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Peña Rodríguez M, Fagan A, Sikaroodi M, Gillevet PM, Bajaj JS. Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis. Clin Transl Gastroenterol 2024; 15:e00659. [PMID: 37937851 PMCID: PMC10887442 DOI: 10.14309/ctg.0000000000000659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
INTRODUCTION Proton pump inhibitors (PPIs) modulate the progression of cirrhosis to hepatic encephalopathy (HE) and can affect the bacterial microbiome. However, the impact of PPI on the virome in cirrhosis using viral-like particle (VLP) analysis is unclear. METHODS We determined the VLP in the stool microbiome in patients with cirrhosis cross-sectionally (ascites, HE, and PPI use analyzed) who were followed up for 6-month hospitalizations and through 2 clinical trials of PPI withdrawal and initiation. RESULTS In a cross-sectional study, PPI users had greater ascites prevalence and 6-month hospitalizations, but VLP α diversity was similar. Among phages, PPI users had lower Autographviridae and higher Streptococcus phages and Herelleviridae than nonusers, whereas opposite trends were seen in ascites and HE. Trends of eukaryotic viruses (higher Adenoviridae and lower Virgaviridae/Smacoviridae) were similar for PPI, HE, and ascites. Twenty-one percent were hospitalized, mostly due to HE. α Diversity was similar in the hospitalized/nonhospitalized/not groups. Higher Gokushovirinae and lower crAssphages were related to hospitalizations such as HE-related cross-sectional VLP changes. As part of the clinical trial, PPIs were added and withdrawn in 2 different decompensated groups over 14 days. No changes in α diversity were observed. Withdrawal reduced crAssphages, and initiation reduced Gokushovirinae and Bacteroides phages. DISCUSSION In cirrhosis, PPI use has a gut microbial VLP phage signature that is different from that in HE and ascites, and VLP changes are linked with hospitalizations over 6 months, independent of clinical biomarkers. Eukaryotic viral patterns were consistent across PPI use, HE, and ascites, indicating a relationship with the progression of cirrhosis. PPIs alone showed modest VLP changes with withdrawal or initiation. Distinct phage and eukaryotic viral patterns are associated with the use of PPIs in cirrhosis.
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Affiliation(s)
| | - Andrew Fagan
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | | | - Jasmohan S. Bajaj
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
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Bajaj JS, Fagan A, Gavis EA, Mousel T, Gallagher ML, Puri P, Fuchs M, Davis BC, Hylemon PB, Zhou H, Ahluwalia V, Cadrain R, Sikaroodi M, Gillevet PM. The RIVET RCT: Rifamycin SV MMX improves muscle mass, physical function, and ammonia in cirrhosis and minimal encephalopathy. Hepatol Commun 2024; 8:e0384. [PMID: 38315140 PMCID: PMC10843468 DOI: 10.1097/hc9.0000000000000384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Minimal hepatic encephalopathy (MHE) negatively affects the prognosis of cirrhosis, but treatment is not standard. Rifamycin SV MMX (RiVM) is a nonabsorbable rifampin derivative with colonic action. METHODS In a phase 2 placebo-controlled, double-blind randomized clinical trial patients with MHE were randomized to RiVM or placebo for 30 days with a 7-day follow-up. The primary endpoint was a change in stool cirrhosis dysbiosis ratio. Gut-brain (cognition, stool/salivary microbiome, ammonia, brain magnetic resonance spectroscopy), inflammation (stool calprotectin/serum cytokines), patient-reported outcomes (sickness impact profile: total/physical/psychosocial, high = worse), and sarcopenia (handgrip, bioelectric impedance) were secondary. Between/within groups and delta (post-pre) comparisons were performed. RESULTS Thirty patients (15/group) were randomized and completed the study without safety concerns. While cirrhosis dysbiosis ratio was statistically similar on repeated measures ANOVA (95% CI: -0.70 to 3.5), ammonia significantly reduced (95% CI: 4.4-29.6) in RiVM with changes in stool microbial α/β-diversity. MHE status was unchanged but only serial dotting (which tests motor strength) improved in RiVM-assigned patients. Delta physical sickness impact profile (95% CI: 0.33 = 8.5), lean mass (95% CI: -3.3 to -0.9), and handgrip strength (95% CI: -8.1 to -1.0) improved in RiVM versus placebo. Stool short-chain fatty acids (propionate, acetate, and butyrate) increased post-RiVM. Serum, urine, and stool bile acid profile changed to nontoxic bile acids (higher hyocholate/ursodeoxycholate and lower deoxycholate/lithocholate) post-RiVM. Serum IL-1β and stool calprotectin decreased while brain magnetic resonance spectroscopy showed higher glutathione concentrations in RiVM. CONCLUSIONS RiVM is well tolerated in patients with MHE with changes in stool microbial composition and function, ammonia, inflammation, brain oxidative stress, and sarcopenia-related parameters without improvement in cognition. RiVM modulates the gut-brain axis and gut-muscle axis in cirrhosis.
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Affiliation(s)
- Jasmohan S. Bajaj
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Andrew Fagan
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Edith A. Gavis
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Travis Mousel
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Mary L. Gallagher
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Puneet Puri
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Michael Fuchs
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Brian C. Davis
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Vishwadeep Ahluwalia
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
- Center for Advanced Brain Imaging, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Robert Cadrain
- Collaborative Advanced Research Imaging Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Jinato T, Sikaroodi M, Fagan A, Sterling RK, Lee H, Puri P, Davis BC, Fuchs M, Gavis E, Gillevet PM, Bajaj JS. Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis. Gut Microbes 2023; 15:2288168. [PMID: 38010871 PMCID: PMC10730154 DOI: 10.1080/19490976.2023.2288168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.
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Affiliation(s)
- Thananya Jinato
- Microbiome Analysis Center, George Mason University, Manassas, VA, USA
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Richard K Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Hannah Lee
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Brian C Davis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | | | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
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Bajaj JS, Peña-Rodriguez M, La Reau A, Phillips W, Fuchs M, Davis BC, Sterling RK, Sikaroodi M, Fagan A, Shamsaddini A, Henseler Z, Ward T, Puri P, Lee H, Gillevet PM. Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis. Gut 2023; 72:759-771. [PMID: 36343978 PMCID: PMC9998342 DOI: 10.1136/gutjnl-2022-328403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE First decompensation development is a critical milestone that needs to be predicted. Transkingdom gut microbial interactions, including archaeal methanogens, may be important targets and predictors but a longitudinal approach is needed. DESIGN Cirrhosis outpatients who provided stool twice were included. Group 1: compensated, group 2: 1 decompensation (decomp), group 3: >1 decompensationwere followed and divided into those who remained stable or decompensated. Bacteria, viral and archaeal presence, α/β diversity and taxa changes over time adjusted for clinical variables were analysed. Correlation networks between kingdoms were analysed. RESULTS 157 outpatients (72 group 1, 33 group 2 and 52 group 3) were followed and 28%-47% developed outcomes. Baseline between those who remained stable/developed outcome: While no α/β diversity differences were seen, commensals were lower and pathobionts were higher in those who decompensated. After decompensation: those experiencing their first decompensation showed greater decrease in α/β-diversity, bacterial change (↑Lactobacillus spp, Streptococcus parasanguinis and ↓ beneficial Lachnospiraceae and Eubacterium hallii) and viral change (↑Siphoviridae, ↓ Myoviridae) versus those with further decompensation. Archaea: 19% had Methanobacter brevii, which was similar between/within groups. Correlation networks: Baseline archaeal-viral-bacterial networks were denser and more homogeneous in those who decompensated versus the rest. Archaea-bacterial correlations collapsed post first decompensation. Lactobacillus phage Lc Nu and C2-like viruses were negatively linked with beneficial bacteria. CONCLUSION In this longitudinal study of cirrhosis outpatients, the greatest transkingdom gut microbial changes were seen in those reaching the first decompensation, compared with subsequent decompensating events. A transkingdom approach may refine prediction and provide therapeutic targets to prevent cirrhosis progression.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | | | | | | | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Brian C Davis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Andrew Fagan
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | | | | | - Tonya Ward
- Diversigen Inc, New Brighton, Minnesota, USA
| | - Puneet Puri
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Bajaj JS, Reddy KR, Tandon P, Garcia-Tsao G, Kamath PS, O'Leary JG, Wong F, Lai J, Vargas H, Thuluvath PJ, Subramanian RM, Pena-Rodriguez M, Sikaroodi M, Thacker LR, Gillevet PM. Association of serum metabolites and gut microbiota at hospital admission with nosocomial infection development in patients with cirrhosis. Liver Transpl 2022; 28:1831-1840. [PMID: 36017804 DOI: 10.1002/lt.26552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/02/2022] [Accepted: 07/18/2022] [Indexed: 02/07/2023]
Abstract
Cirrhosis is complicated by a high rate of nosocomial infections (NIs), which result in poor outcomes and are challenging to predict using clinical variables alone. Our aim was to determine predictors of NI using admission serum metabolomics and gut microbiota in inpatients with cirrhosis. In this multicenter inpatient cirrhosis study, serum was collected on admission for liquid chromatography-mass spectrometry metabolomics, and a subset provided stool for 16SrRNA analysis. Hospital course, including NI development and death, were analyzed. Metabolomic analysis using analysis of covariance (ANCOVA) (demographics, Model for End-Stage Liver Disease [MELD] admission score, white blood count [WBC], rifaximin, and infection status adjusted) and random forest analyses for NI development were performed. Additional values of serum metabolites over clinical variables toward NI were evaluated using logistic regression. Stool microbiota and metabolomic correlations were compared in patients with and without NI development. A total of 602 patients (231 infection admissions) were included; 101 (17%) developed NIs, which resulted in worse inpatient outcomes, including intensive care unit transfer, organ failure, and death. A total of 127 patients also gave stool samples, and 20 of these patients developed NIs. The most common NIs were spontaneous bacterial peritonitis followed by urinary tract infection, Clostridioides difficile, and pneumonia. A total of 247 metabolites were significantly altered on ANCOVA. Higher MELD scores (odds ratio, 1.05; p < 0.0001), admission infection (odds ratio, 3.54; p < 0.0001), and admission WBC (odds ratio, 1.05; p = 0.04) predicted NI (area under the curve, 0.74), which increased to 0.77 (p = 0.05) with lower 1-linolenoyl-glycerolphosphocholine (GPC) and 1-stearoyl-GPC and higher N-acetyltryptophan and N-acetyl isoputreanine. Commensal microbiota were lower and pathobionts were higher in those who developed NIs. Microbial-metabolite correlation networks were complex and dense in patients with NIs, especially sub-networks centered on Ruminococcaceae and Pseudomonadaceae. NIs are common and associated with poor outcomes in cirrhosis. Admission gut microbiota in patients with NIs showed higher pathobionts and lower commensal microbiota. Microbial-metabolomic correlations were more complex, dense, and homogeneous among those who developed NIs, indicating greater linkage strength. Serum metabolites and gut microbiota on admission are associated with NI development in cirrhosis.
