{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T21:00:05Z","timestamp":1790370005707,"version":"4.1.0"},"reference-count":76,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,12,27]],"date-time":"2019-12-27T00:00:00Z","timestamp":1577404800000},"content-version":"vor","delay-in-days":26,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology , Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/PR3260\/BRB\/10\/ 967\/2011"],"award-info":[{"award-number":["BT\/PR3260\/BRB\/10\/ 967\/2011"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant \u201cpriority pathogens\u201d that are posing the greatest threats to human health. Six of these dreaded pathogens are known to infect the human gastrointestinal system. In addition to causing gastrointestinal and systemic infections, these pathogens can also affect the composition of other microbes constituting the healthy gut microbiome. Such aberrations in gut microbiome can significantly affect human physiology and immunity. Identifying the virulence mechanisms of these enteric pathogens are likely to help in developing newer therapeutic strategies to counter them.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Using our previously published in silico approach, we have evaluated (and compared) Host-Pathogen Protein-Protein Interaction (HPI) profiles of four groups of enteric pathogens, namely, different species of<jats:italic>Escherichia<\/jats:italic>,<jats:italic>Shigella<\/jats:italic>,<jats:italic>Salmonella<\/jats:italic>and<jats:italic>Vibrio<\/jats:italic>. Results indicate that in spite of genus\/ species specific variations, most enteric pathogens possess a common repertoire of HPIs. This core set of HPIs are probably responsible for the survival of these pathogen in the harsh nutrient-limiting environment within the gut. Certain genus\/ species specific HPIs were also observed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conslusions<\/jats:title><jats:p>The identified bacterial proteins involved in the core set of HPIs are expected to be helpful in understanding the pathogenesis of these dreaded gut pathogens in greater detail. Possible role of genus\/ species specific variations in the HPI profiles in the virulence of these pathogens are also discussed. The obtained results are likely to provide an opportunity for development of novel therapeutic strategies against the most dreaded gut pathogens.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12864-019-6398-2","type":"journal-article","created":{"date-parts":[[2019,12,27]],"date-time":"2019-12-27T15:02:44Z","timestamp":1577458964000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Investigating host-bacterial interactions among enteric pathogens"],"prefix":"10.1186","volume":"20","author":[{"given":"Tungadri","family":"Bose","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. V.","family":"Venkatesh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharmila S.","family":"Mande","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,27]]},"reference":[{"key":"6398_CR1","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1177\/1756283X13482996","volume":"6","author":"CM Guinane","year":"2013","unstructured":"Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Ther Adv Gastroenterol. 2013;6:295\u2013308.","journal-title":"Ther Adv Gastroenterol"},{"key":"6398_CR2","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/nature11550","volume":"489","author":"CA Lozupone","year":"2012","unstructured":"Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220\u201330.","journal-title":"Nature."