Email this article Specific features of the enteric microbiota composition in patients with alcoholic liver cirrhosis
- Authors: Shalikiani NV1, Bakulin IG1, Dubinkina VB2, Ishchenko DS3,4, Alexeev DG3,4, Tyakht AV3,4, Pavlenko AV5,4, Ilyina EN6, Kostryukova ES2, Taraskina AE6, Skorodumova LO6, Maev IV7, Govorun VM3,4
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Affiliations:
- «Московский клинический научно-практический центр» Департамента здравоохранения города Москвы
- «Московский физико-технический институт»
- «Московский физико-технический институт», Долгопрудныйя
- «НИИ физико-химической медицины» ФМБА России, Москва
- «Московский физико-технический институт», Долгопрудный
- «НИИ физико-химической медицины» ФМБА России
- «Московский государственный медико-стоматологический университет им. А.И. Евдокимова» Минздрава России
- Issue: Vol 87, No 12 (2015)
- Pages: 59-65
- Section: Editorial
- URL: https://journal-vniispk.ru/0040-3660/article/view/31877
- ID: 31877
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Abstract
Aim. To establish the specific features of the taxonomic and functional composition of the enteric microbiota in patients with alcoholic liver cirrhosis (LC). Subjects and methods. Metagenomic analysis was used to study the taxonomic composition and functional potential of the enteric microbiota in 20 patients with alcoholic LC. Total DNA was isolated from the patients’ fecal samples; thereafter full genome sequencing was carried out. The metagenomic analysis yielded the results of the relative taxonomic and functional abundance of microbial species in the test samples. These were comparatively analyzed with the previously published metagenomic datasets of healthy population cohorts in the Russian Federation, as well as in Denmark, China, and the USA. Results. In the majority of patients, the dominant part of the intestinal community represented bacterial species constituting the normal human intestinal flora. At the same time, abnormal gut microbiota composition, which was suggestive of marked dysbacteriosis, was identified in a number of patients. In addition, pooled analysis of the data could identify a number of species with a statistically significantly increase and decrease in the relative abundance as compared to the control groups. Thus, the enteric microbiota of the patients with alcoholic LC showed a high proportion of bacteria characteristic of the oral cavity. Analysis of the pooled metabolic potential of the microbiota in these patients demonstrated the higher abundance of enzyme genes involved in alcohol metabolism. Conclusion. In the patients with alcoholic LC, the microbiota composition changes identified in individual bacterial species may be associated with gastrointestinal comorbidities, such as chronic erosive gastritis, chronic pancreatitis, and gastric ulcer. The alterations occurring in alcoholic cirrhosis promote the penetration and generation of oral cavity-specific microorganisms in the human intestine. This may a potential biomarker for the diagnosis of liver diseases. The bacterial enzyme genes involved in alcohol metabolism have an increased abundance in patients with alcoholic LC and healthy volunteers from the Russian Federation.
About the authors
N V Shalikiani
«Московский клинический научно-практический центр» Департамента здравоохранения города МосквыМосква, Россия
I G Bakulin
«Московский клинический научно-практический центр» Департамента здравоохранения города МосквыМосква, Россия
V B Dubinkina
«Московский физико-технический институт»Долгопрудный, Россия
D S Ishchenko
«Московский физико-технический институт», Долгопрудныйя; «НИИ физико-химической медицины» ФМБА России, Москва
D G Alexeev
«Московский физико-технический институт», Долгопрудныйя; «НИИ физико-химической медицины» ФМБА России, Москва
A V Tyakht
«Московский физико-технический институт», Долгопрудныйя; «НИИ физико-химической медицины» ФМБА России, Москва
A V Pavlenko
«Московский физико-технический институт», Долгопрудный; «НИИ физико-химической медицины» ФМБА России, Москва
E N Ilyina
«НИИ физико-химической медицины» ФМБА РоссииМосква, Россия
E S Kostryukova
«Московский физико-технический институт»Долгопрудный, Россия
A E Taraskina
«НИИ физико-химической медицины» ФМБА РоссииМосква, Россия
L O Skorodumova
«НИИ физико-химической медицины» ФМБА РоссииМосква, Россия
I V Maev
«Московский государственный медико-стоматологический университет им. А.И. Евдокимова» Минздрава РоссииМосква, Россия
V M Govorun
«Московский физико-технический институт», Долгопрудныйя; «НИИ физико-химической медицины» ФМБА России, Москва
References
- World Health Organization et al. Global status report on alcohol and health-2014. World Health Organization; 2014.
- Gramenzi A, Caputo F, Biselli M et al. Review article: alcoholic liver disease — pathophysiological aspects and risk factors. Alimentary Pharmacology and Therapeutics. 2006;24(8):1151-1161. doi: 10.1111/j.1365-2036.2006.03110.x.
