{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T18:44:31Z","timestamp":1791139471581,"version":"4.1.0"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Gut Pathog"],"published-print":{"date-parts":[[2013,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>\n              <jats:italic>Ochrobactrum intermedium<\/jats:italic> is an emerging opportunistic pathogen of humans that is closely related to members of the genus <jats:italic>Brucella<\/jats:italic>. Earlier, we reported the case of an Indian subject with non-ulcer dyspeptic symptoms whose urease positive gastric biopsy revealed the presence of <jats:italic>Helicobacter pylori<\/jats:italic> along with non-<jats:italic>Helicobacter<\/jats:italic> like bacteria, eventually cultured and identified as <jats:italic>O. intermedium<\/jats:italic> strain M86.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here, we describe the unclosed draft genome of the strain M86 with a length of 5,188,688 bp and mean G+C content of 57.9%. We have also identified many putative gene clusters that might be responsible for its persistence in the gastric mucosa.Comparative analysis of genomic features of <jats:italic>Ochrobactrum intermedium<\/jats:italic> strain M86 and <jats:italic>Ochrobactrum intermedium<\/jats:italic> LMG 3301<jats:sup>T<\/jats:sup> was also done.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>This paper attempts to gain whole-genome based insights into the putative gene determinants of <jats:italic>O. intermedium<\/jats:italic> for survival in the highly acidic stomach lumen environment .Identification of genes putatively involved in the various metabolic pathways may lead to a better understanding of the survival of <jats:italic>O. intermdedium<\/jats:italic> in acidic condition.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1757-4749-5-7","type":"journal-article","created":{"date-parts":[[2013,4,4]],"date-time":"2013-04-04T13:04:58Z","timestamp":1365080698000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Draft genome of Ochrobactrum intermedium strain M86 isolated from non-ulcer dyspeptic individual from India"],"prefix":"10.1186","volume":"5","author":[{"given":"Girish","family":"Kulkarni","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhiraj","family":"Dhotre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahesh","family":"Dharne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudarshan","family":"Shetty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Somak","family":"Chowdhury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vatsala","family":"Misra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sriprakash","family":"Misra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milind","family":"Patole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yogesh","family":"Shouche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,4,4]]},"reference":[{"key":"87_CR1","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1099\/00207713-48-3-759","volume":"48","author":"J Velasco","year":"1998","unstructured":"Velasco J, Romero C, Lopez-Goni I, Leiva J, Diaz R, Moriyon I: Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int J Syst Bacteriol. 1998, 48: 759-768. 10.1099\/00207713-48-3-759.","journal-title":"Int J Syst Bacteriol"},{"key":"87_CR2","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1128\/JCM.37.1.241-244.1999","volume":"37","author":"LV Moller","year":"1999","unstructured":"Moller LV, Arends JP, Harmsen HJ, Talens A, Terpstra PM, Slooff J: Ochrobactrum intermedium infection after liver transplantation. J Clin Microbiol. 1999, 37: 241-244.","journal-title":"J Clin Microbiol"},{"key":"87_CR3","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/j.diagmicrobio.2005.05.014","volume":"53","author":"A Apisarnthanarak","year":"2005","unstructured":"Apisarnthanarak A, Kiratisin P, Mundy LM: Evaluation of Ochrobactrum intermedium bacteremia in a patient with bladder cancer. Diagn Microbiol Infect Dis. 2005, 53: 153-155. 10.1016\/j.diagmicrobio.2005.05.014.","journal-title":"Diagn Microbiol Infect Dis"},{"key":"87_CR4","first-page":"183","volume":"41","author":"MS Dharne","year":"2008","unstructured":"Dharne MS, Misra SP, Misra V, Dwivedi M, Patole MS, Shouche YS: Isolation of urease-positive Ochrobactrum intermedium in the stomach of a non-ulcer dyspeptic patient from north India. J Microbiol Immunol Infect. 2008, 41: 183-186.","journal-title":"J Microbiol Immunol Infect"},{"key":"87_CR5","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1023\/A:1005496022881","volume":"45","author":"SS Khanolkar-Gaitonde","year":"2000","unstructured":"Khanolkar-Gaitonde SS, Reubish GK, Lee CK, Stadtlander CT: Isolation of bacteria other than Helicobacter pylori from stomachs of squirrel monkeys (Saimiri spp.) with gastritis. Dig Dis Sci. 2000, 45: 272-80. 10.1023\/A:1005496022881.","journal-title":"Dig Dis Sci"},{"key":"87_CR6","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1136\/gut.32.2.137","volume":"32","author":"KL Heilmann","year":"1991","unstructured":"Heilmann KL, Borchard F: Gastritis due to spiral shaped bacteria other than Helicobacter pylori: clinical, histological, and ultrastructural findings. Gut. 1991, 32: 137-140. 