},{"key":"6398_CR3","doi-asserted-by":"publisher","first-page":"8787","DOI":"10.3748\/wjg.v21.i29.8787","volume":"21","author":"SM Jandhyala","year":"2015","unstructured":"Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015;21:8787\u2013803.","journal-title":"World J Gastroenterol"},{"key":"6398_CR4","unstructured":"WHO publishes list of bacteria for which new antibiotics are urgently needed. https:\/\/www.who.int\/news-room\/detail\/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed. Accessed 7 Nov 2019."},{"key":"6398_CR5","doi-asserted-by":"publisher","first-page":"128","DOI":"10.3389\/fcimb.2017.00128","volume":"7","author":"T Bose","year":"2017","unstructured":"Bose T, Venkatesh KV, Mande SS. Computational analysis of host-pathogen protein interactions between humans and different strains of Enterohemorrhagic Escherichia coli. Front Cell Infect Microbiol. 2017;7:128.","journal-title":"Front Cell Infect Microbiol"},{"key":"6398_CR6","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1186\/s12864-018-4947-8","volume":"19","author":"T Bose","year":"2018","unstructured":"Bose T, Das C, Dutta A, Mahamkali V, Sadhu S, Mande SS. Understanding the role of interactions between host and mycobacterium tuberculosis under hypoxic condition: an in silico approach. BMC Genomics. 2018;19:555.","journal-title":"BMC Genomics"},{"key":"6398_CR7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004483","volume":"11","author":"Y Rossez","year":"2015","unstructured":"Rossez Y, Wolfson EB, Holmes A, Gally DL, Holden NJ. Bacterial flagella: twist and stick, or dodge across the kingdoms. PLoS Pathog. 2015;11:e1004483.","journal-title":"PLoS Pathog"},{"key":"6398_CR8","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1016\/j.coi.2007.06.005","volume":"19","author":"S Mattoo","year":"2007","unstructured":"Mattoo S, Lee YM, Dixon JE. Interactions of bacterial effector proteins with host proteins. Curr Opin Immunol. 2007;19:392\u2013401.","journal-title":"Curr Opin Immunol"},{"key":"6398_CR9","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.freeradbiomed.2016.10.489","volume":"105","author":"M Ellermann","year":"2017","unstructured":"Ellermann M, Arthur JC. Siderophore-mediated iron acquisition and modulation of host-bacterial interactions. Free Radic Biol Med. 2017;105:68\u201378.","journal-title":"Free Radic Biol Med"},{"key":"6398_CR10","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/S1369-5274(99)80008-3","volume":"2","author":"JE Gal\u00e1n","year":"1999","unstructured":"Gal\u00e1n JE. Interaction of Salmonella with host cells through the centisome 63 type III secretion system. Curr Opin Microbiol. 1999;2:46\u201350.","journal-title":"Curr Opin Microbiol"},{"key":"6398_CR11","doi-asserted-by":"publisher","first-page":"2585","DOI":"10.1110\/ps.073228407","volume":"16","author":"FP Davis","year":"2007","unstructured":"Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Sci Publ Protein Soc. 2007;16:2585\u201396.","journal-title":"Protein Sci Publ Protein Soc"},{"key":"6398_CR12","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/s12859-015-0535-y","volume":"16","author":"T Huo","year":"2015","unstructured":"Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z. Prediction of host - pathogen protein interactions between mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics. 2015;16:100.","journal-title":"BMC Bioinformatics."},{"key":"6398_CR13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004088","volume":"11","author":"V Memi\u0161evi\u0107","year":"2015","unstructured":"Memi\u0161evi\u0107 V, Zavaljevski N, Rajagopala SV, Kwon K, Pieper R, DeShazer D, et al. Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms. PLoS Comput Biol. 2015;11:e1004088.","journal-title":"PLoS Comput Biol"},{"key":"6398_CR14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0067472","volume":"8","author":"HA Rapanoel","year":"2013","unstructured":"Rapanoel HA, Mazandu GK, Mulder NJ. Predicting and analyzing interactions between mycobacterium tuberculosis and its human host. PLoS One. 2013;8:e67472.","journal-title":"PLoS One"},{"key":"6398_CR15","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/s12859-017-1550-y","volume":"18","author":"G Mahajan","year":"2017","unstructured":"Mahajan G, Mande SC. Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to mycobacterium tuberculosis. BMC Bioinformatics. 2017;18:201.","journal-title":"BMC Bioinformatics."},{"issue":"Suppl 6","key":"6398_CR16","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1752-0509-7-S6-S6","volume":"7","author":"H Zhou","year":"2013","unstructured":"Zhou H, Rezaei J, Hugo W, Gao S, Jin J, Fan M, et al. Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. BMC Syst Biol. 2013;7(Suppl 6):S6.","journal-title":"BMC Syst Biol"},{"key":"6398_CR17","first-page":"317","volume":"2019","author":"E Guven-Maiorov","year":"1851","unstructured":"Guven-Maiorov E, Tsai C-J, Ma B, Nussinov R. Interface-based structural prediction of novel host-pathogen interactions. Methods Mol Biol. 1851;2019:317\u201335 Clifton NJ.","journal-title":"Methods Mol Biol"},{"key":"6398_CR18","doi-asserted-by":"publisher","first-page":"3925","DOI":"10.1016\/j.jmb.2017.10.023","volume":"429","author":"E Guven-Maiorov","year":"2017","unstructured":"Guven-Maiorov E, Tsai C-J, Ma B, Nussinov R. Prediction of host-pathogen interactions for helicobacter pylori by Interface mimicry and implications to gastric cancer. J Mol Biol. 2017;429:3925\u201341.","journal-title":"J Mol Biol"},{"key":"6398_CR19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005579","volume":"13","author":"E Guven-Maiorov","year":"2017","unstructured":"Guven-Maiorov E, Tsai C-J, Nussinov R. Structural host-microbiota interaction networks. PLoS Comput Biol. 2017;13:e1005579.","journal-title":"PLoS Comput Biol"},{"key":"6398_CR20","doi-asserted-by":"publisher","first-page":"i159","DOI":"10.1093\/bioinformatics\/btm208","volume":"23","author":"MD Dyer","year":"2007","unstructured":"Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen protein-protein interactions. Bioinforma. 2007;23:i159\u201366 Oxf Engl.","journal-title":"Bioinforma"},{"key":"6398_CR21","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1039\/B912129C","volume":"6","author":"K Raman","year":"2010","unstructured":"Raman K, Bhat AG, Chandra N. A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. Mol BioSyst. 2010;6:516\u201330.","journal-title":"Mol BioSyst"},{"key":"6398_CR22","doi-asserted-by":"publisher","unstructured":"Cuesta-Astroz Y, Santos A, Oliveira G, Jensen LJ. Analysis of predicted host\u2013parasite Interactomes reveals commonalities and specificities related to parasitic lifestyle and tissues tropism. Front Immunol. 2019;10. https:\/\/doi.org\/10.3389\/fimmu.2019.00212.","DOI":"10.3389\/fimmu.2019.00212"},{"key":"6398_CR23","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.nmni.2017.09.003","volume":"21","author":"NK Devanga Ragupathi","year":"2017","unstructured":"Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Inbanathan FY, Veeraraghavan B. Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbes New Infect. 2017;21:58\u201362.","journal-title":"New Microbes New Infect"},{"key":"6398_CR24","doi-asserted-by":"publisher","first-page":"1532","DOI":"10.1002\/pro.5560020918","volume":"2","author":"CJ Jeffery","year":"1993","unstructured":"Jeffery CJ, Koshland DE. Vibrio cholerae hlyB is a member of the chemotaxis receptor gene family. Protein Sci Publ Protein Soc. 1993;2:1532\u20135.","journal-title":"Protein Sci Publ Protein Soc."