{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T01:50:05Z","timestamp":1777513805844,"version":"3.51.4"},"reference-count":49,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2018,10,12]],"date-time":"2018-10-12T00:00:00Z","timestamp":1539302400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012553","name":"Chang Gung Memorial Hospital","doi-asserted-by":"publisher","award":["CMRPG8F1861"],"award-info":[{"award-number":["CMRPG8F1861"]}],"id":[{"id":"10.13039\/100012553","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012553","name":"Chang Gung Memorial Hospital","doi-asserted-by":"publisher","award":["CMRPG8G1301"],"award-info":[{"award-number":["CMRPG8G1301"]}],"id":[{"id":"10.13039\/100012553","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"abstract":"<jats:p>Background: The purpose of this study was to profile the bacterium in the ascites and blood of patients with acute surgical abdomen by metagenome analysis. Methods: A total of 97 patients with acute surgical abdomen were included in this study. Accompanied with the standard culture procedures, ascites and blood samples were collected for metagenome analysis to measure the relative abundance of bacteria among groups of patients and between blood and ascites. Results: Metagenomic analysis identified 107 bacterial taxa from the ascites of patients. A principal component analysis (PCA) could separate the bacteria of ascites into roughly three groups: peptic ulcer, perforated or non-perforated appendicitis, and a group which included cholecystitis, small bowel lesion, and colon perforation. Significant correlation between the bacteria of blood and ascites was found in nine bacterial taxa both in blood and ascites with more than 500 sequence reads. However, the PCA failed to separate the variation in the bacteria of blood into different groups of patients, and the bacteria of metagenomic analysis is only partly in accordance with those isolated from a conventional culture method. Conclusion: This study indicated that the metagenome analysis can provide limited information regarding the bacteria in the ascites and blood of patients with acute surgical abdomen.<\/jats:p>","DOI":"10.3390\/jcm7100346","type":"journal-article","created":{"date-parts":[[2018,10,12]],"date-time":"2018-10-12T10:54:03Z","timestamp":1539341643000},"page":"346","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen"],"prefix":"10.3390","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0984-6921","authenticated-orcid":false,"given":"Shao-Chun","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Shyuan","family":"Rau","sequence":"additional","affiliation":[{"name":"Division of Neurosurgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hang-Tsung","family":"Liu","sequence":"additional","affiliation":[{"name":"Division of Trauma Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pao-Jen","family":"Kuo","sequence":"additional","affiliation":[{"name":"Division of Plastic Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng-Chen","family":"Chien","sequence":"additional","affiliation":[{"name":"Division of Plastic Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Min","family":"Hsieh","sequence":"additional","affiliation":[{"name":"Division of Trauma Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ching-Hua","family":"Tsai","sequence":"additional","affiliation":[{"name":"Division of Neurosurgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jung-Fang","family":"Chuang","sequence":"additional","affiliation":[{"name":"Division of Trauma Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun-Ying","family":"Huang","sequence":"additional","affiliation":[{"name":"Division of Trauma Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsiao-Yun","family":"Hsieh","sequence":"additional","affiliation":[{"name":"Division of Plastic Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0945-2746","authenticated-orcid":false,"given":"Ching-Hua","family":"Hsieh","sequence":"additional","affiliation":[{"name":"Division of Plastic Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2018,10,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.micinf.2004.05.017","article-title":"Intra-abdominal infections","volume":"6","author":"Marshall","year":"2004","journal-title":"Microbes Infect."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1038\/nature11553","article-title":"Genomic approaches to studying the human microbiota","volume":"489","author":"Weinstock","year":"2012","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1146\/annurev.mi.31.100177.000543","article-title":"Microbial ecology of the gastrointestinal tract","volume":"31","author":"Savage","year":"1977","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1016\/j.cell.2006.02.017","article-title":"Ecological and evolutionary forces shaping microbial diversity in the human intestine","volume":"124","author":"Ley","year":"2006","journal-title":"Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"ref_6","first-page":"560","article-title":"Gut bacteria in health and disease","volume":"9","author":"Quigley","year":"2013","journal-title":"Gastroenterol. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1097\/MOG.0b013e328339536b","article-title":"The intestinal microbiota in inflammatory bowel diseases: Time to connect with the host","volume":"26","author":"Sokol","year":"2010","journal-title":"Curr. Opin. Gastroenterol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"410s","DOI":"10.1093\/ajcn\/73.2.410s","article-title":"Molecular assessment of intestinal microflora","volume":"73","author":"Tannock","year":"2001","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1097\/01.CCM.0000194725.48928.3A","article-title":"Sepsis in European intensive care units: Results of the SOAP study","volume":"34","author":"Vincent","year":"2006","journal-title":"Crit. Care Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1038\/nbt.2410","article-title":"Genome sequencing in clinical microbiology","volume":"30","author":"Chan","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1038\/nrg1709","article-title":"Metagenomics: DNA sequencing of environmental samples","volume":"6","author":"Tringe","year":"2005","journal-title":"Nat. Rev. Genet."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"62","DOI":"10.7883\/yoken.67.62","article-title":"MePIC, metagenomic pathogen identification for clinical specimens","volume":"67","author":"Takeuchi","year":"2014","journal-title":"Jpn. J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"685","DOI":"10.3389\/fmicb.2017.00685","article-title":"Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach","volume":"8","author":"Kujiraoka","year":"2017","journal-title":"Front. Microb."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Lavezzo, E., Toppo, S., Franchin, E., Di Camillo, B., Finotello, F., Falda, M., Manganelli, R., Palu, G., and Barzon, L. (2013). Genomic comparative analysis and gene function prediction in infectious diseases: Application to the investigation of a meningitis outbreak. BMC Infect. Dis., 13.","DOI":"10.1186\/1471-2334-13-554"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1126\/science.aaf5036","article-title":"Zika virus in the Americas: Early epidemiological and genetic findings","volume":"352","author":"Faria","year":"2016","journal-title":"Science"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"803","DOI":"10.3748\/wjg.v21.i3.803","article-title":"Application of metagenomics in the human gut microbiome","volume":"21","author":"Wang","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"6551","DOI":"10.1128\/AAC.00933-15","article-title":"The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents","volume":"59","author":"Angelin","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/femsec\/fiv168","article-title":"Antibiotic resistance genes across a wide variety of metagenomes","volume":"92","author":"Fitzpatrick","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.clim.2016.07.026","article-title":"The human microbiome in rheumatic autoimmune diseases: A comprehensive review","volume":"170","author":"Coit","year":"2016","journal-title":"Clin. Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"689492","DOI":"10.1155\/2014\/689492","article-title":"The central role of the gut microbiota in chronic inflammatory diseases","volume":"2014","author":"Ferreira","year":"2014","journal-title":"J. Immunol. Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Faria, M.M., Conly, J.M., and Surette, M.G. (2015). The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0557-7"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Gyarmati, P., Kjellander, C., Aust, C., Kalin, M., Ohrmalm, L., and Giske, C.G. (2015). Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0135756"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Turner, P., Suy, K., Tan, L.V., Sar, P., Miliya, T., Hong, N.T.T., Hang, V.T.T., Ny, N.T.H., Soeng, S., and Day, N.P.J. (2017). The aetiologies of central nervous system infections in hospitalised Cambodian children. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-017-2915-6"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Decuypere, S., Meehan, C.J., Van Puyvelde, S., De Block, T., Maltha, J., Palpouguini, L., Tahita, M., Tinto, H., Jacobs, J., and Deborggraeve, S. (2016). Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004470"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/1096-2867(03)90024-7","article-title":"Cytology and fluid analysis of the acute abdomen","volume":"18","author":"Connally","year":"2003","journal-title":"Clin. Tech. Small Anim. Pract."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/1096-2867(03)90026-0","article-title":"The acute abdomen: A surgeon\u2019s approach to diagnosis and treatment","volume":"18","author":"Dye","year":"2003","journal-title":"Clin. Tech. Small Anim. Pract."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/1096-2867(03)90023-5","article-title":"Abdominal paracentesis and diagnostic peritoneal lavage","volume":"18","author":"Walters","year":"2003","journal-title":"Clin. Tech. Small Anim. Pract."},{"key":"ref_28","first-page":"Cr628","article-title":"Bacterial infections in the early period after liver transplantation: Etiological agents and their susceptibility","volume":"15","author":"Kawecki","year":"2009","journal-title":"Med. Sci. Monit."