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Affiliation(s)
- Jasmohan S Bajaj
- Department of Medicine, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - K Rajender Reddy
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Puneeta Tandon
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | | - Patrick S Kamath
- Department of Medicine, Mayo Clinic School of Medicine, Rochester, Minnesota, USA
| | - Jacqueline G O'Leary
- Department of Medicine, Dallas Veterans Affairs Medical Center, Dallas, Texas, USA
| | - Florence Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Lai
- Department of Medicine, University of California, San Francisco, California, USA
| | - Hugo Vargas
- Department of Medicine, Mayo Clinic, Phoenix, Arizona, USA
| | - Paul J Thuluvath
- Department of Medicine, Mercy Medical Center, Baltimore, Maryland, USA
| | - Ram M Subramanian
- Department of Medicine, Emory University Medical Center, Atlanta, Georgia, USA
| | | | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Leroy R Thacker
- Department of Medicine, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Bajaj JS, Rodriguez MP, Fagan A, McGeorge S, Sterling RK, Lee H, Luketic V, Fuchs M, Davis BC, Sikaroodi M, Gillevet PM. Impact of bacterial infections and spontaneous bacterial peritonitis prophylaxis on phage-bacterial dynamics in cirrhosis. Hepatology 2022; 76:1723-1734. [PMID: 35561076 DOI: 10.1002/hep.32571] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/24/2022] [Accepted: 05/06/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Gut microbiota, including bacteria and phages, are altered in cirrhosis, but their role during infections and spontaneous bacterial peritonitis (SBP) prophylaxis is unclear. Our aim was determine metagenomic changes in gut bacteria; phages and their linkages centered around Gram-negative and Gram-positive pathobionts in patients with cirrhosis with/without infections or SBP prophylaxis. APPROACH AND RESULTS We included uninfected (n = 231) and infected (n = 30, SBP n = 19 and urinary tract infection n = 11 before antibiotics) patients who gave stool for bacterial and phage metagenomics. We matched uninfected to infected patients 1:1 on a model for end-stage liver disease (MELD). We also analyzed subgroups of patients with ascites matched on an MELD (n = 73) to patients on SBP prophylaxis (n = 7) and then to SBP infection. Phage and bacterial taxa differences (DESeq2) and correlation networks centered around Escherichia coli and Enterococcus faecium were analyzed. Infections were mostly due to Enterobacteriaceae and Enterococcus spp. On metagenomics, higher fold changes of Enterobacteriaceae members, Enterococcus and Streptococcus spp., and Escherichia phages were seen in infected patients. Correlation networks showed more complex bacteria-phage linkages in infected patients compared with uninfected ones overall and centered around E. coli and E. faecium. SBP prophylaxis induced higher Gram-positive bacteria. In SBP, Enterococcus and Escherichia were higher versus ascites. Correlation networks around E. coli were complex in ascites but sparse with SBP prophylaxis, whereas the reverse was seen with E. faecium. Lytic phages and those associated with antibiotic resistance were correlated with E. faecium. CONCLUSION In cirrhosis, there are significant changes in phage-bacterial linkages in infected patients and those on SBP prophylaxis compared to the remaining patients. SBP prophylaxis enriches complexity of E. faecium-centered but induces a collapse in E. coli-centered phage-bacterial correlations.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Sara McGeorge
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Richard K Sterling
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Hannah Lee
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Velimir Luketic
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
| | - Brian C Davis
- Division of Gastroenterology, Hepatology and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare System Medical CenterVirginiaUSA
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Zawada SG, von Fricken ME, Weppelmann TA, Sikaroodi M, Gillevet PM. Genetic variation of Borreliella burgdorferi in Fairfax County, Virginia, targeting the OspC gene in white-footed mice. Front Microbiol 2022; 13:998365. [DOI: 10.3389/fmicb.2022.998365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/20/2022] [Indexed: 11/20/2022] Open
Abstract
Outer surface protein C (OspC) is a commonly used marker in population studies of Borreliella to differentiate types and establish evolution over time. Investigating the ospC genetic types of Borreliella burgdorferi across multiple organ tissues of white-footed mice has the potential to contribute to our understanding of Lyme disease and the wide spectrum of clinical presentation associated with infection. In this study, five unique tissue types were sampled from 90 mice and screened for B. burgdorferi infections. This initial screening revealed a 63% overall B. burgdorferi infection rate in the mice collected (57/90). A total of 163 tissues (30.4%) tested positive for B. burgdorferi infections and when mapped to Borreliella types, 143,894 of the initial 322,480 reads mapped to 10 of the reference sequences in the ospC strain library constructed for this study at a 97% MOI. Two tissue types, the ear and the tongue, each accounted for 90% of the observed Borreliella sequence diversity in the tissue samples surveyed. The largest amount of variation was observed in an individual ear tissue sample with six ospC sequence types, which is equivalent to 60% of the observed variation seen across all tested specimens, with statistically significant associations observed between tissue type and detected Borreliella. There is strong evidence for genetic variability in B. burgdorferi within local white-footed mouse populations and even within individual hosts by tissue type. These findings may shed light on drivers of infection sequalae in specific tissues in humans and highlights the need for expanded surveillance on the epigenetics of B. burgdorferi across reservoirs, ticks, and infected patients.
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Wolstenholme JT, Saunders JM, Smith M, Kang JD, Hylemon PB, González-Maeso J, Fagan A, Zhao D, Sikaroodi M, Herzog J, Shamsaddini A, Peña-Rodríguez M, Su L, Tai YL, Zheng J, Cheng PC, Sartor RB, Gillevet PM, Zhou H, Bajaj JS. Reduced alcohol preference and intake after fecal transplant in patients with alcohol use disorder is transmissible to germ-free mice. Nat Commun 2022; 13:6198. [PMID: 36261423 PMCID: PMC9581985 DOI: 10.1038/s41467-022-34054-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/07/2022] [Indexed: 01/11/2023] Open
Abstract
Alcohol use disorder is a major cause of morbidity, which requires newer treatment approaches. We previously showed in a randomized clinical trial that alcohol craving and consumption reduces after fecal transplantation. Here, to determine if this could be transmitted through microbial transfer, germ-free male C57BL/6 mice received stool or sterile supernatants collected from the trial participants pre-/post-fecal transplant. We found that mice colonized with post-fecal transplant stool but not supernatants reduced ethanol acceptance, intake and preference versus pre-fecal transplant colonized mice. Microbial taxa that were higher in post-fecal transplant humans were also associated with lower murine alcohol intake and preference. A majority of the differentially expressed genes (immune response, inflammation, oxidative stress response, and epithelial cell proliferation) occurred in the intestine rather than the liver and prefrontal cortex. These findings suggest a potential for therapeutically targeting gut microbiota and the microbial-intestinal interface to alter gut-liver-brain axis and reduce alcohol consumption in humans.
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Affiliation(s)
- Jennifer T Wolstenholme
- VCU-Alcohol Research Center and Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Justin M Saunders
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Maren Smith
- VCU-Alcohol Research Center and Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jason D Kang
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Phillip B Hylemon
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Derrick Zhao
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Jeremy Herzog
- National Gnotobiotic Rodent Research Center, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Marcela Peña-Rodríguez
- University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Lianyong Su
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Yun-Ling Tai
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jing Zheng
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Po-Cheng Cheng
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - R Balfour Sartor
- National Gnotobiotic Rodent Research Center, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Huiping Zhou
- Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA.
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Saraf VS, Ali Zaidi SS, Zhu J, Gillevet P, Sikaroodi M, Bokhari H, Javed S. Pathogenic microbe detection in placental tissues supports placental pathobiome association with preterm birth risk in Pakistani women: A brief snapshot. Placenta 2022; 126:160-163. [PMID: 35839624 DOI: 10.1016/j.placenta.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 10/17/2022]
Abstract
Preterm birth (PTB) poses great risk to neonatal health in Pakistan with few tertiary health care facilities. Role of intrauterine microbiome in maintaining healthy pregnancy has been highlighted. However, there is ongoing debate whether a true placental microbiome exist. We analyzed placental and vaginal microbiome through V3-V4 16srRNA sequencing and observed increased abundance of proteobacteria, with concomitant decline in the firmicutes population in preterm vagina. Simplistic placental microflora included many environmental microbes with PTB placenta carrying pathogenic microbes like ureaplasma and mycoplasma species. We observed contribution of environmental, vaginal and skin contamination in term versus pathobiome signatures in preterm placenta.
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Affiliation(s)
- Viqar Sayeed Saraf
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, Pakistan
| | - Syed Shujaat Ali Zaidi
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, Pakistan; Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Jay Zhu
- Department of Microbiology, University of Pennsylvania, USA
| | | | | | - Habib Bokhari
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, Pakistan; Biosciences Department, Kohsar University Murree, Murree, Punjab, Pakistan.
| | - Sundus Javed
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, Pakistan.
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Bajaj JS, Fagan A, McGeorge S, Sterling RK, Rogal S, Sikaroodi M, Gillevet PM. Area Deprivation Index and Gut-Brain Axis in Cirrhosis. Clin Transl Gastroenterol 2022; 13:e00495. [PMID: 35537854 PMCID: PMC9236605 DOI: 10.14309/ctg.0000000000000495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Neighborhood deprivation has been associated with chronic diseases and with gut microbial alterations. Although cirrhosis is associated with gut microbiome changes and hepatic encephalopathy (HE), their association is unclear. METHODS Demographics and cirrhosis details (model for end-stage liver disease [MELD], prior HE, and medications) were recorded from outpatients with cirrhosis. Area deprivation index (ADI), which ranks neighborhoods by socioeconomic disadvantage, was recorded as state decile and national percentile (high = worse for both) and dichotomized on the median. Patients underwent cognitive testing to diagnose minimal HE (MHE). Stool microbiota was analyzed using 16S ribosomal RNA for α/β-diversity. Multivariable analysis was used to evaluate the factors independently associated with MHE. RESULTS A total of 321 people with cirrhosis (60 years, 78% men, 75% non-Hispanic White, 24% non-Hispanic African American, 4% Hispanic) were included. 45% had prior HE and 56% MHE. For ADI, the national percentile was 49.1 ± 21.8 while the state decile was 6.1 ± 2.3. ADI was not associated with race, ethnicity, MELD, or HE-related variables on regression. Regarding microbiota, α-diversity was lower in MHE and prior HE patients but similar across ADI rankings. Low vs high ADIs were associated with different β-diversity in univariable but not multivariable analyses. Multivariable analyses showed positive associations with MELD, prior HE, and lactate producers ( Lactobacillus and Lacticaseibacillus ) and negative associations with short-chain fatty acid producers ( Blautia , Lachnoclostridium , and Anaerobutyricum ) with MHE. DISCUSSION Cirrhosis-related variables may be more influential in determining gut microbiome composition and cognitive impairment than ADI. Therefore, the focus should be on improving cirrhosis care, regardless of ADI, but studies evaluating other measures of social determinants are needed in cirrhosis.
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Affiliation(s)
- Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Shari Rogal
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Álvares-da-Silva MR, Oliveira CP, Fagan A, Longo L, Thoen RU, Yoshimura Zitelli PM, Tanaka Ferreira RM, Mcgeorge S, Shamsaddini A, Farias AQ, Sikaroodi M, Gillevet PM, Bajaj JS. Interaction of Microbiome, Diet, and Hospitalizations Between Brazilian and American Patients With Cirrhosis. Clin Gastroenterol Hepatol 2022; 20:930-940. [PMID: 33813071 PMCID: PMC8486893 DOI: 10.1016/j.cgh.2021.03.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Gut microbiota are affected by diet, country, and affect outcomes in cirrhosis. Western diets are associated with dysbiosis. Comparisons with other diets is needed. We aimed to compare cirrhosis patients from the United States with cirrhosis patients from Brazil with respect to diet, microbiota, and impact on hospitalizations. METHODS Healthy controls and compensated/decompensated outpatients with cirrhosis from the United States and Brazil underwent dietary recall and stool for 16S ribosomal RNA sequencing. Demographics and medications/cirrhosis details were compared within and between countries. Patients with cirrhosis were followed up for 90-day hospitalizations. Regression for Shannon diversity was performed within cirrhosis. Regression for hospitalizations adjusting for clinical and microbial variables was performed. RESULTS Model for end-stage liver disease (MELD), diabetes, ascites, and albumin were similar, but more Americans were men, had higher hepatic encephalopathy and alcohol/hepatitis C etiology, with lower nonalcoholic fatty liver disease than Brazilians. Brazilians had higher cereal, rice, and yogurt intake vs the United States. As disease progressed, cereals, rice/beans, coffee, and chocolate consumption was reduced. Microbial diversity was higher in Brazilians. Within cirrhosis, high diversity was related to Brazilian origin (P < .0001), age, and cereal intake (P = .05), while high MELD scores (P = .009) and ascites (P = .05) did the reverse. Regardless of stage, beneficial taxa and taxa associated with grant and yogurt intake were higher (Ruminococcaceae, Christensenellacae, and Prevotellaceae), while pathobionts (Porphyromonadaceae, Sutterellaceae, and Enterobacteriaceae) were lower in Brazilians. More Americans were hospitalized vs Brazilians (P = .002). On regression, MELD (P = .001) and ascites (P = .001) were associated with higher hospitalizations, while chocolate (P = .03) and Brazilian origin (P = .001) were associated with lower hospitalizations with/without microbiota inclusion. CONCLUSIONS Brazilian cirrhotic patients follow a diet richer in cereals and yogurt, which is associated with higher microbial diversity and beneficial microbiota and could contribute toward lower hospitalizations compared with a Western-diet-consuming American cohort.