},{"key":"6398_CR25","doi-asserted-by":"publisher","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","volume":"44","author":"M Kanehisa","year":"2016","unstructured":"Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457\u201362.","journal-title":"Nucleic Acids Res"},{"key":"6398_CR26","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27\u201330.","journal-title":"Nucleic Acids Res"},{"key":"6398_CR27","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1111\/j.1574-695X.2007.00323.x","volume":"51","author":"V Patil","year":"2007","unstructured":"Patil V, Kumar A, Kuruppath S, Nandi D. Peptidase N encoded by Salmonella enterica serovar Typhimurium modulates systemic infection in mice. FEMS Immunol Med Microbiol. 2007;51:431\u201342.","journal-title":"FEMS Immunol Med Microbiol"},{"key":"6398_CR28","doi-asserted-by":"publisher","first-page":"105","DOI":"10.2147\/IJGM.S15618","volume":"4","author":"P Ghezzi","year":"2011","unstructured":"Ghezzi P. Role of glutathione in immunity and inflammation in the lung. Int J Gen Med. 2011;4:105\u201313.","journal-title":"Int J Gen Med"},{"key":"6398_CR29","unstructured":"Antoine Danchin antoine danchin [at] normalesup [dot]org. Sulfur metabolism in bacteria. 2011. http:\/\/www.normalesup.org\/~adanchin\/science\/sulfur-review.html. Accessed 1 Jan 2018."},{"key":"6398_CR30","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1093\/mp\/ssq001","volume":"3","author":"J-C Davidian","year":"2010","unstructured":"Davidian J-C, Kopriva S. Regulation of sulfate uptake and assimilation\u2014the same or not the same? Mol Plant. 2010;3:314\u201325.","journal-title":"Mol Plant"},{"key":"6398_CR31","unstructured":"AID_2013060511545426.pdf. http:\/\/file.scirp.org\/pdf\/AID_2013060511545426.pdf. Accessed 1 Jan 2018."},{"key":"6398_CR32","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1124\/mol.115.098756","volume":"88","author":"ER Lazarowski","year":"2015","unstructured":"Lazarowski ER, Harden TK. UDP-sugars as extracellular signaling molecules: cellular and physiologic consequences of P2Y14 receptor activation. Mol Pharmacol. 2015;88:151\u201360.","journal-title":"Mol Pharmacol"},{"key":"6398_CR33","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1007\/s11302-016-9524-5","volume":"12","author":"JI Sesma","year":"2016","unstructured":"Sesma JI, Weitzer CD, Livraghi-Butrico A, Dang H, Donaldson S, Alexis NE, et al. UDP-glucose promotes neutrophil recruitment in the lung. Purinergic Signal. 2016;12:627\u201335.","journal-title":"Purinergic Signal"},{"issue":"11","key":"6398_CR34","doi-asserted-by":"publisher","first-page":"e1002360","DOI":"10.1371\/journal.ppat.1002360","volume":"7","author":"Catherine L. Shelton","year":"2011","unstructured":"Shelton CL, Raffel FK, Beatty WL, Johnson SM, Mason KM. Sap transporter mediated import and subsequent degradation of antimicrobial peptides in Haemophilus. PLoS Pathog. 2011;7. https:\/\/doi.org\/10.1371\/journal.ppat.1002360.","journal-title":"PLoS Pathogens"},{"key":"6398_CR35","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1038\/cmi.2015.95","volume":"13","author":"E-K Jo","year":"2016","unstructured":"Jo E-K, Kim JK, Shin D-M, Sasakawa C. Molecular mechanisms regulating NLRP3 inflammasome activation. Cell Mol Immunol. 2016;13:148\u201359.","journal-title":"Cell Mol Immunol"},{"key":"6398_CR36","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.4049\/jimmunol.1400145","volume":"193","author":"J Thinwa","year":"2014","unstructured":"Thinwa J, Segovia JA, Bose S, Dube PH. Integrin-mediated first signal for inflammasome activation in intestinal epithelial cells. J Immunol. 