{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T22:19:20Z","timestamp":1780352360422,"version":"3.54.1"},"reference-count":42,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T00:00:00Z","timestamp":1753833600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Moscow Center for Innovative Technologies in Healthcare"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Currently, due to the complexity of obtaining samples, specific features of laboratory processing and analysis of the results, there is a lack of data on the microbial signature of the small intestine in healthy and diseased states of the upper gastrointestinal tract. Objective: To investigate the characteristics of the small intestinal microbiome in acute pancreatitis of varying severity and to identify correlations with clinical factors. Methods: This study included 30 patients with acute pancreatitis of varying severity treated between 1 January 2019 and 31 December 2021. The composition of the microbiota was analyzed by metagenomic sequencing of the 16S rRNA gene from jejunal samples. Results: The mortality rate in the study group was 23.3%. The small intestinal microbiome was dominated by Streptococcus (median relative abundance 19.2%, interquartile range 6.4\u201335.1%), Veillonella (3.4%; 0.6\u20137%), Granulicatella (2.7%; 0.6\u20135%), Fusobacterium (2.2%; 0.3\u20135.9%), Prevotella (1.5%; 0.3\u20138%), Haemophilus (0.9%; 0.2\u201310%), Gemella (0.8%; 0.2\u20134.3%), and Lactobacillus (0.2%; 0.1\u20130.9%). More severe disease was associated with decreased abundance of Neisseria mucosa, Parvimonas micra, and Megasphaera micronuciformis. In contrast, the relative abundance of the genera Streptococcus (species S. rubneri\/parasanguinis\/australis), Actinomyces, and several genera within the family Enterobacteriaceae was higher in these patients. Conclusions: The state of the microbiota has important prognostic value and correlates with the duration from the onset of the pain syndrome to the time of receiving qualified care in the hospital.<\/jats:p>","DOI":"10.3390\/diagnostics15151911","type":"journal-article","created":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:00:41Z","timestamp":1753884041000},"page":"1911","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Microbiome of the Proximal Small Intestine in Patients with Acute Pancreatitis"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0170-7775","authenticated-orcid":false,"given":"Vladimir V.","family":"Kiselev","sequence":"first","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanislav I.","family":"Koshechkin","sequence":"additional","affiliation":[{"name":"Nobias Technologies LLC, 14B Berezovaya Alleya St., Bldg. 2, Prem. 2\/4, 127273 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey V.","family":"Kurenkov","sequence":"additional","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera E.","family":"Odintsova","sequence":"additional","affiliation":[{"name":"Nobias Technologies LLC, 14B Berezovaya Alleya St., Bldg. 2, Prem. 2\/4, 127273 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria S.","family":"Zhigalova","sequence":"additional","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7358-2537","authenticated-orcid":false,"given":"Alekxandr V.","family":"Tyakht","sequence":"additional","affiliation":[{"name":"FSBIS Institute of Gene Biology, Russian Academy of Sciences, 34\/5 Vavilova St., 119334 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey S.","family":"Petrikov","sequence":"additional","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"},{"name":"Scientific and Educational Institute of Continuing Professional Education Named After N.D. Yushchuk, Federal State Budgetary Educational Institution of Higher Education, \u201cRussian University of Medicine\u201d of the Ministry of Health of the Russian Federation, 4 Dolgorukovskaya St., 127006 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr A.","family":"Yartsev","sequence":"additional","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5731-3310","authenticated-orcid":false,"given":"Ilya V.","family":"Dmitriev","sequence":"additional","affiliation":[{"name":"Sklifosovsky Research Institute for Emergency Medicine, 3 Bolshaya Sukharevskaya Square, 129090 Moscow, Russia"},{"name":"Federal State Autonomous Educational Institution of Higher Education, Pirogov Russian National Research Medical University, 1\/6 Ostrovitianova St., 117513 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1136\/flgastro-2018-101102","article-title":"Practical guide to the management of acute pancreatitis","volume":"10","author":"Goodchild","year":"2019","journal-title":"Frontline Gastroenterol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1097\/JP9.0000000000000168","article-title":"Acute pancreatitis: Pathogenesis and emerging therapies","volume":"7","author":"Zaman","year":"2024","journal-title":"J Pancreatol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/s41575-018-0087-5","article-title":"Global epidemiology and holistic prevention of pancreatitis","volume":"16","author":"Petrov","year":"2019","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1053\/j.gastro.2021.09.043","article-title":"Global Incidence of Acute Pancreatitis Is Increasing Over Time: A Systematic Review and Meta-Analysis","volume":"162","author":"Iannuzzi","year":"2022","journal-title":"Gastroenterology"},{"key":"ref_5","unstructured":"Popova, T.S., Tamazashvili, T.S., and Shestopalov, A.E. (1991). Syndrome of Intestinal Insufficiency in Surgery, Medicine."