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Affiliation(s)
| | | | - Andrew Fagan
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, United States
| | - Larisse Longo
- Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rutiane U. Thoen
- Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | - Sara Mcgeorge
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, United States
| | | | | | | | | | - Jasmohan S. Bajaj
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, United States
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12
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Saboo K, Petrakov NV, Shamsaddini A, Fagan A, Gavis EA, Sikaroodi M, McGeorge S, Gillevet PM, Iyer RK, Bajaj JS. Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning. J Hepatol 2022; 76:600-607. [PMID: 34793867 PMCID: PMC8858861 DOI: 10.1016/j.jhep.2021.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Saliva and stool microbiota are altered in cirrhosis. Since stool is logistically difficult to collect compared to saliva, it is important to determine their relative diagnostic and prognostic capabilities. We aimed to determine the ability of stool vs. saliva microbiota to differentiate between groups based on disease severity using machine learning (ML). METHODS Controls and outpatients with cirrhosis underwent saliva and stool microbiome analysis. Controls vs. cirrhosis and within cirrhosis (based on hepatic encephalopathy [HE], proton pump inhibitor [PPI] and rifaximin use) were classified using 4 ML techniques (random forest [RF], support vector machine, logistic regression, and gradient boosting) with AUC comparisons for stool, saliva or both sample types. Individual microbial contributions were computed using feature importance of RF and Shapley additive explanations. Finally, thresholds for including microbiota were varied between 2.5% and 10%, and core microbiome (DESeq2) analysis was performed. RESULTS Two hundred and sixty-nine participants, including 87 controls and 182 patients with cirrhosis, of whom 57 had HE, 78 were on PPIs and 29 on rifaximin were included. Regardless of the ML model, stool microbiota had a significantly higher AUC in differentiating groups vs. saliva. Regarding individual microbiota: autochthonous taxa drove the difference between controls vs. patients with cirrhosis, oral-origin microbiota the difference between PPI users/non-users, and pathobionts and autochthonous taxa the difference between rifaximin users/non-users and patients with/without HE. These were consistent with the core microbiome analysis results. CONCLUSIONS On ML analysis, stool microbiota composition is significantly more informative in differentiating between controls and patients with cirrhosis, and those with varying cirrhosis severity, compared to saliva. Despite logistic challenges, stool should be preferred over saliva for microbiome analysis. LAY SUMMARY Since it is harder to collect stool than saliva, we wanted to test whether microbes from saliva were better than stool in differentiating between healthy people and those with cirrhosis and, among those with cirrhosis, those with more severe disease. Using machine learning, we found that microbes in stool were more accurate than saliva alone or in combination, therefore, stool should be preferred for analysis and collection wherever possible.
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Affiliation(s)
- Krishnakant Saboo
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nikita V Petrakov
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA, USA
| | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA, USA
| | | | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA, USA
| | | | - Ravishankar K Iyer
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA, USA.
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Bajaj JS, Shamsaddini A, Acharya C, Fagan A, Sikaroodi M, Gavis E, McGeorge S, Khoruts A, Fuchs M, Sterling RK, Lee H, Gillevet PM. Multiple bacterial virulence factors focused on adherence and biofilm formation associate with outcomes in cirrhosis. Gut Microbes 2022; 13:1993584. [PMID: 34743650 PMCID: PMC8582993 DOI: 10.1080/19490976.2021.1993584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND & AIMS Altered gut microbiota is associated with poor outcomes in cirrhosis, including infections and hepatic encephalopathy (HE). However, the role of bacterial virulence factors (VFs) is unclear. Aim: Define association of VFs with cirrhosis severity and infections, their linkage with outcomes, and impact of fecal microbiota transplant (FMT). METHODS VF abundances were determined using metagenomic analysis in stools from controls and cirrhosis patients (compensated, HE-only, ascites-only, both and infected). Patients were followed for 90-day hospitalizations and 1-year death. Stool samples collected before/after a placebo-controlled FMT trial were also analyzed. Bacterial species and VFs for all species and selected pathogens (Escherichia, Klebsiella, Pseudomonas, Staphylococcus, Streptococcus, and Enterococcus spp) were compared between groups. Multi-variable analyses were performed for clinical biomarkers and VFs for outcome prediction. Changes in VFs pre/post-FMT and post-FMT/placebo were analyzed. Results: We included 233 subjects (40 controls, 43 compensated, 30 HE-only, 20 ascites-only, 70 both, and 30 infected). Decompensated patients, especially those with infections, had higher VFs coding for siderophores, biofilms, and adhesion factors versus the rest. Biofilm and adhesion VFs from Enterobacteriaceae and Enterococcus spp associated with death and hospitalizations independent of clinical factors regardless of when all VFs or selected pathogens were analyzed. FMT was associated with reduced VF post-FMT versus pre-FMT and post-placebo groups. CONCLUSIONS Virulence factors from multiple species focused on adhesion and biofilms increased with decompensation and infections, associated with death and hospitalizations independent of clinical factors, and were attenuated with FMT. Strategies focused on targeting multiple virulence factors could potentially impact outcomes in cirrhosis. PRESENTATIONS Portions of this manuscript were an oral presentation in the virtual International Liver Congress 2021. ABBREVIATIONS VF: virulence factors, HE: hepatic encephalopathy, FMT: Fecal microbiota transplant, PPI: proton pump inhibitors, LPS: lipopolysaccharides, VFDB: Virulence factor database, OTU: operational taxonomic units, SBP: spontaneous bacterial peritonitis, UTI: urinary tract infections, MRSA: methicillin resistant Staphylococcus aureus, VRE: vancomycin-resistant Enterococcus, MAAsLin2: Microbiome Multivariable Associations with Linear Models, LPS: lipopolysaccharides, AKI: acute kidney injury.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA,CONTACT Jasmohan S Bajaj Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, 1201 Broad Rock Boulevard, Richmond, Virginia23249, USA
| | | | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Sara McGeorge
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Alexander Khoruts
- Gastroenterology, Hepatology and Nutrition, Center for Immunology and Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Hall NC, Sikaroodi M, Hogan D, Jones RC, Gillevet PM. The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs). Environ Manage 2022; 69:89-110. [PMID: 34860281 PMCID: PMC8758610 DOI: 10.1007/s00267-021-01529-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.
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Affiliation(s)
- Natalie C Hall
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA, USA.
| | - Masoumeh Sikaroodi
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
| | - Dianna Hogan
- U.S. Geological Survey, Deputy Regional Director for Science, Southeast Region, Reston, VA, USA
| | - R Christian Jones
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Potomac Environmental Research and Education Center (PEREC), George Mason University, Woodbridge, VA, USA
| | - Patrick M Gillevet
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
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Shamsaddini A, Gillevet PM, Acharya C, Fagan A, Gavis E, Sikaroodi M, McGeorge S, Khoruts A, Albhaisi S, Fuchs M, Sterling RK, Bajaj JS. Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis. Gastroenterology 2021; 161:508-521.e7. [PMID: 33857456 PMCID: PMC9069394 DOI: 10.1053/j.gastro.2021.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes. METHODS In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning. RESULTS A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs. CONCLUSIONS Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.
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Affiliation(s)
| | | | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | | | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Alexander Khoruts
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Somaya Albhaisi
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
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Zhang Y, Kang JD, Zhao D, Ghosh SS, Wang Y, Tai Y, Gonzalez-Maeso J, Sikaroodi M, Gillevet PM, Lippman HR, Hylemon PB, Zhou H, Bajaj JS. Hepatic Branch Vagotomy Modulates the Gut-Liver-Brain Axis in Murine Cirrhosis. Front Physiol 2021; 12:702646. [PMID: 34248683 PMCID: PMC8268007 DOI: 10.3389/fphys.2021.702646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Background Cirrhosis and hepatic encephalopathy (HE) are linked with an altered gut-liver-brain axis, however, the relative contribution of hepatic vagal innervation is unclear. We aimed to determine the impact of hepatic vagotomy on the gut microbiome, brain, and liver in murine cirrhosis. Methods 10–15-week-old male C57BL/6 mice with and without hepatic vagotomy underwent carbon tetrachloride (CCl4) gavage for 8 weeks. Frontal cortex [inflammation, glial/microglial activation, BDNF (brain-derived neurotrophic factor)], liver [histology including inflammation and steatosis, fatty acid synthesis (sterol-responsive binding protein-1) SREBP-1, insulin-induced gene-2 (Insig2) and BDNF], and colonic mucosal microbiota (16srRNA microbial sequencing) were evaluated on sacrifice. Conventional mice with and without cirrhosis were compared to vagotomized counterparts. Results Conventional control vs. cirrhosis: Cirrhosis resulted in dysbiosis, hepatic/neuro-inflammation with glial/microglial activation, and low brain BDNF vs. controls. Conventional control vs. vagotomy controls: Vagotomized control mice had a lower colonic dysbiosis than conventional mice but the rest of the hepatic/brain parameters were similar. Conventional cirrhosis vs. vagotomized cirrhosis: After vagotomy + cirrhosis, we found lower dysbiosis but continuing neuroinflammation in the absence of glial/microglial activation vs. conventional cirrhosis. Vagotomy + Cirrhosis groups showed higher hepatic steatosis due to higher SREBP1 and low Insig2 protein and altered activation of key genes involved in hepatic lipid metabolism and inflammation. BDNF levels in the brain were higher but low in the liver in vagotomy + cirrhosis, likely a protective mechanism. Conclusions Hepatic vagal innervation affects the gut microbial composition, hepatic inflammation and steatosis, and cortical inflammation and BDNF expression and could be a critical modulator of the gut-liver-brain axis with consequences for HE development.
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Affiliation(s)
- Yuan Zhang
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Jason D Kang
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Derrick Zhao
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Siddartha S Ghosh
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, United States
| | - Yanyan Wang
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Yunling Tai
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, United States
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, VA, United States
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, VA, United States
| | - H Robert Lippman
- Department of Pathology, Central Virginia Veterans Health Care System, Richmond, VA, United States
| | - Phillip B Hylemon
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Huiping Zhou
- Division of Microbiology and Immunology, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology, and Nutrition, Central Virginia Veterans Health Care System, Virginia Commonwealth University, Richmond, VA, United States
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Bajaj JS, Sikaroodi M, Shamsaddini A, Henseler Z, Santiago-Rodriguez T, Acharya C, Fagan A, Hylemon PB, Fuchs M, Gavis E, Ward T, Knights D, Gillevet PM. Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy. Gut 2021; 70:1162-1173. [PMID: 32998876 DOI: 10.1136/gutjnl-2020-322470] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Altered bacterial composition is associated with disease progression in cirrhosis but the role of virome, especially phages, is unclear. DESIGN Cross-sectional and pre/post rifaximin cohorts were enrolled. Cross-sectional: controls and cirrhotic outpatients (compensated, on lactulose (Cirr-L), on rifaximin (Cirr-LR)) were included and followed for 90-day hospitalisations. Pre/post: compensated cirrhotics underwent stool collection pre/post 8 weeks of rifaximin. Stool metagenomics for bacteria and phages and their correlation networks were analysed in controls versus cirrhosis, within cirrhotics, hospitalised/not and pre/post rifaximin. RESULTS Cross-sectional: 40 controls and 163 cirrhotics (63 compensated, 43 Cirr-L, 57 Cirr-LR) were enrolled. Cirr-L/LR groups were similar on model for end-stage liver disease (MELD) score but Cirr-L developed greater hospitalisations versus Cirr-LR (56% vs 30%, p=0.008). Bacterial alpha/beta diversity worsened from controls through Cirr-LR. While phage alpha diversity was similar, beta diversity was different between groups. Autochthonous bacteria linked negatively, pathobionts linked positively with MELD but only modest phage-MELD correlations were seen. Phage-bacterial correlation network complexity was highest in controls, lowest in Cirr-L and increased in Cirr-LR. Microviridae and Faecalibacterium phages were linked with autochthonous bacteria in Cirr-LR, but not Cirr-L hospitalised patients had greater pathobionts, lower commensal bacteria and phages focused on Streptococcus, Lactococcus and Myoviridae. Pre/post: No changes in alpha/beta diversity of phages or bacteria were seen postrifaximin. Phage-bacterial linkages centred around urease-producing Streptococcus species collapsed postrifaximin. CONCLUSION Unlike bacteria, faecal phages are sparsely linked with cirrhosis characteristics and 90-day outcomes. Phage and bacterial linkages centred on urease-producing, ammonia-generating Streptococcus species were affected by disease progression and rifaximin therapy and were altered in patients who experienced 90-day hospitalisations.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | | | | | | | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Phillip B Hylemon
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Tonya Ward
- Diversigen, New Brighton, Minnesota, USA
| | - Dan Knights
- Diversigen, New Brighton, Minnesota, USA.,Department of Computer Science and Engineering, U, University of Minnesota, Minneapolis, MN, USA.,Minnesota Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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18
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Albhaisi S, Shamsaddini A, Fagan A, McGeorge S, Sikaroodi M, Gavis E, Patel S, Davis BC, Acharya C, Sterling RK, Matherly S, Fuchs M, Gillevet PM, Bajaj JS. Gut Microbial Signature of Hepatocellular Cancer in Men With Cirrhosis. Liver Transpl 2021; 27:629-640. [PMID: 33492761 DOI: 10.1002/lt.25994] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/12/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
The gut microbiome is altered in cirrhosis. Recent evidence has suggested a key role for the gut microbiota in the progression of cirrhosis and the development of hepatocellular carcinoma (HCC). We studied the differences in the microbial composition in patients with cirrhosis with prior and future HCC in the context of other complications (eg, infections, hepatic encephalopathy). The following 2 cohorts were recruited prospectively: the prior HCC cohort, in which outpatients with HCC within 2 years were age-matched, sex-matched, and Model for End-Stage Liver Disease (MELD) score-matched with those without HCC; and the future HCC cohort, in which patients were followed for 2 years and divided into future HCC versus no HCC after age, sex, and MELD-score matching and other complications were also recorded. Microbiota composition and predicted function were analyzed with ribosomal RNA sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PiCRUST)and compared between (1) prior HCC versus none and (2) future HCC versus none, and in the future cohort, comparisons were also made between those patients who developed (1) HCC only versus without complications, (2) HCC only versus non-HCC complications only, and (3) HCC + other complications versus non-HCC complications only. A total of 142 men (76 total in the prior cohort [38 with/38 without HCC] and 66 total in the future cohort [33 with/33 without future HCC]) were included. The groups had similar etiology, lactulose/rifaximin/proton pump inhibitor use, diabetes mellitus, and non-HCC complications. Microbial diversity was similar between prior HCC/not or future HCC/not. On DESeq2 higher Clostridium sensu stricto and Anaerotruncus were significantly associated with protection from HCC, whereas the reverse was seen with Raoultella and Haemophilus regardless of prior/future HCC comparisons. Functions focused on urea cycle, bioenergetics, tryptophan, and toluene metabolism were different between the groups. Rothia was specific for other complications. Despite age, sex, and MELD-score matching and accounting for other complications, gut microbiota composition and the predicted function are different in men with cirrhosis with and without prior HCC and can be extended toward future HCC development.