2014;193:1373\u201382 Baltim Md 1950.","journal-title":"J Immunol"},{"key":"6398_CR37","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1189\/jlb.0607362","volume":"83","author":"F Martinon","year":"2008","unstructured":"Martinon F. Detection of immune danger signals by NALP3. J Leukoc Biol. 2008;83:507\u201311.","journal-title":"J Leukoc Biol"},{"key":"6398_CR38","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1757-4749-2-8","volume":"2","author":"RSD Reis","year":"2010","unstructured":"Reis RSD, Horn F. Enteropathogenic Escherichia coli, Samonella, Shigella and Yersinia: cellular aspects of host-bacteria interactions in enteric diseases. Gut Pathog. 2010;2:8.","journal-title":"Gut Pathog"},{"key":"6398_CR39","doi-asserted-by":"publisher","DOI":"10.1590\/S0100-736X2008001000015","volume-title":"Occurrence of virulence-related sequences and phylogenetic analysis of commensal and pathogenic avian Escherichia coli strains (APEC)","author":"TA de Campos","year":"2008","unstructured":"de Campos TA, Lago JC, Nakazato G, Stehling EG, Brocchi M, de Castro AF, et al. Occurrence of virulence-related sequences and phylogenetic analysis of commensal and pathogenic avian Escherichia coli strains (APEC). 2008."},{"key":"6398_CR40","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1128\/IAI.71.4.1919-1928.2003","volume":"71","author":"LJ Runyen-Janecky","year":"2003","unstructured":"Runyen-Janecky LJ, Reeves SA, Gonzales EG, Payne SM. Contribution of the Shigella flexneri sit, Iuc, and Feo iron acquisition systems to iron acquisition in vitro and in cultured cells. Infect Immun. 2003;71:1919\u201328.","journal-title":"Infect Immun"},{"key":"6398_CR41","doi-asserted-by":"publisher","first-page":"12679","DOI":"10.1074\/jbc.M111.336180","volume":"287","author":"DL Ulrich","year":"2012","unstructured":"Ulrich DL, Lynch J, Wang Y, Fukuda Y, Nachagari D, Du G, et al. ATP-dependent mitochondrial porphyrin importer ABCB6 protects against phenylhydrazine toxicity. J Biol Chem. 2012;287:12679\u201390.","journal-title":"J Biol Chem"},{"key":"6398_CR42","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.carres.2012.02.027","volume":"356","author":"LK Greenfield","year":"2012","unstructured":"Greenfield LK, Whitfield C. Synthesis of lipopolysaccharide O-antigens by ABC transporter-dependent pathways. Carbohydr Res. 2012;356:12\u201324.","journal-title":"Carbohydr Res"},{"key":"6398_CR43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0070829","volume":"8","author":"I Wallrodt","year":"2013","unstructured":"Wallrodt I, Jelsbak L, Thorndahl L, Thomsen LE, Lemire S, Olsen JE. The putative thiosulfate sulfurtransferases PspE and GlpE contribute to virulence of Salmonella Typhimurium in the mouse model of systemic disease. PLoS One. 2013;8:e70829.","journal-title":"PLoS One"},{"key":"6398_CR44","doi-asserted-by":"publisher","unstructured":"Urdaneta V, Casades\u00fas J. Interactions between Bacteria and bile salts in the gastrointestinal and Hepatobiliary tracts. Front Med. 2017;4. https:\/\/doi.org\/10.3389\/fmed.2017.00163.","DOI":"10.3389\/fmed.2017.00163"},{"key":"6398_CR45","doi-asserted-by":"publisher","unstructured":"Simon Davis DA, Parish CR. Heparan sulfate: a ubiquitous glycosaminoglycan with multiple roles in immunity. Front Immunol. 2013;4. https:\/\/doi.org\/10.3389\/fimmu.2013.00470.","DOI":"10.3389\/fimmu.2013.00470"},{"key":"6398_CR46","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1093\/jb\/mvg189","volume":"134","author":"R Chambert","year":"2003","unstructured":"Chambert R, Pereira Y, Petit-Glatron MF. Purification and characterization of YfkN, a trifunctional nucleotide phosphoesterase secreted by Bacillus subtilis. J Biochem (Tokyo). 2003;134:655\u201360.","journal-title":"J Biochem (Tokyo)"},{"key":"6398_CR47","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/1757-4749-5-28","volume":"5","author":"C Das","year":"2013","unstructured":"Das C, Dutta A, Rajasingh H, Mande SS. Understanding the sequential activation of type III and type VI secretion Systems in Salmonella typhimurium using Boolean modeling. Gut Pathog. 