10.1136\/gut.32.2.137.","journal-title":"Gut"},{"key":"87_CR7","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1016\/S0046-8177(03)00287-9","volume":"34","author":"MT Hala","year":"2003","unstructured":"Hala MT, El-Zimaty , Ramchatesingh J, Clarrige JE, Abudayyeh S, Osato MS, Graham D: Enterococcal gastritis. Human Pathol. 2003, 34: 944-945. 10.1016\/S0046-8177(03)00287-9.","journal-title":"Human Pathol"},{"key":"87_CR8","doi-asserted-by":"publisher","first-page":"1756","DOI":"10.1111\/j.1572-0241.2006.00698.x","volume":"101","author":"G Brandi","year":"2006","unstructured":"Brandi G, Biavati B, Calabrese C, Granata M, Nannetti A, Mattarelli P, Di Febo G, Saccoccio G, Biasco G: Urease-positive bacteria other than Helicobacter pylori in human gastric juice and mucosa. Am J Gastroenterol. 2006, 101: 1756-61. 10.1111\/j.1572-0241.2006.00698.x.","journal-title":"Am J Gastroenterol"},{"key":"87_CR9","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1128\/iai.65.1.49-54.1997","volume":"65","author":"L Sung","year":"1997","unstructured":"Sung L, Changsung K, Young C: Successful cultivation of a potentially pathogenic coccoid organism with tropism for gastric mucin. Infect Immun. 1997, 65: 49-52.","journal-title":"Infect Immun"},{"key":"87_CR10","first-page":"45","volume":"99","author":"B Chevreux","year":"1999","unstructured":"Chevreux B, Wetter T, Suhai S: Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol. 1999, 99: 45-56.","journal-title":"Comput Sci Biol"},{"key":"87_CR11","first-page":"9","volume":"8","author":"RK Aziz","year":"2008","unstructured":"Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008, 8: 9-75.","journal-title":"BMC Genomics"},{"key":"87_CR12","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1093\/bioinformatics\/btq090","volume":"26","author":"C Hemmerich","year":"2010","unstructured":"Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q: An Ergatis-based prokaryotic genome annotation web server. Bioinformatics. 2010, 26: 1122-1124. 10.1093\/bioinformatics\/btq090.","journal-title":"Bioinformatics"},{"key":"87_CR13","doi-asserted-by":"publisher","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","volume":"27","author":"AL Delcher","year":"1999","unstructured":"Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27: 4636-4641. 10.1093\/nar\/27.23.4636.","journal-title":"Nucleic Acids Res"},{"key":"87_CR14","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1093\/nar\/gkr485","volume":"39","author":"Y Zhou","year":"2011","unstructured":"Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res. 2011, 39: 347-352. 10.1093\/nar\/gkq749.","journal-title":"Nucleic Acids Res"},{"key":"87_CR15","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1128\/CMR.00054-05","volume":"19","author":"JG Kusters","year":"2006","unstructured":"Kusters JG, van Vliet AH, Kuipers EJ: Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev. 2006, 19: 449-490. 10.1128\/CMR.00054-05.","journal-title":"Clin Microbiol Rev"},{"key":"87_CR16","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1099\/jmm.0.46116-0","volume":"54","author":"C Teyssier","year":"2005","unstructured":"Teyssier C, Marchandin H, Jean-Pierre H, Darbas H, Sim\u00e9on De Buochberg M, Diego I, Gouby A, Jumas-Bilak E: Molecular and phenotypic features for identification of the opportunistic pathogens Ochrobactrum spp. J Med Microbiol. 2005, 54: 945-953. 10.1099\/jmm.0.46116-0.","journal-title":"J Med Microbiol"},{"key":"87_CR17","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1093\/jac\/47.6.745","volume":"47","author":"CS Higgins","year":"2001","unstructured":"Higgins CS, Avison MB, Jamieson L, Simm AM, Bennett PM, Walsh TR: Characterization, cloning and sequence analysis of the inducible Ochrobactrum anthropi AmpC \u00df-lactamase. J Antimicrob Chemother. 2001, 47: 745-754. 10.1093\/jac\/47.6.745.","journal-title":"J Antimicrob Chemother"},{"key":"87_CR18","doi-asserted-by":"publisher","first-page":"2324","DOI":"10.1128\/AAC.45.8.2324-2330.2001","volume":"45","author":"D Nadjar","year":"2001","unstructured":"Nadjar D, Labia R, Cerceau C, Bizet C, Philippon A, Arlet G: Molecular characterization of chromosomal class C \u00df-lactamase and its regulatory gene in Ochrobactrum anthropi. Antimicrob Agents Chemother. 2001, 45: 2324-2330. 10.1128\/AAC.45.8.2324-2330.2001.","journal-title":"Antimicrob Agents Chemother"}],"container-title":["Gut Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1757-4749-5-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T23:27:13Z","timestamp":1630538833000},"score":1,"resource":{"primary":{"URL":"https:\/\/gutpathogens.biomedcentral.com\/articles\/10.1186\/1757-4749-5-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["87"],"URL":"https:\/\/doi.org\/10.1186\/1757-4749-5-7","relation":{},"ISSN":["1757-4749"],"issn-type":[{"value":"1757-4749","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,4]]},"assertion":[{"value":"1 March 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 March 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 April 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"7"}}