM et al (2016) Molecular characterisation, genotyping and survival of Aeromonas hydrophila isolated from milk, dairy products and humans in Egypt. Int Dairy J 63:52\u201358. https:\/\/doi.org\/10.1016\/j.idairyj.2016.07.011","journal-title":"Int Dairy J"},{"key":"11116_CR95","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1017\/S095026889700798X","volume":"119","author":"A Dalsgaard","year":"1997","unstructured":"Dalsgaard A, Glerup P, H\u00f8ybye L-L et al (1997) Vibrio furnissii isolated from humans in Peru: a possible human pathogen? Epidemiol Infect 119:143\u2013149. https:\/\/doi.org\/10.1017\/S095026889700798X","journal-title":"Epidemiol Infect"},{"key":"11116_CR96","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.mimet.2017.10.014","volume":"144","author":"I Takajo","year":"2018","unstructured":"Takajo I, Yamada A, Umeki K et al (2018) Development of a simple and practical method of discrimination between Vibrio furnissii and V. fluvialis based on single-nucleotide polymorphisms of 16S rRNA genes observed in V. furnissii but not in V. fluvialis. J Microbiol Methods 144:22\u201328","journal-title":"J Microbiol Methods"},{"key":"11116_CR97","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1007\/s12199-016-0528-0","volume":"21","author":"K Miyagi","year":"2016","unstructured":"Miyagi K, Hirai I, Sano K (2016) Distribution of Aeromonas species in environmental water used in daily life in Okinawa Prefecture, Japan. Environ Health Prev Med 21:287\u2013294. https:\/\/doi.org\/10.1007\/s12199-016-0528-0","journal-title":"Environ Health Prev Med"},{"key":"11116_CR98","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01635","author":"R Rafique","year":"2016","unstructured":"Rafique R, Rashid M, Monira S et al (2016) Transmission of infectious Vibrio cholerae through drinking water among the household contacts of cholera patients (CHoBI7 trial). Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2016.01635","journal-title":"Front Microbiol"},{"key":"11116_CR99","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/B978-0-323-44585-6.00006-0","volume-title":"Diagnostic pathology of infectious disease (second edition)","author":"N Pecora","year":"2018","unstructured":"Pecora N, Milner DA (2018) 6 - New technologies for the diagnosis of infection. In: Kradin RL (ed) Diagnostic pathology of infectious disease (second edition). Elsevier, Amsterdam, pp 104\u2013117"},{"key":"11116_CR100","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.868890","author":"RBG Pessoa","year":"2022","unstructured":"Pessoa RBG, de Oliveira WF, dos Santos Correia MT et al (2022) Aeromonas and human health disorders: clinical approaches. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2022.868890","journal-title":"Front Microbiol"},{"key":"11116_CR101","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1007\/s10156-010-0050-Z","volume":"16","author":"K Matsumoto","year":"2010","unstructured":"Matsumoto K, Ohshige K, Tomita Y et al (2010) Clinical features of Vibrio vulnificus infections in the coastal areas of the Ariake Sea, Japan. J Infect Chemother 16:272\u2013279. https:\/\/doi.org\/10.1007\/s10156-010-0050-Z","journal-title":"J Infect Chemother"},{"key":"11116_CR102","doi-asserted-by":"publisher","first-page":"163332","DOI":"10.1016\/j.scitotenv.2023.163332","volume":"881","author":"I-AI Ibangha","year":"2023","unstructured":"Ibangha I-AI, Digwo DC, Ozochi CA et al (2023) A meta-analysis on the distribution of pathogenic Vibrio species in water sources and wastewater in Africa. Sci Total Environ 881:163332. https:\/\/doi.org\/10.1016\/j.scitotenv.2023.163332","journal-title":"Sci Total Environ"},{"key":"11116_CR103","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2023.e13323","author":"A Bodaghi","year":"2023","unstructured":"Bodaghi A, Fattahi N, Ramazani A (2023) Biomarkers: promising and valuable tools towards diagnosis, prognosis and treatment of Covid-19 and other diseases. Heliyon. https:\/\/doi.org\/10.1016\/j.heliyon.2023.e13323","journal-title":"Heliyon"},{"key":"11116_CR104","doi-asserted-by":"publisher","first-page":"1964","DOI":"10.1128\/iai.00059-13","volume":"81","author":"RJ Bager","year":"2013","unstructured":"Bager RJ, Nesta B, Pors SE et al (2013) The fimbrial protein FlfA from Gallibacterium anatis is a virulence factor and vaccine candidate. Infect Immun 81:1964\u20131973. https:\/\/doi.org\/10.1128\/iai.00059-13","journal-title":"Infect