2013;5:28.","journal-title":"Gut Pathog"},{"key":"6398_CR48","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.mib.2003.12.005","volume":"7","author":"JH Brumell","year":"2004","unstructured":"Brumell JH, Grinstein S. Salmonella redirects phagosomal maturation. Curr Opin Microbiol. 2004;7:78\u201384.","journal-title":"Curr Opin Microbiol"},{"key":"6398_CR49","doi-asserted-by":"publisher","first-page":"3419","DOI":"10.1128\/IAI.70.7.3419-3426.2002","volume":"70","author":"AR Mey","year":"2002","unstructured":"Mey AR, Wyckoff EE, Oglesby AG, Rab E, Taylor RK, Payne SM. Identification of the Vibrio cholerae Enterobactin receptors VctA and IrgA: IrgA is not required for virulence. Infect Immun. 2002;70:3419\u201326.","journal-title":"Infect Immun"},{"key":"6398_CR50","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1093\/infdis\/jiv593","volume":"213","author":"WE Yang","year":"2016","unstructured":"Yang WE, Suchindran S, Nicholson BP, McClain MT, Burke T, Ginsburg GS, et al. Transcriptomic analysis of the host response and innate resilience to Enterotoxigenic Escherichia coli infection in humans. J Infect Dis. 2016;213:1495\u2013504.","journal-title":"J Infect Dis"},{"key":"6398_CR51","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.yexcr.2015.09.018","volume":"340","author":"F Beilstein","year":"2016","unstructured":"Beilstein F, Carri\u00e8re V, Leturque A, Demignot S. Characteristics and functions of lipid droplets and associated proteins in enterocytes. Exp Cell Res. 2016;340:172\u20139.","journal-title":"Exp Cell Res"},{"key":"6398_CR52","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1471-2180-6-14","volume":"6","author":"JP Weerasinghe","year":"2006","unstructured":"Weerasinghe JP, Dong T, Schertzberg MR, Kirchhof MG, Sun Y, Schellhorn HE. Stationary phase expression of the arginine biosynthetic operon argCBH in Escherichia coli. BMC Microbiol. 2006;6:14.","journal-title":"BMC Microbiol"},{"key":"6398_CR53","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1111\/j.1753-4887.2008.00082.x","volume":"66","author":"RL Guerrant","year":"2008","unstructured":"Guerrant RL, Ori\u00e1 RB, Moore SR, Ori\u00e1 MO, Lima AA. Malnutrition as an enteric infectious disease with long-term effects on child development. Nutr Rev. 2008;66:487\u2013505.","journal-title":"Nutr Rev"},{"key":"6398_CR54","doi-asserted-by":"publisher","first-page":"5217","DOI":"10.1128\/IAI.73.8.5217-5221.2005","volume":"73","author":"SP Faucher","year":"2005","unstructured":"Faucher SP, Curtiss R, Daigle F. Selective capture of Salmonella enterica Serovar Typhi genes expressed in macrophages that are absent from the Salmonella enterica Serovar Typhimurium genome. Infect Immun. 2005;73:5217\u201321.","journal-title":"Infect Immun"},{"key":"6398_CR55","doi-asserted-by":"publisher","first-page":"e00624","DOI":"10.1128\/mBio.00624-12","volume":"4","author":"J Dolores","year":"2013","unstructured":"Dolores J, Satchell KJF. Analysis of Vibrio cholerae Genome Sequences Reveals Unique rtxA Variants in Environmental Strains and an rtxA-Null Mutation in Recent Altered El Tor Isolates. mBio. 2013;4:e00624\u201312.","journal-title":"mBio"},{"key":"6398_CR56","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1111\/j.1365-2958.2009.06629.x","volume":"72","author":"L Bourassa","year":"2009","unstructured":"Bourassa L, Camilli A. Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae. Mol Microbiol. 