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1159\/000067684","article-title":"International Association of Pancreatology. IAP Guidelines for the Surgical Management of Acute Pancreatitis","volume":"2","author":"Uhl","year":"2002","journal-title":"Pancreatology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1111\/j.1572-0241.2006.00856.x","article-title":"Practice Parameters Committee of the American College of Gastroenterology. Practice guidelines in acute pancreatitis","volume":"101","author":"Banks","year":"2006","journal-title":"Am. J. Gastroenterol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1097\/00003246-199510000-00007","article-title":"Multiple organ dysfunction score: A reliable descriptor of a complex clinical outcome","volume":"23","author":"Marshall","year":"1995","journal-title":"Crit. Care Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1097\/MPA.0000000000000355","article-title":"Dysbiosis of Intestinal Microbiota Associated with Inflammation Involved in the Progression of Acute Pancreatitis","volume":"44","author":"Tan","year":"2015","journal-title":"Pancreas"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cmet.2017.02.007","article-title":"Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity","volume":"25","author":"Ahuja","year":"2017","journal-title":"Cell Metab."},{"key":"ref_11","first-page":"81","article-title":"Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers","volume":"31","author":"Zhang","year":"2018","journal-title":"Biomed. Environ. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1007\/s00535-018-1529-0","article-title":"Gut microbiota dysbiosis worsens the severity of acute pancreatitis in patients and mice","volume":"54","author":"Zhu","year":"2019","journal-title":"J. Gastroenterol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.dld.2023.10.011","article-title":"Acute pancreatitis is associated with gut dysbiosis in children","volume":"56","author":"Dike","year":"2024","journal-title":"Dig. Liver Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.pan.2014.09.001","article-title":"Spectrum of microorganisms in infected walled-off pancreatic necrosis\u2013impact on organ failure and mortality","volume":"14","author":"Schmidt","year":"2014","journal-title":"Pancreatology"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7376","DOI":"10.12659\/MSM.916808","article-title":"Association Between Gut Bacterial Diversity and Mortality in Septic Shock Patients: A Cohort Study","volume":"25","author":"Yin","year":"2019","journal-title":"Med. Sci. Monit."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2187","DOI":"10.3748\/wjg.v26.i18.2187","article-title":"Role of gut microbiota on intestinal barrier function in acute pancreatitis","volume":"26","author":"Li","year":"2020","journal-title":"World J. Gastroenterol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"210","DOI":"10.23934\/2223-9022-2023-12-2-210-216","article-title":"Restoration of intestinal propulsion in patients with severe acute pancreatitis in the conditions of the resuscitation and intensive care unit","volume":"12","author":"Kiselev","year":"2023","journal-title":"Russ. Sklifosovsky J. Emerg. Med. Care"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"Arumugam","year":"2011","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1128\/AEM.01403-14","article-title":"DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies","volume":"80","author":"Hugerth","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1134\/S0026261719060110","article-title":"Analysis of 16S rRNA primer systems for profiling of thermophilic microbial communities","volume":"88","author":"Merkel","year":"2019","journal-title":"Microbiology"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5019","DOI":"10.3748\/wjg.v27.i30.5019","article-title":"Gut microbiome in acute pancreatitis: A review based on current literature","volume":"27","author":"Patel","year":"2021","journal-title":"World J. Gastroenterol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.jcmgh.2019.07.006","article-title":"The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions","volume":"9","author":"Kastl","year":"2020","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e0150721","DOI":"10.1128\/msystems.01507-21","article-title":"Paneth Cells Protect against Acute Pancreatitis via Modulating Gut Microbiota Dysbiosis","volume":"7","author":"Fu","year":"2022","journal-title":"mSystems"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1152\/physrev.1965.45.3.555","article-title":"Membrane (Contact) Digestion","volume":"45","author":"Ugolev","year":"1965","journal-title":"Physiol. Rev."