Immun"},{"key":"11116_CR105","doi-asserted-by":"publisher","first-page":"e679045","DOI":"10.1155\/2012\/679045","volume":"2012","author":"E Casa-Esper\u00f3n","year":"2012","unstructured":"Casa-Esper\u00f3n E (2012) Horizontal transfer and the evolution of host-pathogen interactions. Int J Evol Biol 2012:e679045. https:\/\/doi.org\/10.1155\/2012\/679045","journal-title":"Int J Evol Biol"},{"key":"11116_CR106","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/j.gene.2018.05.084","volume":"670","author":"R Hurtado","year":"2018","unstructured":"Hurtado R, Carhuaricra D, Soares S et al (2018) Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida. Gene 670:193\u2013206. https:\/\/doi.org\/10.1016\/j.gene.2018.05.084","journal-title":"Gene"},{"key":"11116_CR107","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1007\/s13213-019-01539-7","volume":"69","author":"S Nathamuni","year":"2019","unstructured":"Nathamuni S, Jangam AK, Katneni VK et al (2019) Insights on genomic diversity of Vibrio spp. through Pan-genome analysis. Ann Microbiol 69:1547\u20131555. https:\/\/doi.org\/10.1007\/s13213-019-01539-7","journal-title":"Ann Microbiol"},{"key":"11116_CR108","doi-asserted-by":"publisher","first-page":"8215","DOI":"10.1128\/JB.01039-07","volume":"189","author":"T-K Wu","year":"2007","unstructured":"Wu T-K, Wang Y-K, Chen Y-C et al (2007) Identification of a Vibrio furnissii oligopeptide permease and characterization of its in vitro hemolytic activity. J Bacteriol 189:8215\u20138223. https:\/\/doi.org\/10.1128\/JB.01039-07","journal-title":"J Bacteriol"},{"key":"11116_CR109","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00805","author":"P Raghunath","year":"2015","unstructured":"Raghunath P (2015) Roles of thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) in Vibrio parahaemolyticus. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2014.00805","journal-title":"Front Microbiol"},{"key":"11116_CR110","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.micpath.2018.07.021","volume":"123","author":"Q Cai","year":"2018","unstructured":"Cai Q, Zhang Y (2018) Structure, function and regulation of the thermostable direct hemolysin (TDH) in pandemic Vibrio parahaemolyticus. Microb Pathog 123:242\u2013245. https:\/\/doi.org\/10.1016\/j.micpath.2018.07.021","journal-title":"Microb Pathog"},{"key":"11116_CR111","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/nrmicro.2017.27","volume":"15","author":"AN Spaan","year":"2017","unstructured":"Spaan AN, van Strijp JAG, Torres VJ (2017) Leukocidins: staphylococcal bi-component pore-forming toxins find their receptors. Nat Rev Microbiol 15:435\u2013447. https:\/\/doi.org\/10.1038\/nrmicro.2017.27","journal-title":"Nat Rev Microbiol"},{"key":"11116_CR112","doi-asserted-by":"publisher","first-page":"8137","DOI":"10.1128\/jb.186.23.8137-8143.2004","volume":"186","author":"BK Boardman","year":"2004","unstructured":"Boardman BK, Fullner Satchell KJ (2004) Vibrio cholerae strains with mutations in an atypical type I secretion system accumulate RTX toxin intracellularly. J Bacteriol 186:8137\u20138143. https:\/\/doi.org\/10.1128\/jb.186.23.8137-8143.2004","journal-title":"J Bacteriol"},{"key":"11116_CR113","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1073\/pnas.96.3.1071","volume":"96","author":"W Lin","year":"1999","unstructured":"Lin W, Fullner KJ, Clayton R et al (1999) Identification of a Vibrio cholerae RTX toxin gene cluster that is tightly linked to the cholera toxin prophage. Proc Natl Acad Sci 96:1071\u20131076. https:\/\/doi.org\/10.1073\/pnas.96.3.1071","journal-title":"Proc Natl Acad Sci"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11116-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-025-11116-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11116-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T12:29:20Z","timestamp":1763728160000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-025-11116-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,6]]},"references-count":113,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["11116"],"URL":"https:\/\/doi.org\/10.1007\/s11030-025-11116-7","relation":{},"ISSN":["1381-1991","1573-501X"],"issn-type":[{"type":"print","value":"1381-1991"},{"type":"electronic","value":"1573-501X"}],"subject":[],"published":{"date-parts":[[2025,2,6]]},"assertion":[{"value":"1 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 February 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}