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Affiliation(s)
- Somaya Albhaisi
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | | | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Samarth Patel
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Brian C Davis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Richard K Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Scott Matherly
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
| | | | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Healthcare System, Richmond, VA
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19
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Bajaj JS, Gavis EA, Fagan A, Wade JB, Thacker LR, Fuchs M, Patel S, Davis B, Meador J, Puri P, Sikaroodi M, Gillevet PM. A Randomized Clinical Trial of Fecal Microbiota Transplant for Alcohol Use Disorder. Hepatology 2021; 73:1688-1700. [PMID: 32750174 DOI: 10.1002/hep.31496] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Alcohol use disorder (AUD) is associated with microbial alterations that worsen with cirrhosis. Fecal microbiota transplant (FMT) could be a promising approach. APPROACH AND RESULTS In this phase 1, double-blind, randomized clinical trial, patients with AUD-related cirrhosis with problem drinking (AUDIT-10 > 8) were randomized 1:1 into receiving one placebo or FMT enema from a donor enriched in Lachnospiraceae and Ruminococcaceae. Six-month safety was the primary outcome. Alcohol craving questionnaire, alcohol consumption (urinary ethylglucuronide/creatinine), quality of life, cognition, serum IL-6 and lipopolysaccharide-binding protein, plasma/stool short-chain fatty acids (SCFAs), and stool microbiota were tested at baseline and day 15. A 6-month follow-up with serious adverse event (SAE) analysis was performed. Twenty patients with AUD-related cirrhosis (65 ± 6.4 years, all men, Model for End-Stage Liver Disease 8.9 ± 2.7) with similar demographics, cirrhosis, and AUD severity were included. Craving reduced significantly in 90% of FMT versus 30% in placebo at day 15 (P = 0.02) with lower urinary ethylglucuronide/creatinine (P = 0.03) and improved cognition and psychosocial quality of life. There was reduction in serum IL-6 and lipopolysaccharide-binding protein and increased butyrate/isobutyrate compared with baseline in FMT but not placebo. Microbial diversity increased with higher Ruminococcaceae and other SCFAs, producing taxa following FMT but not placebo, which were linked with SCFA levels. At 6 months, patients with any SAEs (8 vs. 2, P = 0.02), AUD-related SAEs (7 vs. 1, P = 0.02), and SAEs/patient (median [interquartile range], 1.5 [1.25] vs. 0 [0.25] in FMT, P = 0.02) were higher in placebo versus FMT. CONCLUSIONS This phase 1 trial shows that FMT is safe and associated with short-term reduction in alcohol craving and consumption with favorable microbial changes versus placebo in patients with alcohol-associated cirrhosis with alcohol misuse. There was also a reduction in AUD-related events over 6 months in patients assigned to FMT.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - James B Wade
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA
| | - Leroy R Thacker
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Samarth Patel
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Brian Davis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Jill Meador
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
| | - Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, VA
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20
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Jung J, Gillevet PM, Sikaroodi M, Andrews J, Song B, Shields JD. Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus. Dis Aquat Organ 2021; 143:147-158. [PMID: 33629659 DOI: 10.3354/dao03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.
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Affiliation(s)
- Jibom Jung
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
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21
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Bajaj JS, Shamsaddini A, Fagan A, Sterling RK, Gavis E, Khoruts A, Fuchs M, Lee H, Sikaroodi M, Gillevet PM. Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials. Hepatol Commun 2021; 5:258-271. [PMID: 33553973 PMCID: PMC7850310 DOI: 10.1002/hep4.1639] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | | | - Andrew Fagan
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Richard K Sterling
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Edith Gavis
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Alexander Khoruts
- Gastroenterology, Hepatology, and NutritionBiotechnology Institute University of MinnesotaMinneapolisMNUSA
| | - Michael Fuchs
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Hannah Lee
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
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22
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Saboo K, Shamsaddini A, Iyer MV, Hu C, Fagan A, Gavis EA, White MB, Fuchs M, Heuman DM, Sikaroodi M, Iyer RK, Gillevet PM, Bajaj JS. Sex is associated with differences in gut microbial composition and function in hepatic encephalopathy. J Hepatol 2021; 74:80-88. [PMID: 32679299 PMCID: PMC7749850 DOI: 10.1016/j.jhep.2020.06.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Altered microbiota can affect the gut-liver-brain axis in cirrhosis and hepatic encephalopathy (HE), but the impact of sex on these changes is unclear. We aimed to determine differences in fecal microbiota composition/functionality between men and women with cirrhosis and HE on differing treatments. METHODS Cross-sectional stool microbiome composition (16s rRNA sequencing) and microbial functional analyses were performed in men and women with cirrhosis, and controls. Patients with HE on rifaximin+lactulose (HE-Rif), patients with HE on lactulose only (HE-Lac) and those with cirrhosis without HE (No-HE) were compared to controls using random forest classifier. Men and women were also compared. RESULTS A total of 761 individuals were included, 619 with cirrhosis (466 men, 153 women) and 142 controls (92 men, 50 women). Men were older and more frequently used proton pump inhibitors (PPIs), but model for end-stage liver disease score, No-HE (n = 319), HE-lac (n = 130) and HE-Rif (n = 170) proportions were similar. PPI/age-adjusted AUC of differentiation between controls vs. all cirrhosis, and controls vs. No-HE were higher within women than men, but the adjusted AUC for No-HE vs. HE-Rif was higher in men. Control vs. HE-Rif differentiation was similar across sexes. Men vs. women were different in all cirrhosis, No-HE and HE-Lac but not HE-Rif on PERMANOVA and AUC analyses. Autochthonous taxa decreased and pathobionts increased with disease progression regardless of sex. In men, Lactobacillaceae were higher in HE-Lac but decreased in HE-Rif, along with Veillonellaceae. Pathways related to glutamate and aromatic compound degradation were higher in men at all stages. Degradation of androstenedione, an estrogenic precursor, was lower in men vs. women in HE-Rif, likely enhancing feminization. CONCLUSIONS There are differences in gut microbial function and composition between men and women with cirrhosis, which could be implicated in differential responses to HE therapies. Further studies linking these differences to sex-specific outcomes are needed. LAY SUMMARY Patients with cirrhosis develop changes in their brain function, and men often develop feminization with disease progression. However, the interaction between sex, microbiota and disease severity is unclear. We found that as disease progressed in men, their microbial composition began to approach that observed in women, with changes in specific microbes that are associated with male hormone metabolism.
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Affiliation(s)
- Krishnakant Saboo
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Mihir V Iyer
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chang Hu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Melanie B White
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Douglas M Heuman
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | | | - Ravishankar K Iyer
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA.
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23
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Bajaj JS, Shamsaddini A, Fagan A, McGeorge S, Gavis E, Sikaroodi M, Brenner LA, Wade JB, Gillevet PM. Distinct gut microbial compositional and functional changes associated with impaired inhibitory control in patients with cirrhosis. Gut Microbes 2021; 13:1953247. [PMID: 34346283 PMCID: PMC8344770 DOI: 10.1080/19490976.2021.1953247] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Most cirrhosis etiologies, such as alcohol, hepatitis C, and obesity, involve behavior that require the loss of inhibitory control. Once cirrhosis develops, patients can also develop cognitive impairment due to minimal hepatic encephalopathy (MHE). Both processes could have distinct imprints on the gut-liver-brain axis. Determine the impact of inhibitory control versus traditional cirrhosis-related cognitive performance on gut microbial composition and function. Outpatients with cirrhosis underwent two tests for MHE: inhibitory control test (MHEICT, computerized associated with response inhibition) and psychometric hepatic encephalopathy score (MHEPHES, paper-pencil HE-specific associated with subcortical impairment) along with stool collection for metagenomics. MHEICT/not, MHEPHES/not, and discordant (positive on one test but negative on the other) were analyzed for demographics, bacterial species, and gut-brain modules (GBM) using multi-variable analyses. Ninety-seven patients [47 (49%) MHEPHES, 76 (78%) MHEICT, 41 discordant] were enrolled. MHEPHES/not: Cirrhosis severity was worse in MHEPHES without differences in alpha/beta diversity on bacterial species or GBMs. Pathobionts (Enterobacteriaceae) and γ-amino-butryic acid (GABA) synthesis GBM were higher in MHEPHES. MHEICT/not: We found similar cirrhosis severity and metagenomic alpha/beta diversity in MHEICT versus not. However, alpha/beta diversity of GBMs were different in MHEICT versus No-MHE patients. Alistipes ihumii, Prevotella copri, and Eubacterium spp. were higher, while Enterococcus spp. were uniquely lower in MHEICT versus no-MHE and discordant comparisons. GBMs belonging to tryptophan, menaquinone, GABA, glutamate, and short-chain fatty acid synthesis were also unique to MHEICT. Gut microbial signature of impaired inhibitory control, which is associated with addictive disorders that can lead to cirrhosis, is distinct from cirrhosis-related cognitive impairment.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | - Lisa A. Brenner
- Departments of Physical Medicine and Rehabilitation, Psychiatry, & Neurology, VA Rocky Mountain Mental Illness Research Education and Clinical Center, Aurora, Colorado, and University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - James B Wade
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
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24
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Dal Forno M, Lawrey JD, Sikaroodi M, Gillevet PM, Schuettpelz E, Lücking R. Extensive photobiont sharing in a rapidly radiating cyanolichen clade. Mol Ecol 2020; 30:1755-1776. [PMID: 33080083 DOI: 10.1111/mec.15700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Recent studies have uncovered remarkable diversity in Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of Rhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to R. interruptum and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont-mycobiont co-speciation, but one of the monophyletic lineages of Rhizonema appears to partner predominantly with one of the two major clades of Cora (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the Rhizonema species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers," in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.