- Atkinson K, Rao R. Role of protein tyrosine phosphorylation in acetaldehyde-induced disruption of epithelial tight junctions. Am J Physiol Gastrointest Liver Physiol. 2001;280:1280-1288.
- Bull-Otterson L, Feng W, Kirpich I et al. Metagenomic Analyses of Alcohol Induced Pathogenic Alterations in the Intestinal Microbiome and the Effect of Lactobacillus rhamnosus GG Treatment. PLoSONE. 2013;8(1):e53028. doi: 10.1371/journal.pone.0053028.
- Bajaj J, Heuman D, Hylemon P et al. Altered profile of human gut microbiome is associated with cirrhosis and its complications. Journal of Hepatology. 2014;60(5):940-947. doi: 10.1016/j.jhep.2013.12.019.
- Chen Y, Yang F, Lu H et al. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology. 2011;54(2):562-572. doi: 10.1002/hep.24423.
- Mutlu E, Gillevet P, Rangwala H et al. Colonic microbiome is altered in alcoholism. AJP: Gastrointestinal and Liver Physiology. 2012;302(9):G966-G978. doi: 10.1152/ajpgi.00380.2011.
- Liu Q, Duan Z, Ha D, Bengmark S, Kurtovic J, Riordan S. Synbiotic modulation of gut flora: Effect on minimal hepatic encephalopathy in patients with cirrhosis. Hepatology. 2004;39(5):1441-1449. doi: 10.1002/hep.20194.
- Leclercq S, Matamoros S, Cani P et al. Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity. Proceedings of the National Academy of Sciences. 2014;111(42):E4485-E4493. doi: 10.1073/pnas.1415174111.
- Qin N, Yang F, Li A et al. Alterations of the human gut microbiome in liver cirrhosis. Nature. 2014;513(7516):59-64. doi: 10.1038/nature13568.
- Miller TL, Wolin MJ. Fermentations by saccharolytic intestinal bacteria. The American Journal of Clinical Nutrition. 1979;32(1):164-172.
- Nosova T. Acetaldehyde production and metabolism by human indigenous and probiotic lactobacillus and bifidobacterium strains. Alcohol and Alcoholism. 2000;35(6):561-568. doi: 10.1093/alcalc/35.6.561.
- Tyakht A, Popenko A, Belenikin M, Altukhov I, Pavlenko A, Kostryukova E, Selezneva O, Larin A, Karpova I, Alexeev D. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. Source Code Biol Med. 2012;7(1):13. doi: 10.1186/1751—0473-7-13.
- Tyakht A, Kostryukova E, Popenko A, Belenikin M, Pavlenko A, Larin A, Karpova I, Selezneva O, Semashko T, Ospanova E, Babenko V, Maev I, Cheremushkin S, Kucheryavyy Y, Shcherbakov P, Grinevich V, Efimov O, Sas E, Abdulkhakov R, Abdulkhakov S, Lyalyukova E, Livzan M, Vlassov V, Sagdeev R,Tsukanov V, Osipenko M, Kozlova I, Tkachev A, Sergienko V, Alexeev D, Govorun V. Human gut microbiota community structures in urban and rural populations in Russia. Nature Communications. 2013;4:2469. doi: 10.1038/ncomms3469.
- Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285): 59-65. doi: 10.1038/nature08821.
- Huttenhower C, Gevers D, Knight R et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-214. doi: 10.1038/nature11234.
- Qin J, Li Y, Cai Z et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55-60. doi: 10.1038/nature11450.
- Kanehisa M. The KEGG database. Silico simulation of biological processes. 2002;247:91-103.
- Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. 2012;9(8):811-814. doi: 10.1038/nmeth.2066.
- Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25.
- Кострюкова Е.С., Карпова И.Ю., Ларин А.К., Попенко А.С., Тяхт А.В., Ильина Е.Н. Вариабельность относительного содержания геномной ДНК человека при метагеномном анализе микробиоты кишечника. Биомедицинская химия. 2014;60(6):695-701. doi: 10.18097/pbmc20146006695.
- Gevers D, Kugathasan S, Denson L et al. The Treatment-Naive Microbiome in New-Onset Crohn’s Disease. Cell Host & Microbe. 2014;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.
- Taur Y, Xavier J, Lipuma L et al. Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation. Clinical Infectious Diseases. 2012;55(7):905-914. doi: 10.1093/cid/cis580.
- Ferrier L, Bérard F, Debrauwer L et al. Impairment of the Intestinal Barrier by Ethanol Involves Enteric Microflora and Mast Cell Activation in Rodents. The American Journal of Pathology. 2006;168(4):1148-1154. doi: 10.2353/ajpath.2006.050617.
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