2009;72:124\u201338.","journal-title":"Mol Microbiol"},{"key":"6398_CR57","doi-asserted-by":"publisher","first-page":"20897","DOI":"10.1074\/jbc.M110.121707","volume":"285","author":"K Pal","year":"2010","unstructured":"Pal K, Kumar S, Sharma S, Garg SK, Alam MS, Xu HE, et al. Crystal structure of full-length mycobacterium tuberculosis H37Rv glycogen branching enzyme insights of N-terminal \u03b2-sandwich in substrate specificity and enzymatic activity. J Biol Chem. 2010;285:20897\u2013903.","journal-title":"J Biol Chem"},{"key":"6398_CR58","doi-asserted-by":"publisher","first-page":"3739","DOI":"10.1128\/JCM.01286-11","volume":"49","author":"MS Son","year":"2011","unstructured":"Son MS, Megli CJ, Kovacikova G, Qadri F, Taylor RK. Characterization of Vibrio cholerae O1 El Tor biotype variant clinical isolates from Bangladesh and Haiti, including a molecular genetic analysis of virulence genes. J Clin Microbiol. 2011;49:3739\u201349.","journal-title":"J Clin Microbiol"},{"key":"6398_CR59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0053504","volume":"8","author":"S Pradhan","year":"2013","unstructured":"Pradhan S, Mallick SK, Chowdhury R. Vibrio cholerae classical biotype is converted to the viable non-Culturable state when cultured with the El Tor biotype. PLoS One. 2013;8:e53504.","journal-title":"PLoS One"},{"key":"6398_CR60","doi-asserted-by":"publisher","first-page":"5725","DOI":"10.1128\/JB.00980-12","volume":"194","author":"C Hill","year":"2012","unstructured":"Hill C. Virulence or niche factors: What\u2019s in a name? J Bacteriol. 2012;194:5725\u20137.","journal-title":"J Bacteriol"},{"key":"6398_CR61","doi-asserted-by":"publisher","first-page":"7074","DOI":"10.4049\/jimmunol.0900001","volume":"182","author":"T Arase","year":"2009","unstructured":"Arase T, Uchida H, Kajitani T, Ono M, Tamaki K, Oda H, et al. The UDP-glucose receptor P2RY14 triggers innate mucosal immunity in the female reproductive tract by inducing IL-8. J Immunol. 2009;182:7074\u201384 Baltim Md 1950.","journal-title":"J Immunol"},{"key":"6398_CR62","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12552","volume":"5","author":"L Gehre","year":"2016","unstructured":"Gehre L, Gorgette O, Perrinet S, Prevost M-C, Ducatez M, Giebel AM, et al. Sequestration of host metabolism by an intracellular pathogen. eLife. 2016;5:e12552.","journal-title":"eLife."},{"key":"6398_CR63","doi-asserted-by":"crossref","first-page":"5208","DOI":"10.1016\/S0021-9258(19)41297-0","volume":"250","author":"O Doi","year":"1975","unstructured":"Doi O, Nojima S. Lysophospholipase of Escherichia coli. J Biol Chem. 1975;250:5208\u201314.","journal-title":"J Biol Chem"},{"key":"6398_CR64","doi-asserted-by":"publisher","first-page":"1793","DOI":"10.1128\/jb.176.6.1793-1795.1994","volume":"176","author":"H Cho","year":"1994","unstructured":"Cho H, Cronan JE. \u201cProtease I\u201d of Escherichia coli functions as a thioesterase in vivo. J Bacteriol. 1994;176:1793\u20135.","journal-title":"J Bacteriol"},{"key":"6398_CR65","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1006\/bbrc.1997.5797","volume":"231","author":"YL Lee","year":"1997","unstructured":"Lee YL, Chen JC, Shaw JF. The thioesterase I of Escherichia coli has arylesterase activity and shows stereospecificity for protease substrates. Biochem Biophys Res Commun. 1997;231:452\u20136.","journal-title":"Biochem Biophys Res Commun"},{"key":"6398_CR66","doi-asserted-by":"publisher","first-page":"24616","DOI":"10.1074\/jbc.M111.247601","volume":"286","author":"SS Chavadi","year":"2011","unstructured":"Chavadi SS, Edupuganti UR, Vergnolle O, Fatima I, Singh SM, Soll CE, et al. Inactivation of tesA reduces Cell Wall lipid production and increases drug susceptibility in mycobacteria. J Biol Chem. 2011;286:24616\u201325.","journal-title":"J Biol Chem"},{"key":"6398_CR67","doi-asserted-by":"publisher","first-page":"4432","DOI":"10.1093\/nar\/gkf566","volume":"30","author":"Q Jin","year":"2002","unstructured":"Jin Q, Yuan Z, Xu J, Wang Y, Shen Y, Lu W, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002;30:4432\u201341.","journal-title":"Nucleic Acids