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Lluch, J., Servant, F., Paisse, S., Valle, C., Valiere, S., Kuchly, C., Vilchez, G., Donnadieu, C., Courtney, M., and Burcelin, R. (2015). The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0142334"},{"key":"ref_31","first-page":"109","article-title":"High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism","volume":"8","author":"McCann","year":"2014","journal-title":"Bioinf. Boil. Insights"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1037\/0033-2909.103.2.265","article-title":"Relation of sample size to the stability of component patterns","volume":"103","author":"Guadagnoli","year":"1988","journal-title":"Psychol. Bull."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.aca.2018.03.044","article-title":"Estimating the number of components and detecting outliers using Angle Distribution of Loading Subspaces (ADLS) in PCA analysis","volume":"1020","author":"Liu","year":"2018","journal-title":"Anal. Chim. Acta"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"587","DOI":"10.4040\/jkan.2013.43.5.587","article-title":"A guide on the use of factor analysis in the assessment of construct validity","volume":"43","author":"Kang","year":"2013","journal-title":"J. Korean Acad. Nurs."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e00366-12","DOI":"10.1128\/mBio.00366-12","article-title":"Microbial composition of human appendices from patients following appendectomy","volume":"4","author":"Guinane","year":"2013","journal-title":"mBio"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1016\/S0140-6736(15)00275-5","article-title":"Acute appendicitis: Modern understanding of pathogenesis, diagnosis, and management","volume":"386","author":"Bhangu","year":"2015","journal-title":"Lancet"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1016\/S0140-6736(84)91816-6","article-title":"Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration","volume":"1","author":"Marshall","year":"1984","journal-title":"Lancet"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1007\/s11894-017-0577-6","article-title":"The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors","volume":"19","author":"Minalyan","year":"2017","journal-title":"Curr. Gastroenterol. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1073\/pnas.0506655103","article-title":"Molecular analysis of the bacterial microbiota in the human stomach","volume":"103","author":"Bik","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e01361-14","DOI":"10.1128\/mBio.01361-14","article-title":"Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness","volume":"5","author":"Zaborin","year":"2014","journal-title":"mBio"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/j.1469-0691.2012.03867.x","article-title":"Changes in the intestinal microbiota from adulthood through to old age","volume":"18","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/cid\/cir797","article-title":"Metagenomic analysis of brain abscesses identifies specific bacterial associations","volume":"54","author":"Lonjon","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Abayasekara, L.M., Perera, J., Chandrasekharan, V., Gnanam, V.S., Udunuwara, N.A., Liyanage, D.S., Bulathsinhala, N.E., Adikary, S., Aluthmuhandiram, J.V.S., and Thanaseelan, C.S. (2017). Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: A comparative study. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-017-2727-8"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3590","DOI":"10.1128\/iai.62.8.3590-3593.1994","article-title":"Structure-function relationships for polysaccharide-induced intra-abdominal abscesses","volume":"62","author":"Tzianabos","year":"1994","journal-title":"Infect. Immun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2574","DOI":"10.1111\/j.1462-2920.2009.01982.x","article-title":"Towards the human intestinal microbiota phylogenetic core","volume":"11","author":"Tap","year":"2009","journal-title":"Environ. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"D443","DOI":"10.1093\/nar\/gkn656","article-title":"ARDB\u2014Antibiotic Resistance Genes Database","volume":"37","author":"Liu","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Rowe, W., Baker, K.S., Verner-Jeffreys, D., Baker-Austin, C., Ryan, J.J., Maskell, D., and Pearce, G. (2015). Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0133492"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/j.tim.2017.11.002","article-title":"Human Gut Microbiome: Function Matters","volume":"26","author":"Wilmes","year":"2018","journal-title":"Trends Microbiol."}],"container-title":["Journal of Clinical Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2077-0383\/7\/10\/346\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:25:19Z","timestamp":1760196319000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2077-0383\/7\/10\/346"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,12]]},"references-count":49,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2018,10]]}},"alternative-id":["jcm7100346"],"URL":"https:\/\/doi.org\/10.3390\/jcm7100346","relation":{},"ISSN":["2077-0383"],"issn-type":[{"value":"2077-0383","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,12]]}}}