Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning

Saboo, Krishnakant; Petrakov, Nikita V.; Shamsaddini, Amirhossein; Fagan, Andrew; Gavis, Edith A.; Sikaroodi, Masoumeh; McGeorge, Sara; Gillevet, Patrick M.; Iyer, Ravishankar K.; Bajaj, Jasmohan S.

doi:10.1016/j.jhep.2021.11.011

Title: Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning

Journal Article · 28 February 2022 · Journal of Hepatology

DOI: https://doi.org/10.1016/j.jhep.2021.11.011 · OSTI ID:1845347

;

; Fagan, Andrew; Gavis, Edith A.; Sikaroodi, Masoumeh;

; Gillevet, Patrick M.; Iyer, Ravishankar K.;

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Sponsoring Organization:: USDOE Office of Electricity (OE), Advanced Grid Research & Development. Power Systems Engineering Research

OSTI ID:: 1845347

Journal Information:: Journal of Hepatology, Journal Name: Journal of Hepatology Journal Issue: 3 Vol. 76; ISSN 0168-8278

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (23)

Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy: HEPATOLOGY, Vol. XX, No. X, 2015 Bajaj, Jasmohan S.; Betrapally, Naga S.; Hylemon, Phillip B. Hepatology, Vol. 62, Issue 4 https://doi.org/10.1002/hep.27819	journal	May 2015
The Use of Rifaximin in Patients With Cirrhosis Caraceni, Paolo; Vargas, Victor; Solà, Elsa Hepatology, Vol. 74, Issue 3 https://doi.org/10.1002/hep.31708	journal	June 2021
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians Allaband, Celeste; McDonald, Daniel; Vázquez-Baeza, Yoshiki Clinical Gastroenterology and Hepatology, Vol. 17, Issue 2 https://doi.org/10.1016/j.cgh.2018.09.017	journal	January 2019
Alterations in Skin Microbiomes of Patients With Cirrhosis Bajaj, Jasmohan S.; Fagan, Andrew; Sikaroodi, Masoumeh Clinical Gastroenterology and Hepatology, Vol. 17, Issue 12 https://doi.org/10.1016/j.cgh.2019.03.028	journal	November 2019
Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome Sung, Chang Mu; Lin, Yu-fei; Chen, Kuan-Fu Cellular and Molecular Gastroenterology and Hepatology, Vol. 8, Issue 2 https://doi.org/10.1016/j.jcmgh.2019.04.008	journal	January 2019
Gut Microbiota as Biosensors in Patients With Cirrhosis Bajaj, Jasmohan S. Cellular and Molecular Gastroenterology and Hepatology, Vol. 8, Issue 2 https://doi.org/10.1016/j.jcmgh.2019.04.016	journal	January 2019
Altered profile of human gut microbiome is associated with cirrhosis and its complications Bajaj, Jasmohan S.; Heuman, Douglas M.; Hylemon, Phillip B. Journal of Hepatology, Vol. 60, Issue 5 https://doi.org/10.1016/j.jhep.2013.12.019	journal	May 2014
Alterations of the human gut microbiome in liver cirrhosis Qin, Nan; Yang, Fengling; Li, Ang Nature, Vol. 513, Issue 7516 https://doi.org/10.1038/nature13568	journal	July 2014
Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis Bajaj, Jasmohan S.; Acharya, Chathur; Fagan, Andrew American Journal of Gastroenterology, Vol. 113, Issue 8 https://doi.org/10.1038/s41395-018-0085-9	journal	January 2018
Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure Trebicka, Jonel; Bork, Peer; Krag, Aleksander Nature Reviews Gastroenterology & Hepatology, Vol. 18, Issue 3 https://doi.org/10.1038/s41575-020-00376-3	journal	November 2020
Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis Horvath, Angela; Rainer, Florian; Bashir, Mina Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-48352-5	journal	August 2019
Chronic Liver Diseases and the Microbiome—Translating Our Knowledge of Gut Microbiota to Management of Chronic Liver Disease Acharya, Chathur; Bajaj, Jasmohan S. Gastroenterology, Vol. 160, Issue 2 https://doi.org/10.1053/j.gastro.2020.10.056	journal	January 2021
Is treating the gut microbiome the key to achieving better outcomes in cirrhosis? Hatton, Grace; Shawcross, Debbie L. Expert Review of Gastroenterology & Hepatology, Vol. 13, Issue 1 https://doi.org/10.1080/17474124.2019.1543587	journal	October 2018
Targeting the gut-liver-immune axis to treat cirrhosis Tranah, Thomas Henry; Edwards, Lindsey A.; Schnabl, Bernd Gut, Vol. 70, Issue 5 https://doi.org/10.1136/gutjnl-2020-320786	journal	October 2020
Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation Bajaj, Jasmohan S.; Hylemon, Phillip B.; Ridlon, Jason M. American Journal of Physiology-Gastrointestinal and Liver Physiology, Vol. 303, Issue 6 https://doi.org/10.1152/ajpgi.00152.2012	journal	September 2012
Paneth cell defects in Crohn’s disease patients promote dysbiosis Liu, Ta-Chiang; Gurram, Bhaskar; Baldridge, Megan T. JCI Insight, Vol. 1, Issue 8 https://doi.org/10.1172/jci.insight.86907	journal	June 2016
Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics Tuomisto, Sari; Pessi, Tanja; Collin, Pekka BMC Gastroenterology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-230X-14-40	journal	February 2014
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples Segata, Nicola; Haake, Susan; Mannon, Peter Genome Biology, Vol. 13, Issue 6 https://doi.org/10.1186/gb-2012-13-6-r42	journal	January 2012
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox Wirbel, Jakob; Zych, Konrad; Essex, Morgan Genome Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s13059-021-02306-1	journal	March 2021
BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline Shamsaddini, Amirhossein; Dadkhah, Kimia; Gillevet, Patrick M. PLOS ONE, Vol. 15, Issue 6 https://doi.org/10.1371/journal.pone.0234860	journal	June 2020
Diversity of the autochthonous colonic microbiota Nava, Gerardo M.; Stappenbeck, Thaddeus S. Gut Microbes, Vol. 2, Issue 2 https://doi.org/10.4161/gmic.2.2.15416	journal	March 2011
Extensive transmission of microbes along the gastrointestinal tract Schmidt, Thomas SB; Hayward, Matthew R.; Coelho, Luis P. eLife, Vol. 8 https://doi.org/10.7554/eLife.42693	journal	February 2019

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