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Affiliation(s)
- Manuela Dal Forno
- Botanical Research Institute of Texas, Fort Worth, TX, USA.,Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - James D Lawrey
- Department of Biology, George Mason University, Fairfax, VA, USA
| | | | | | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Robert Lücking
- Botanical Garden and Botanical Museum Berlin, Berlin, Germany.,Research Associate, Science & Education, The Field Museum, Chicago, IL, USA
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Bajaj JS, Reddy KR, O’Leary JG, Vargas HE, Lai JC, Kamath PS, Tandon P, Wong F, Subramanian RM, Thuluvath P, Fagan A, White MB, Gavis EA, Sehrawat T, de la Rosa Rodriguez R, Thacker LR, Sikaroodi M, Garcia-Tsao G, Gillevet PM. Serum Levels of Metabolites Produced by Intestinal Microbes and Lipid Moieties Independently Associated With Acute-on-Chronic Liver Failure and Death in Patients With Cirrhosis. Gastroenterology 2020; 159:1715-1730.e12. [PMID: 32687928 PMCID: PMC7680282 DOI: 10.1053/j.gastro.2020.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Inpatients with cirrhosis have high rates of acute-on-chronic failure (ACLF) development and high mortality within 30 days of admission to the hospital. Better biomarkers are needed to predict these outcomes. We performed metabolomic analyses of serum samples from patients with cirrhosis at multiple centers to determine whether metabolite profiles might identify patients at high risk for ACLF and death. METHODS We performed metabolomic analyses, using liquid chromatography, of serum samples collected at time of admission to 12 North American tertiary hepatology centers from 602 patients in the North American Consortium for the Study of End-Stage Liver Disease sites from 2015 through 2017 (mean age, 56 years; 61% men; mean model for end-stage liver disease score, 19.5). We performed analysis of covariance, adjusted for model for end-stage liver disease at time of hospital admission, serum levels of albumin and sodium, and white blood cell count, to identify metabolites that differed between patients who did vs did not develop ACLF and patients who did vs did not die during hospitalization and within 30 days. We performed random forest analysis to identify specific metabolite(s) that were associated with outcomes and area under the curve (AUC) analyses to analyze them in context of clinical parameters. We analyzed microbiomes of stool samples collected from 133 patients collected at the same time and examined associations with serum metabolites. RESULTS Of the 602 patients analyzed, 88 developed ACLF (15%), 43 died in the hospital (7%), and 72 died within 30 days (12%). Increased levels of compounds of microbial origin (aromatic compounds, secondary or sulfated bile acids, and benzoate) and estrogen metabolites, as well as decreased levels of phospholipids, were associated with development of ACLF, inpatient, and 30-day mortality and were also associated with fecal microbiomes. Random forest analysis and logistic regression showed that levels of specific microbially produced metabolites identified patients who developed ACLF with an AUC of 0.84 (95% confidence interval [CI] 0.78-0.88; P = .001), patients who died while in the hospital with an AUC of 0.81 (95% CI 0.74-0.85; P = .002), and patients who died within 30 days with an AUC of 0.77 (95% CI 0.73-0.81; P = .02). The metabolites were significantly additive to clinical parameters for predicting these outcomes. Metabolites associated with outcomes were also correlated with microbiomes of stool samples. CONCLUSIONS In an analysis of serum metabolites and fecal microbiomes of patients hospitalized with cirrhosis at multiple centers, we associated metabolites of microbial origin and lipid moieties with development of ACLF and death as an inpatient or within 30 days, after controlling for clinical features.
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Affiliation(s)
- Jasmohan S Bajaj
- Department of Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia.
| | | | | | | | | | | | | | | | | | | | - Andrew Fagan
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, USA
| | - Melanie B White
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, USA
| | - Edith A Gavis
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, USA
| | | | | | - Leroy R Thacker
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, USA
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26
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Smirnova E, Puri P, Muthiah MD, Daitya K, Brown R, Chalasani N, Liangpunsakul S, Shah VH, Gelow K, Siddiqui MS, Boyett S, Mirshahi F, Sikaroodi M, Gillevet P, Sanyal AJ. Fecal Microbiome Distinguishes Alcohol Consumption From Alcoholic Hepatitis But Does Not Discriminate Disease Severity. Hepatology 2020; 72:271-286. [PMID: 32056227 PMCID: PMC7752764 DOI: 10.1002/hep.31178] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity, and (3) infer the functional relevance of shifts in microbial ecology. APPROACH AND RESULTS The fecal microbiome in patients with moderate alcoholic hepatitis (MAH) or severe alcoholic hepatitis (SAH) was compared with healthy controls (HCs) and heavy drinking controls (HDCs). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFAs) were measured using a liquid chromatography-mass spectrometry platform. A total of 78 participants (HC, n = 24; HDC, n = 20; MAH, n = 10; SAH, n = 24) were studied. HDC had a distinct signature compared with HC with depletion of Bacteroidetes (46% vs. 26%; P = 0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared with HDC (area under the curve = 0.826); differential abundance of Ruminococcaceae, Veillonellaceae, Lachnospiraceae, Porphyromonadaceae, and Rikenellaceae families were the key contributors to these differences. The beta diversity was significantly different among the groups (permutational multivariate analysis of variance [PERMANOVA] P < 0.001). SAH was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, P = 0.20 and 0.01, respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48%, respectively; P = 0.09, HDC vs. SAH). Microbial taxa did not distinguish between MAH and SAH (PERMANOVA P = 0.785). SCFAs producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal SCFAs among alcoholic hepatitis patients. CONCLUSIONS There are distinct changes in fecal microbiome associated with the development, but not severity, of alcoholic hepatitis.
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Affiliation(s)
- Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA
| | - Puneet Puri
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | - Mark D. Muthiah
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Division of Gastroenterology and Hepatology, National University Hospital, Singapore
| | - Kalyani Daitya
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | - Robert Brown
- Dept. of Microbiology, George Mason University, VA
| | - Naga Chalasani
- Div. of Gastroenterology, Dept. of Internal Medicine, Indiana University, Indianapolis
| | - Suthat Liangpunsakul
- Div. of Gastroenterology, Dept. of Internal Medicine, Indiana University, Indianapolis
| | - Vijay H. Shah
- Div. of Gastroenterology, Dept. of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kayla Gelow
- Dept. of Biostatistics, Indiana University, Indianapolis, Indiana
| | - Mohammed S. Siddiqui
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | - Sherry Boyett
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | - Faridoddin Mirshahi
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | | | | | - Arun J. Sanyal
- Div. of Gastroenterology, Hepatology and Nutrition, Dept. of Internal Medicine, Virginia Commonwealth University, Richmond, VA
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27
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Bajaj JS, Torre A, Rojas ML, Fagan A, Nandez IE, Gavis EA, De Leon Osorio O, White MB, Fuchs M, Sikaroodi M, Gillevet PM. Cognition and hospitalizations are linked with salivary and faecal microbiota in cirrhosis cohorts from the USA and Mexico. Liver Int 2020; 40:1395-1407. [PMID: 32181561 DOI: 10.1111/liv.14437] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/15/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Gut microbiota are affected by diet and ethnicity, which impacts cognition and hospitalizations in cirrhosis. AIM Study interactions of diet with microbiota and impact on hospitalizations and cognition in American and Mexican cohorts. METHODS Controls and age-balanced patients with compensated/decompensated cirrhosis were included and followed for 90-day hospitalizations. A subset underwent minimal hepatic encephalopathy (MHE) testing. Parameters such as dietary, salivary and faecal microbiota (diversity, taxa analysis, cirrhosis dysbiosis ratio CDR:high = good) between/within countries were analysed. Regression analyses for hospitalizations and MHE were performed. RESULTS In all, 275 age-balanced subjects (133 US [40 Control, 50 Compensated, 43 Decompensated] and 142 Mexican [41 Control, 49 Compensated, 52 Decompensated]) were enrolled. MELD/cirrhosis severity was comparable. Diet showed lower protein and animal fat intake in all decompensated patients, but this was worse in Mexico. Diversity was lower in stool and saliva in decompensated patients, and worse in Mexican cohorts. Prevotellaceae were lower in decompensated cirrhosis, particularly those with lower animal fat/protein consumption across countries. Hospitalizations were higher in Mexico vs the USA (26% vs 14%, P = .04). On regression, Prevotellaceae, Ruminococcaceae and Lachnospiraceae lowered hospitalization risk independent of MELD and ascites. MHE testing was performed in 120 (60/country and 20/subgroup) subjects and MHE rate was similar. MELD and decompensation increased while CDR and Prevotellaceae decreased the risk of MHE. CONCLUSIONS Changes in diet and microbiota, especially related to animal fat and protein intake and Prevotellaceae, are associated with MHE and hospitalizations in Mexican patients with cirrhosis compared to an American cohort. Nutritional counselling to increase protein intake in cirrhosis could help prevent these hospitalizations.
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Affiliation(s)
- Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Aldo Torre
- Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Mayra L Rojas
- Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Andrew Fagan
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Ivvone E Nandez
- Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Edith A Gavis
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Omar De Leon Osorio
- Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Melanie B White
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
| | - Michael Fuchs
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA
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28
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Saunders JM, Moreno JL, Ibi D, Sikaroodi M, Kang DJ, Muñoz-Moreno R, Dalmet SS, García-Sastre A, Gillevet PM, Dozmorov MG, Bajaj JS, González-Maeso J. Gut microbiota manipulation during the prepubertal period shapes behavioral abnormalities in a mouse neurodevelopmental disorder model. Sci Rep 2020; 10:4697. [PMID: 32170216 PMCID: PMC7070045 DOI: 10.1038/s41598-020-61635-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/02/2020] [Indexed: 02/08/2023] Open
Abstract
Previous studies demonstrate an association between activation of the maternal immune system during pregnancy and increased risk of neurodevelopmental psychiatric conditions, such as schizophrenia and autism, in the offspring. Relatively recent findings also suggest that the gut microbiota plays an important role in shaping brain development and behavior. Here we show that maternal immune activation (MIA) accomplished by infection with a mouse-adapted influenza virus during pregnancy induced up-regulation of frontal cortex serotonin 5-HT2A receptor (5-HT2AR) density in the adult offspring, a phenotype previously observed in postmortem frontal cortex of schizophrenic subjects. 5-HT2AR agonist-induced head-twitch behavior was also augmented in this preclinical mouse model. Using the novel object recognition (NOR) test to evaluate cognitive performance, we demonstrate that MIA induced NOR deficits in adult offspring. Oral antibiotic treatment of prepubertal mice prevented this cognitive impairment, but not increased frontal cortex 5-HT2AR density or psychedelic-induced head-twitch behavior in adult MIA offspring. Additionally, gut microbiota transplantation from MIA mice produced behavioral deficits in antibiotic-treated mock mice. Adult MIA offspring displayed altered gut microbiota, and relative abundance of specific components of the gut microbiota, including Ruminococcaceae, correlated with frontal cortex 5-HT2AR density. Together, these findings provide a better understanding of basic mechanisms by which prenatal insults impact offspring brain function, and suggest gut-brain axis manipulation as a potential therapeutic approach for neurodevelopmental psychiatric conditions.
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Affiliation(s)
- Justin M Saunders
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - José L Moreno
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.,VIVEbiotech S.L., E-20009, Donostia/San Sebastián, Spain
| | - Daisuke Ibi
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.,Department of Chemical Pharmacology, Meijo University, Nagoya, 468-8503, Japan
| | - Masoumeh Sikaroodi
- Center for Microbiome Analysis, George Mason University, Manassas, VA, 20110, USA
| | - Dae Joong Kang
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, 23298, USA
| | - Raquel Muñoz-Moreno
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Swati S Dalmet
- Center for Microbiome Analysis, George Mason University, Manassas, VA, 20110, USA
| | - Adolfo García-Sastre
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Medicine - Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Patrick M Gillevet
- Center for Microbiome Analysis, George Mason University, Manassas, VA, 20110, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, 23298, USA
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.