Res"},{"key":"6398_CR68","doi-asserted-by":"publisher","first-page":"4449","DOI":"10.1093\/emboj\/cdf457","volume":"21","author":"F Lafont","year":"2002","unstructured":"Lafont F, Tran Van Nhieu G, Hanada K, Sansonetti P, van der Goot FG. Initial steps of Shigella infection depend on the cholesterol\/sphingolipid raft-mediated CD44-IpaB interaction. EMBO J. 2002;21:4449\u201357.","journal-title":"EMBO J"},{"key":"6398_CR69","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/S0005-2736(02)00359-0","volume":"1562","author":"MR Yen","year":"2002","unstructured":"Yen MR, Peabody CR, Partovi SM, Zhai Y, Tseng YH, Saier MH. Protein-translocating outer membrane porins of gram-negative bacteria. Biochim Biophys Acta. 2002;1562:6\u201331.","journal-title":"Biochim Biophys Acta"},{"key":"6398_CR70","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1128\/MMBR.00001-07","volume":"71","author":"J Lubelski","year":"2007","unstructured":"Lubelski J, Konings WN, Driessen AJM. Distribution and physiology of ABC-type transporters contributing to multidrug resistance in Bacteria. Microbiol Mol Biol Rev. 2007;71:463\u201376.","journal-title":"Microbiol Mol Biol Rev"},{"issue":"Web Server issu","key":"6398_CR71","doi-asserted-by":"publisher","first-page":"W585","DOI":"10.1093\/nar\/gkm259","volume":"35","author":"P Horton","year":"2007","unstructured":"Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35(Web Server issue):W585\u20137.","journal-title":"Nucleic Acids Res"},{"key":"6398_CR72","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","volume":"26","author":"NY Yu","year":"2010","unstructured":"Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26:1608\u201315.","journal-title":"Bioinformatics"},{"key":"6398_CR73","doi-asserted-by":"publisher","first-page":"D808","DOI":"10.1093\/nar\/gks1094","volume":"41","author":"A Franceschini","year":"2013","unstructured":"Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41:D808\u201315.","journal-title":"Nucleic Acids Res"},{"key":"6398_CR74","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498\u2013504.","journal-title":"Genome Res"},{"key":"6398_CR75","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1186\/s12859-016-1013-x","volume":"17","author":"BK Kuntal","year":"2016","unstructured":"Kuntal BK, Dutta A, Mande SS. CompNet: a GUI based tool for comparison of multiple biological interaction networks. BMC Bioinformatics. 2016;17:185.","journal-title":"BMC Bioinformatics"},{"key":"6398_CR76","doi-asserted-by":"publisher","first-page":"D447","DOI":"10.1093\/nar\/gku1003","volume":"43","author":"D Szklarczyk","year":"2015","unstructured":"Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: protein\u2013protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43:D447\u201352.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-019-6398-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12864-019-6398-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-019-6398-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,14]],"date-time":"2021-02-14T08:26:06Z","timestamp":1613291166000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-019-6398-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12]]},"references-count":76,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["6398"],"URL":"https:\/\/doi.org\/10.1186\/s12864-019-6398-2","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12]]},"assertion":[{"value":"19 August 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 December 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 December 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Dr. Sharmila S. Mande and Mr. Tungadri Bose are employees of Tata Consultancy Services Limited. All other authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1022"}}