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.pan.2015.01.006","article-title":"Classifying the severity of acute pancreatitis: Towards a way forward","volume":"15","author":"Windsor","year":"2015","journal-title":"Pancreatology"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"(2013). Working Group IAP\/APA Acute Pancreatitis Guidelines. IAP\/APA evidence-based guidelines for the management of acute pancreatitis. Pancreatology, 13, e1\u2013e15.","DOI":"10.1016\/j.pan.2013.07.063"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"World Medical Association (2013). World Medical Association Declaration of Helsinki: Ethical principles for medical research involving human subjects. JAMA, 310, 2191\u20132194.","DOI":"10.1001\/jama.2013.281053"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"132","DOI":"10.23934\/2223-9022-2025-14-1-132-140","article-title":"Microbiome of the Initial Small Intestine in Patients with Severe Acute Pancreatitis: A Pilot Study","volume":"14","author":"Kiselyov","year":"2025","journal-title":"Russ. Sklifosovsky J. Emerg. Med. Care"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Fadrosh, D.W., Ma, B., Gajer, P., Sengamalay, N., Ott, S., Brotman, R.M., and Ravel, J. (2014). An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome, 2.","DOI":"10.1186\/2049-2618-2-6"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_31","unstructured":"Horton, N.J., and Kleinman, K. (2020). Using R and RStudio for Data Management, Statistical Analysis, and Graphics, Chapman & Hall\/CRC. [2nd ed.]."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e0015522","DOI":"10.1128\/msystems.00155-22","article-title":"Approximation of a Microbiome Composition Shift by a Change in a Single Balance Between Two Groups of Taxa","volume":"7","author":"Odintsova","year":"2022","journal-title":"mSystems"},{"key":"ref_33","unstructured":"Aitchison, J. (2011). The Statistical Analysis of Compositional Data, Springer."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Gloor, G.B., Macklaim, J.M., Pawlowsky-Glahn, V., and Egozcue, J.J. (2017). Microbiome Datasets Are Compositional: And This Is Not Optional. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.02224"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.chemolab.2015.02.019","article-title":"zCompositions\u2014R package for multivariate imputation of left-censored data under a compositional approach","volume":"143","year":"2015","journal-title":"Chemom. Intell. Lab. Syst."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1177\/15353702231187645","article-title":"Oral microbiota in human health and disease: A perspective","volume":"248","author":"Santacroce","year":"2023","journal-title":"Exp. Biol. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/s41575-019-0242-7","article-title":"Microbiota in pancreatic health and disease: The next frontier in microbiome research","volume":"17","author":"Thomas","year":"2020","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/s41401-020-00532-0","article-title":"Gut microbiota in pancreatic diseases: Possible new therapeutic strategies","volume":"42","author":"Pan","year":"2021","journal-title":"Acta Pharmacol. Sin."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1016\/j.tim.2024.02.013","article-title":"Small intestinal microbiota: From taxonomic composition to metabolism","volume":"32","author":"Yersin","year":"2024","journal-title":"Trends Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Zou, M., Yang, Z., Fan, Y., Gong, L., Han, Z., Ji, L., Hu, X., and Wu, D. (2022). Gut microbiota on admission as predictive biomarker for acute necrotizing pancreatitis. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.988326"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pan.2020.12.013","article-title":"Microbiome changes associated with acute and chronic pancreatitis: A systematic review","volume":"21","author":"Brubaker","year":"2021","journal-title":"Pancreatology"}],"container-title":["Diagnostics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-4418\/15\/15\/1911\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:19:06Z","timestamp":1760033946000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-4418\/15\/15\/1911"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,30]]},"references-count":42,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["diagnostics15151911"],"URL":"https:\/\/doi.org\/10.3390\/diagnostics15151911","relation":{},"ISSN":["2075-4418"],"issn-type":[{"value":"2075-4418","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,30]]}}}