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29
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Bajaj JS, Acharya C, Sikaroodi M, Gillevet PM, Thacker LR. Cost-effectiveness of integrating gut microbiota analysis into hospitalisation prediction in cirrhosis. GastroHep 2020; 2:79-86. [PMID: 33071650 PMCID: PMC7567123 DOI: 10.1002/ygh2.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Admissions in cirrhosis are expensive and often unpredictable based on purely clinical variables. Admissions could be related to complications associated with gut microbial changes, which can improve prognostication. However, the cost-effectiveness is unclear. AIMS Determine cost-effectiveness of adding gut microbiota analysis to clinical parameters in prediction and subsequent reduction of admissions in cirrhosis. METHODS Using a Markov model of 1000 cirrhosis patients over 90 days, we modeled microbiota testing using 16srRNA ($250/sample), low-depth ($350/sample) and high-depth ($650/sample) metagenomics added to standard-of-care (SOC) for prevention of admissions using standard outcome costs and rates of development. We generated quality of life years (QALY) and Incremental cost-effectiveness ratios (ICER) for the base scenarios and performed sensitivity analyses by varying costs for outcomes (transplant, death, admission) and admission rates (40%, range 25%-60%). RESULTS Using fixed costs of outcomes and outcome rates, microbiota analysis was cost-saving ($47K-$97K) at $250 and $350/sample if admissions were reduced by 5%over SOC and >10% with $650/sample. When costs of LT, death and admissions were varied, these cost-savings remained robust provided there was >2.1% reduction (range 1.3%-3.2%) for $250/sample, >2.9% (range 1.8%-4.4%) for $350/sample and >5.4% (range 3.3%-8.2%) for $650/sample. These cost-savings remained robust even when the assumed admission rate was varied for all sample cost values. CONCLUSIONS Gut microbiota analysis is cost-effective for predicting and potentially preventing 90-day admissions in cirrhosis over current standard of care. This cost-saving remained robust even after sensitivity analyses that varied the background admission rates.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | | | | | - Leroy R Thacker
- Department of Biostatistics, Virginia Commonwealth University Medical Center, Richmond, Virginia
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30
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Liu R, Kang JD, Sartor RB, Sikaroodi M, Fagan A, Gavis EA, Zhou H, Hylemon PB, Herzog JW, Li X, Lippman RH, Gonzalez-Maeso J, Wade JB, Ghosh S, Gurley E, Gillevet PM, Bajaj JS. Neuroinflammation in Murine Cirrhosis Is Dependent on the Gut Microbiome and Is Attenuated by Fecal Transplant. Hepatology 2020; 71:611-626. [PMID: 31220352 PMCID: PMC6923631 DOI: 10.1002/hep.30827] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/16/2019] [Indexed: 12/14/2022]
Abstract
Cirrhosis and hepatic encephalopathy (HE) is associated with an altered gut-liver-brain axis. Fecal microbial transplant (FMT) after antibiotics improves outcomes in HE, but the impact on brain function is unclear. The aim of this study is to determine the effect of colonization using human donors in germ-free (GF) mice on the gut-liver-brain axis. GF and conventional mice were made cirrhotic using carbon tetrachloride and compared with controls in GF and conventional state. Additional GF mice were colonized with stool from controls (Ctrl-Hum) and patients with cirrhosis (Cirr-Hum). Stools from patients with HE cirrhosis after antibiotics were pooled (pre-FMT). Stools from the same patients 15 days after FMT from a healthy donor were also pooled (post-FMT). Sterile supernatants were created from pre-FMT and post-FMT samples. GF mice were colonized using stools/sterile supernatants. For all mice, frontal cortex, liver, and small/large intestines were collected. Cortical inflammation, synaptic plasticity and gamma-aminobutyric acid (GABA) signaling, and liver inflammation and intestinal 16s ribosomal RNA microbiota sequencing were performed. Conventional cirrhotic mice had higher degrees of neuroinflammation, microglial/glial activation, GABA signaling, and intestinal dysbiosis compared with other groups. Cirr-Hum mice had greater neuroinflammation, microglial/glial activation, and GABA signaling and lower synaptic plasticity compared with Ctrl-Hum mice. This was associated with greater dysbiosis but no change in liver histology. Pre-FMT material colonization was associated with neuroinflammation and microglial activation and dysbiosis, which was reduced significantly with post-FMT samples. Sterile pre-FMT and post-FMT supernatants did not affect brain parameters. Liver inflammation was unaffected. Conclusion: Fecal microbial colonization from patients with cirrhosis results in higher degrees of neuroinflammation and activation of GABAergic and neuronal activation in mice regardless of cirrhosis compared with those from healthy humans. Reduction in neuroinflammation by using samples from post-FMT patients to colonize GF mice shows a direct effect of fecal microbiota independent of active liver inflammation or injury.
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Affiliation(s)
- Runping Liu
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Jason D. Kang
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - R. Balfour Sartor
- National Gnotobiotic Rodent Resource Center, Departments of Medicine, Microbiology, and Immunology, University of North Carolina, Chapel Hill, NC
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Edith A. Gavis
- Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Huiping Zhou
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Phillip B. Hylemon
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Jeremy W. Herzog
- National Gnotobiotic Rodent Resource Center, Departments of Medicine, Microbiology, and Immunology, University of North Carolina, Chapel Hill, NC
| | - Xiaojiaoyang Li
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Robert H. Lippman
- Department of Pathology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - James B. Wade
- Department of Psychiatry, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Siddhartha Ghosh
- Division of Nephrology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Emily Gurley
- Division of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | | | - Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
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31
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Cox IJ, Idilman R, Fagan A, Turan D, Ajayi L, Le Guennec AD, Taylor-Robinson SD, Karakaya F, Gavis E, Andrew Atkinson R, Williams R, Sikaroodi M, Nizam S, Gillevet PM, Bajaj JS. Metabolomics and microbial composition increase insight into the impact of dietary differences in cirrhosis. Liver Int 2020; 40:416-427. [PMID: 31544308 PMCID: PMC6980909 DOI: 10.1111/liv.14256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Dietary changes can modulate gut microbiota and interact with cirrhosis. Our prior study demonstrated that microbial diversity was higher in cirrhotics from Turkish vs the USA, which was associated with lower risk of 90-day hospitalizations. We aimed to define gut microbial functional and metabolomic changes to increase insight into benefits of the Mediterranean compared to Western diets. METHODS In all, 139 Turkish (46 controls/50 compensated/43 decompensated) and 157 American subjects (48 controls/59 compensated/50 decompensated) were studied. Turkish subjects consumed a modified Mediterranean diet with daily fermented milk intake, whereas Americans consumed a Western diet. Predicted gut microbial functionalities and plasma metabolomics were compared between/within countries. Correlation network differences between microbiota and metabolites in cirrhotics from Turkey vs the USA were evaluated. RESULTS Predicted microbial function showed lower amino acid, bioenergetics and lipid pathways, with functions related to vitamin B, glycan, xenobiotic metabolism, DNA/RNA synthesis, in cirrhotics from Turkey compared to the USA. Plasma metabolomics demonstrated higher relative lactate levels in Turkey vs the USA. The metabolite changes in decompensated cirrhosis, compared to controls, showed similar trends in Turkey and the USA, with reduced lipids and phosphocholines. Phosphocholines were significantly lower in patients hospitalized in 90 days (P = .03). Correlation networks in cirrhotics demonstrated linkage differences between beneficial taxa, Blautia and Oscillispira, and lactate and unsaturated lipids, in Turkey compared to American patients. CONCLUSIONS A modified Mediterranean diet was associated with altered plasma metabolomics and beneficially alters microbiota functionality and correlations compared to Western diet in cirrhosis. These altered diet-microbial interactions could potentially affect the 90-day hospitalization risk.
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Affiliation(s)
- I Jane Cox
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | | | - Andrew Fagan
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | | | - Lola Ajayi
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | - Adrien D Le Guennec
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | | | | | - Edith Gavis
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - R Andrew Atkinson
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Roger Williams
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | | | | | | | - Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
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32
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Zawada SG, von Fricken ME, Weppelmann TA, Sikaroodi M, Gillevet PM. Optimization of tissue sampling for Borrelia burgdorferi in white-footed mice (Peromyscus leucopus). PLoS One 2020; 15:e0226798. [PMID: 31978068 PMCID: PMC6980393 DOI: 10.1371/journal.pone.0226798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/04/2019] [Indexed: 11/18/2022] Open
Abstract
Peromyscus leucopus (the white-footed mouse) is a known reservoir of the Lyme disease spirochete Borrelia burgdorferi. Sampling of white-footed mice allows for year-round B. burgdorferi surveillance as well as opportunities to establish the diversity of the different variants in a geographic region. This study explores the prevalence of B. burgdorferi infections in the tissues of white-footed mice, investigates the correlations between B. burgdorferi infected tissues, and determines the optimum field methods for surveillance of B. burgdorferi in P. leucopus. A total of 90 mice and 573 tissues (spleen, liver, ear, tongue, tail, heart, and kidney) were screened via nested PCR for B. burgdorferi infections. A large number of infections were found in the 90 mice as well as multiple infections within individual mice. Infections in a single mouse tissue (spleen, liver, ear, tongue and tail) were predictive of concurrent infection in other tissues of the same mouse at a statistically significant level. Ear tissue accounted for 68.4% of detected infections, which increased to 78.9% of the infected mice with the inclusion of tail samples. The use of ear punch or tail snip samples (used individually or in tandem) have multiple advantages over current Lyme disease ecological studies and surveillance methodologies, including lower associated costs, minimization of delays, year-round B. burgdorferi testing opportunities, as well as longitudinal monitoring of B. burgdorferi in defined geographic regions. In the absence of an effective vaccine, personal prevention measures are currently the most effective way to reduce Lyme disease transmission to humans. Thus, the identification and monitoring of environmental reservoirs to inform at-risk populations remains a priority. The sampling methods proposed in this study provide a reasonable estimate of B. burgdorferi in white-footed mice in a timely and cost-effective manner.
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Affiliation(s)
- Sonya G. Zawada
- Department of Environmental Science & Public Policy, George Mason University, Fairfax, Virginia, United States of America
- Department of Biology, University of Mary Washington, Fredericksburg, Virginia, United States of America
- * E-mail:
| | - Michael E. von Fricken
- Department of Global and Community Health, George Mason University, Fairfax, Virginia, United States of America
| | - Thomas A. Weppelmann
- Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Masoumeh Sikaroodi
- Department of Biology, George Mason University, Fairfax, Virginia, United States of America
| | - Patrick M. Gillevet
- Department of Biology, George Mason University, Fairfax, Virginia, United States of America
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Bajaj JS, Salzman N, Acharya C, Takei H, Kakiyama G, Fagan A, White MB, Gavis EA, Holtz ML, Hayward M, Nittono H, Hylemon PB, Cox IJ, Williams R, Taylor-Robinson SD, Sterling RK, Matherly SC, Fuchs M, Lee H, Puri P, Stravitz RT, Sanyal AJ, Ajayi L, Le Guennec A, Atkinson RA, Siddiqui MS, Luketic V, Pandak WM, Sikaroodi M, Gillevet PM. Microbial functional change is linked with clinical outcomes after capsular fecal transplant in cirrhosis. JCI Insight 2019; 4:133410. [PMID: 31751317 PMCID: PMC6975263 DOI: 10.1172/jci.insight.133410] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUNDHepatic encephalopathy (HE) is associated with poor outcomes. A prior randomized, pilot trial demonstrated safety after oral capsular fecal microbial transplant (FMT) in HE, with favorable changes in microbial composition and cognition. However, microbial functional changes are unclear. The aim of this study was to determine the effect of FMT on the gut-brain axis compared with placebo, using microbial function based on bile acids (BAs), inflammation (serum IL-6, LPS-binding protein [LBP]), and their association with EncephalApp.METHODSTwenty cirrhotic patients were randomized 1:1 into groups that received 1-time FMT capsules from a donor enriched in Lachnospiraceae and Ruminococcaceae or placebo capsules, with 5-month follow-up for safety outcomes. Stool microbiota and BA; serum IL-6, BA, and LBP; and EncephalApp were analyzed at baseline and 4 weeks after FMT/placebo. Correlation networks among microbiota, BAs, EncephalApp, IL-6, and LBP were performed before/after FMT.RESULTSFMT-assigned participants had 1 HE recurrence and 2 unrelated infections. Six placebo-assigned participants developed negative outcomes. FMT, but not placebo, was associated with reduced serum IL-6 and LBP and improved EncephalApp. FMT-assigned participants demonstrated higher deconjugation and secondary BA formation in feces and serum compared with baseline. No change was seen in placebo. Correlation networks showed greater complexity after FMT compared with baseline. Beneficial taxa, such as Ruminococcaceae, Verrucomicrobiaceae, and Lachnospiraceae, were correlated with cognitive improvement and decrease in inflammation after FMT. Fecal/serum secondary/primary ratios and PiCRUST secondary BA pathways did not increase in participants who developed poor outcomes.CONCLUSIONGut microbial function in cirrhosis is beneficially affected by capsular FMT, with improved inflammation and cognition. Lower secondary BAs in FMT recipients could select for participants who develop negative outcomes.TRIAL REGISTRATIONClinicaltrials.gov NCT03152188.FUNDINGNational Center for Advancing Translational Sciences NIH grant R21TR002024, VA Merit Review grant 2I0CX001076, the United Kingdom National Institute for Health Research Biomedical Facility at Imperial College London, the British Heart Foundation, Wellcome Trust, and King's College London.
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Affiliation(s)
- Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Nita Salzman
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | - Genta Kakiyama
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Melanie B. White
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Edith A. Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Mary L. Holtz
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael Hayward
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - I. Jane Cox
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | - Roger Williams
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | | | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Scott C. Matherly
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Hannah Lee
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - R. Todd Stravitz
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Arun J. Sanyal
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Lola Ajayi
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | - Adrien Le Guennec
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King’s College London, London, United Kingdom
| | - R. Andrew Atkinson
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King’s College London, London, United Kingdom
| | - Mohammad S. Siddiqui
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Velimir Luketic
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - William M. Pandak
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Bajaj JS, Salzman NH, Acharya C, Sterling RK, White MB, Gavis EA, Fagan A, Hayward M, Holtz ML, Matherly S, Lee H, Osman M, Siddiqui MS, Fuchs M, Puri P, Sikaroodi M, Gillevet PM. Fecal Microbial Transplant Capsules Are Safe in Hepatic Encephalopathy: A Phase 1, Randomized, Placebo-Controlled Trial. Hepatology 2019; 70:1690-1703. [PMID: 31038755 PMCID: PMC6819208 DOI: 10.1002/hep.30690] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2019] [Indexed: 12/11/2022]
Abstract
Hepatic encephalopathy (HE) can cause major morbidity despite standard of care (SOC; rifaximin/lactulose). Fecal microbial transplant (FMT) enemas postantibiotics are safe, but the effect of FMT without antibiotics using the capsular route requires investigation. The aim of this work was to determine the safety, tolerability, and impact on mucosal/stool microbiota and brain function in HE after capsular FMT in a randomized, single-blind, placebo-controlled clinical trial in Virginia. Patients with cirrhosis with recurrent HE with MELD (Model for End-Stage Liver Disease) <17 on SOC were randomized 1:1 into receiving 15 FMT capsules versus placebo from a single donor enriched in Lachnospiraceae and Ruminococcaceae. Endoscopies with duodenal and sigmoid biopsies, stool analysis, cognition, serum lipopolysaccharide-binding protein (LBP), and duodenal antimicrobial peptide (AMP) expression at baseline were used. Clinical follow-up with SOC maintenance was performed until 5 months. FMT-assigned patients underwent repeat endoscopies 4 weeks postenrollment. Twenty subjects on lactulose/rifaximin were randomized 1:1. MELD score was similar at baseline (9.6 vs. 10.2) and study end (10.2 vs. 10.5). Six patients in the placebo group required hospitalizations compared to 1 in FMT, which was deemed unrelated to FMT. Infection/HE episodes were similar between groups. Baseline microbial diversity was similar in all tissues between groups. Post-FMT, duodenal mucosal diversity (P = 0.01) increased with higher Ruminococcaceae and Bifidobacteriaceae and lower Streptococcaceae and Veillonellaceae. Reduction in Veillonellaceae were noted post-FMT in sigmoid (P = 0.04) and stool (P = 0.05). Duodenal E-cadherin (P = 0.03) and defensin alpha 5 (P = 0.03) increased whereas interleukin-6 (P = 0.02) and serum LBP (P = 0.009) reduced post-FMT. EncephalApp performance improved post-FMT only (P = 0.02). Conclusion: In this phase 1 study, oral FMT capsules are safe and well tolerated in patients with cirrhosis and recurrent HE. FMT was associated with improved duodenal mucosal diversity, dysbiosis, and AMP expression, reduced LBP, and improved EncephalApp performance. Further studies are needed to prove efficacy.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Nita H Salzman
- Pediatrics and Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Melanie B White
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Edith A Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Michael Hayward
- Pediatrics and Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary L. Holtz
- Pediatrics and Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Scott Matherly
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | | | | | - Michael Fuchs
- Pediatrics and Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Puneet Puri
- Pediatrics and Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
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Bajaj JS, Fagan A, Sikaroodi M, Kakiyama G, Takei H, Degefu Y, Pandak WM, Hylemon PB, Fuchs M, John B, Heuman DM, Gavis E, Nittono H, Patil R, Gillevet PM. Alterations in Skin Microbiomes of Patients With Cirrhosis. Clin Gastroenterol Hepatol 2019; 17:2581-2591.e15. [PMID: 30905718 PMCID: PMC6754819 DOI: 10.1016/j.cgh.2019.03.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Patients with cirrhosis have intestinal dysbiosis and are prone to itching and skin or soft-tissue infections. The skin microbiome, and its relationship with intestinal microbiome, have not been characterized. We investigated alterations in skin microbiota of patients with cirrhosis and their association with intestinal microbiota and modulators of itch. METHODS We collected skin swabs at 7 sites and blood and stool samples from 20 healthy individuals (control subjects; mean age, 59 years) and 50 patients with cirrhosis (mean age, 61 years; mean model for end-stage disease score, 12; 20 with decompensation). Skin and stool samples were analyzed by 16s rRNA sequencing and serum samples were analyzed by liquid chromatography and mass spectrometry for levels of bile acids (BAs) and by an ELISA for autotaxin (an itch modulator). Participants were analyzed by the visual analog itch scale (VAS, 0-10,10 = maximum intensity). Data were compared between groups (cirrhosis vs control subjects, with vs without decompensation, VAS 5 or higher vs less than 5). Correlation networks between serum levels of BAs and skin microbiomes were compared between patients with cirrhosis with vs without itching. RESULTS The composition of microbiomes at all skin sites differed between control subjects and patients with cirrhosis and between patients with compensated vs decompensated cirrhosis. Skin microbiomes of patients with cirrhosis (especially those with decompensation) contained a higher relative abundance of Gammaproteobacteria, Streptococaceae, and Staphylococcaceae, and fecal microbiomes contained a higher relative abundance of Gammaproteobacteria, than control subjects. These bacterial taxa were associated with serum levels of autotaxin and BAs, which were higher in patients with VAS scores ≥5. Based on network statistics, microbial and BA interactions at all sites were more complex in patients with greater levels of itching in the shin, the most common site of itch. CONCLUSIONS We identified alterations in skin microbiome of patients with cirrhosis (in Gammaproteobacteria, Streptococcaceae, and Staphylococcaceae)-especially in patients with decompensation; fecal microbiomes of patients with cirrhosis had a higher relative abundance of Gammaproteobacteria than control subjects. These specific microbial taxa are associated with itching intensity and itch modulators, such as serum levels of BAs and autotaxin.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia.
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Masoumeh Sikaroodi
- Center for Microbiome Analysis, George Mason University,
Manassas, VA, USA
| | - Genta Kakiyama
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Hajme Takei
- Junshin Clinic Bile Acid Institute, Tokyo, Japan
| | - Yordanos Degefu
- Center for Microbiome Analysis, George Mason University,
Manassas, VA, USA
| | - William M Pandak
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Phillip B Hylemon
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Binu John
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Douglas M Heuman
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition,
Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA,
USA
| | | | - Rohan Patil
- Center for Microbiome Analysis, George Mason University,
Manassas, VA, USA
| | - Patrick M Gillevet
- Center for Microbiome Analysis, George Mason University,
Manassas, VA, USA
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Bajaj JS, Sikaroodi M, Fagan A, Heuman D, Gilles H, Gavis EA, Fuchs M, Gonzalez-Maeso J, Nizam S, Gillevet PM, Wade JB. Posttraumatic stress disorder is associated with altered gut microbiota that modulates cognitive performance in veterans with cirrhosis. Am J Physiol Gastrointest Liver Physiol 2019; 317:G661-G669. [PMID: 31460790 PMCID: PMC6879889 DOI: 10.1152/ajpgi.00194.2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/12/2019] [Accepted: 08/18/2019] [Indexed: 02/07/2023]
Abstract
Posttraumatic stress disorder (PTSD) is associated with cirrhosis in veterans, and therapeutic results are suboptimal. An altered gut-liver-brain axis exists in cirrhosis due to hepatic encephalopathy (HE), but the added impact of PTSD is unclear. The aim of this study was to define linkages between gut microbiota and cognition in cirrhosis with/without PTSD. Cirrhotic veterans (with/without prior HE) underwent cognitive testing [PHES, inhibitory control test (ICT), and block design test (BDT)], serum lipopolysaccharide-binding protein (LBP) and stool collection for 16S rRNA microbiota composition, and predicted function analysis (PiCRUST). PTSD was diagnosed using DSM-V criteria. Correlation networks between microbiota and cognition were created. Patients with/without PTSD and with/without HE were compared. Ninety-three combat-exposed male veterans [ (58 yr, MELD 11, 34% HE, 31% combat-PTSD (42 no-HE/PTSD, 19 PTSD-only, 22 HE-only, 10 PTSD+HE)] were included. PTSD patients had similar demographics, alcohol history, MELD, but worse ICT/BDT, and higher antidepressant use and LBP levels. Microbial diversity was lower in PTSD (2.1 ± 0.5 vs. 2.5 ± 0.5, P = 0.03) but unaffected by alcohol/antidepressant use. PTSD (P = 0.02) and MELD (P < 0.001) predicted diversity on regression. PTSD patients showed higher pathobionts (Enterococcus and Escherichia/Shigella) and lower autochthonous genera belonging to Lachnospiraceaeae and Ruminococcaceae regardless of HE. Enterococcus was correlated with poor cognition, while the opposite was true for autochthonous taxa regardless of PTSD/HE. Escherichia/Shigella was only linked with poor cognition in PTSD patients. Gut-brain axis-associated microbiota functionality was altered in PTSD. In male cirrhotic veterans, combat-related PTSD is associated with cognitive impairment, lower microbial diversity, higher pathobionts, and lower autochthonous taxa composition and altered gut-brain axis functionality compared with non-PTSD combat-exposed patients. Cognition was differentially linked to gut microbiota, which could represent a new therapeutic target.NEW & NOTEWORTHY Posttraumatic stress disorder (PTSD) in veterans with cirrhosis was associated with poor cognitive performance. This was associated with lower gut microbial diversity in PTSD with higher pathobionts belonging to Enterococcus and Escherichia/Shigella and lower beneficial taxa belonging to Lachnospiraceaeae and Ruminococcaceae, with functional alterations despite accounting for prior hepatic encephalopathy, psychoactive drug use, or model for end-stage liver disease score. Given the suboptimal response to current therapies for PTSD, targeting the gut microbiota could benefit the altered gut-brain axis in these patients.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Douglas Heuman
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - HoChong Gilles
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia
- McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Shahzor Nizam
- Microbiome Analysis Center, George Mason University, Manassas, Virginia
| | | | - James B Wade
- Department of Psychiatry, Virginia Commonwealth University Medical Center, Richmond, Virginia
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Solano-Aguilar G, Shao J, Urban J, Lakshman S, Jang S, Lozano V, Sikaroodi M, Gupta R, Gillevet P, Molokin A, Vinyard B, Humphrys M, Proszkowiec-Weglarz M, Beshah E, Lamon-Fava S, Walker M, Matthan N, Lichtenstein A. Dietary Patterns Differentially Affect Microbiome Composition and Function in a Porcine Model of Obesity-related Metabolic Disorder (OR23-04-19). Curr Dev Nutr 2019. [DOI: 10.1093/cdn/nzz040.or23-04-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
To determine the impact of two isocaloric diets containing (38% ,15% and 47% energy from fat, protein and carbohydrate, respectively): Western diet (WD) rich in saturated fat, refined carbohydrate, low in fiber and high in cholesterol, and a heart healthy diet (HHD) rich in unsaturated fat, unrefined carbohydrate, fruits/vegetables, high in fiber and low in cholesterol, on the composition and function of the gut microbiome
Methods
Thirty-Ossabaw pigs were fed WD or HHD diets with half within each group therapeutically treated with statin (atorvastatin [Lipitor]). The fecal microbiome was analyzed one and six months after dietary intervention by 16S rRNA sequencing and metagenomic function was empirically inferred
Results
Genus diversity was transiently affected with a reduced Shannon Diversity index one month after feeding the WD or HHD (FDR P < 0.05) with no change between groups at 6 months. Bacterial communities were clustered and separated by diet independent of gender and separated by treatment with statin in the HHD only. Verrucomicrobiaceae (Akkermansia) and Methanobacteriales (Methanobrevibacter) were increased in pigs as early as one month after feeding the HHD, as was Clostridiales and Bifidobacterium (associated with optimal intestinal health). There was an enrichment of Proteobacteria (Succinivibrionaceae, Desulfovibrionaceae) in pigs fed the WD. Additional members of the Firmicutes phylum were detected. Diet-dependent associations (all P < 0.05) were identified between Lachnospiraceae members and early host dyslipidemia, inflammation, and atheromatous lesions in the left anterior descending proximal (LAD) and LAD/Left circumflex (LCX) bifurcation six months post-intervention.
Conclusions
These data document for the first time a distinctive bacterial profile in Ossabaw pigs with a diet-induced dyslipidemia and early stage atherosclerosis. Taken together these results represent a new model to examine mechanistic pathways of dietary patterns and/or drug interactions and its effect on modulating microbiome in developing atherosclerosis.
Funding Sources
USDA project 8040-51530-056-00 and Inter Agency USDA Agreement 588-1950-9-001 between BHNRC and Jean Mayer USDA-HNRCA
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Affiliation(s)
| | | | - Joseph Urban
- Agricultural Research Service, United States Department of Agrigulture
| | | | | | | | | | | | | | | | | | | | | | | | - Stefania Lamon-Fava
- Cardiovascular Nutrition Lab, JM USDA-HNRCA at Tufts University, Boston, MA, USA
| | | | - Nirupa Matthan
- Cardiovascular Nutrition Lab, JM USDA HNRCA At Tufts University, Boston, MA, USA
| | - Alice Lichtenstein
- Friedman School of Nutrition Science and Policy at Tufts University; HNRCA at Tufts University
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Dadkhah E, Sikaroodi M, Korman L, Hardi R, Baybick J, Hanzel D, Kuehn G, Kuehn T, Gillevet PM. Gut microbiome identifies risk for colorectal polyps. BMJ Open Gastroenterol 2019; 6:e000297. [PMID: 31275588 PMCID: PMC6577315 DOI: 10.1136/bmjgast-2019-000297] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
Objective To characterise the gut microbiome in subjects with and without polyps and evaluate the potential of the microbiome as a non-invasive biomarker to screen for risk of colorectal cancer (CRC). Design Presurgery rectal swab, home collected stool, and sigmoid biopsy samples were obtained from 231 subjects undergoing screening or surveillance colonoscopy. 16S rRNA analysis was performed on 552 samples (231 rectal swab, 183 stool, 138 biopsy) and operational taxonomic units (OTU) were identified using UPARSE. Non-parametric statistical methods were used to identify OTUs that were significantly different between subjects with and without polyps. These informative OTUs were then used to build classifiers to predict the presence of polyps using advanced machine learning models. Results We obtained clinical data on 218 subjects (87 females, 131 males) of which 193 were White, 21 African-American, and 4 Asian-American. Colonoscopy detected polyps in 56% of subjects. Modelling of the non-invasive home stool samples resulted in a classification accuracy >75% for Naïve Bayes and Neural Network models using informative OTUs. A naïve holdout analysis performed on home stool samples resulted in an average false negative rate of 11.5% for the Naïve Bayes and Neural Network models, which was reduced to 5% when the two models were combined. Conclusion Gut microbiome analysis combined with advanced machine learning represents a promising approach to screen patients for the presence of polyps, with the potential to optimise the use of colonoscopy, reduce morbidity and mortality associated with CRC, and reduce associated healthcare costs.
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Affiliation(s)
- Ezzat Dadkhah
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Louis Korman
- Capital Digestive Care, Chevy Chase, Maryland, USA
| | | | | | | | | | | | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Bajaj JS, Fagan A, Gavis EA, Kassam Z, Sikaroodi M, Gillevet PM. Long-term Outcomes of Fecal Microbiota Transplantation in Patients With Cirrhosis. Gastroenterology 2019; 156:1921-1923.e3. [PMID: 30664879 PMCID: PMC6475479 DOI: 10.1053/j.gastro.2019.01.033] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia.
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Zain Kassam
- Finch Therapeutics Group, Somerville, Massachusetts, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Solano-Aguilar GI, Jang S, Lakshman S, Gupta R, Beshah E, Sikaroodi M, Vinyard B, Molokin A, Gillevet PM, Urban JF. The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function. Nutrients 2018; 10:nu10111721. [PMID: 30424006 PMCID: PMC6266512 DOI: 10.3390/nu10111721] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/28/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
A study was designed to determine the potential prebiotic effect of dietary mushrooms on the host immune response, and intestinal microbiota composition and function. Thirty-one six-week-old pigs were fed a pig grower diet alone or supplemented with either three or six servings of freeze-dried white button (WB)-mushrooms for six weeks. Host immune response was evaluated in peripheral blood mononuclear cells (PBMC), and alveolar macrophages (AM) after stimulation with Salmonella typhymurium-Lipopolysaccharide (LPS). Isolated DNA from fecal and proximal colon contents were used for 16S rDNA taxonomic analysis and linear discriminant analysis effect size (LEfSe) to determine bacterial abundance and metabolic function. Pigs gained weight with no difference in body composition or intestinal permeability. Feeding mushrooms reduced LPS-induced IL-1β gene expression in AM (P < 0.05) with no change in LPS-stimulated PBMC or the intestinal mucosa transcriptome. LEfSe indicated increases in Lachnospiraceae, Ruminococcaceae within the order Clostridiales with a shift in bacterial carbohydrate metabolism and biosynthesis of secondary metabolites in the mushroom-fed pigs. These results suggested that feeding WB mushrooms significantly reduced the LPS-induced inflammatory response in AM and positively modulated the host microbiota metabolism by increasing the abundance of Clostridiales taxa that are associated with improved intestinal health.
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Affiliation(s)
- Gloria I Solano-Aguilar
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Saebyeol Jang
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Sukla Lakshman
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Richi Gupta
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Ethiopia Beshah
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Bryan Vinyard
- Statistics Group, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Aleksey Molokin
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Joseph F Urban
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
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Bajaj JS, Matin P, White MB, Fagan A, Deeb JG, Acharya C, Dalmet SS, Sikaroodi M, Gillevet PM, Sahingur SE. Periodontal therapy favorably modulates the oral-gut-hepatic axis in cirrhosis. Am J Physiol Gastrointest Liver Physiol 2018; 315:G824-G837. [PMID: 30118351 PMCID: PMC6293251 DOI: 10.1152/ajpgi.00230.2018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cirrhosis is associated with a systemic proinflammatory milieu, endotoxemia, and gut dysbiosis. The oral cavity could be an additional source of inflammation. We aimed to determine the effect of periodontal therapy in cirrhosis through evaluating endotoxemia, inflammation, cognition, and quality of life (QOL). Age-matched cirrhotic and noncirrhotic subjects exhibiting chronic gingivitis and/or mild or moderate periodontitis underwent periodontal therapy with follow-up at 30 days. Saliva/stool for microbial composition and serum for Model for End-stage Liver Disease (MELD) score, endotoxin and lipopolysaccharide binding protein (LBP) and immune-inflammatory markers (IL-1β; IL-6; histatins 1, 3, 5; and lysozyme) were collected at baseline and day 30. The cognitive function and QOL were also evaluated similarly. A separate group of cirrhotic patients were followed for the same duration without periodontal therapy. Cirrhotics, especially those with hepatic encephalopathy (HE), demonstrated improved dysbiosis in stool and saliva, and improved endotoxin, LBP, and salivary and serum inflammatory mediators following periodontal therapy. These parameters, which were higher in HE at baseline, became statistically similar posttherapy. Pretherapy vs. posttherapy QOL and cognition also improved in HE patients following oral interventions. On the other hand, LBP and endotoxin increased over time in cirrhotic patients not receiving therapy, but the rest of the parameters, including microbiota remained similar over time in the no-therapy group. This proof-of-concept study demonstrates that periodontal therapy in cirrhosis, especially in those with HE, is associated with improved oral and gut dysbiosis, systemic inflammation, MELD score, and cognitive function, which was not observed in those who did not receive therapy over the same time period. NEW & NOTEWORTHY Systematic periodontal therapy in cirrhotic outpatients improved endotoxemia, as well as systemic and local inflammation, and modulated salivary and stool microbial dysbiosis over 30 days. This was associated with improved quality of life and cognition in patients with prior hepatic encephalopathy. In a cirrhotic group that was not provided periodontal therapy, there was an increase in endotoxin and lipopolysaccharide binding protein in the same duration. The oral cavity could be an important underdefined source of inflammation in cirrhosis.
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Affiliation(s)
- Jasmohan S. Bajaj
- 1Department of Internal Medicine, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Payam Matin
- 2Department of Periodontics, Virginia Commonwealth University, Richmond, Virginia
| | - Melanie B. White
- 1Department of Internal Medicine, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Andrew Fagan
- 1Department of Internal Medicine, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Janina Golob Deeb
- 2Department of Periodontics, Virginia Commonwealth University, Richmond, Virginia
| | - Chathur Acharya
- 1Department of Internal Medicine, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Swati S. Dalmet
- 3Microbiome Analysis Center, George Mason University, Manassas, Virginia
| | - Masoumeh Sikaroodi
- 3Microbiome Analysis Center, George Mason University, Manassas, Virginia
| | | | - Sinem E. Sahingur
- 2Department of Periodontics, Virginia Commonwealth University, Richmond, Virginia
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Bajaj JS, Kakiyama G, Savidge T, Takei H, Kassam ZA, Fagan A, Gavis EA, Pandak WM, Nittono H, Hylemon PB, Boonma P, Haag A, Heuman DM, Fuchs M, John B, Sikaroodi M, Gillevet PM. Antibiotic-Associated Disruption of Microbiota Composition and Function in Cirrhosis Is Restored by Fecal Transplant. Hepatology 2018; 68:1549-1558. [PMID: 29665102 DOI: 10.1002/hep.30037] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 12/11/2022]
Abstract
UNLABELLED Patients with cirrhosis are often exposed to antibiotics that can lead to resistance and fungal overgrowth. The role of fecal microbial transplant (FMT) in restoring gut microbial function is unclear in cirrhosis. In a Food and Drug Administration-monitored phase 1 clinical safety trial, patients with decompensated cirrhosis on standard therapies (lactulose and rifaximin) were randomized to standard-of-care (SOC, no antibiotics/FMT) or 5 days of broad-spectrum antibiotics followed by FMT from a donor enriched in Lachnospiraceae and Ruminococcaceae. Microbial composition (diversity, family-level relative abundances), function (fecal bile acid [BA] deconjugation, 7α-dehydroxylation, short-chain fatty acids [SCFAs]), and correlations between Lachnospiraceae, Ruminococcaceae, and clinical variables were analyzed at baseline, postantibiotics, and 15 days post-FMT. FMT was well tolerated. Postantibiotics, there was a reduced microbial diversity and autochthonous taxa relative abundance. This was associated with an altered fecal SCFA and BA profile. Correlation linkage changes from beneficial at baseline to negative after antibiotics. All of these parameters became statistically similar post-FMT to baseline levels. No changes were seen in the SOC group. CONCLUSION In patients with advanced cirrhosis on lactulose and rifaximin, FMT restored antibiotic-associated disruption in microbial diversity and function. (Hepatology 2018; 00:000-000).
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Affiliation(s)
- Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Genta Kakiyama
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Tokyo, Japan
| | | | - Andrew Fagan
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Edith A Gavis
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - William M Pandak
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | | | - Phillip B Hylemon
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Prapaporn Boonma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Anthony Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Douglas M Heuman
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Michael Fuchs
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Binu John
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
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Bajaj JS, Acharya C, Fagan A, White MB, Gavis E, Heuman DM, Hylemon PB, Fuchs M, Puri P, Schubert ML, Sanyal AJ, Sterling RK, Stravitz TR, Siddiqui MS, Luketic V, Lee H, Sikaroodi M, Gillevet PM. Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis. Am J Gastroenterol 2018; 113:1177-1186. [PMID: 29872220 DOI: 10.1038/s41395-018-0085-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/01/2018] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Cirrhosis is associated with gut microbial dysbiosis, high readmissions and proton pump inhibitor (PPI) overuse, which could be inter-linked. Our aim was to determine the effect of PPI use, initiation and withdrawl on gut microbiota and readmissions in cirrhosis. METHODS Four cohorts were enrolled. Readmissions study: Cirrhotic inpatients were followed throughout the hospitalization and 30/90-days post-discharge. PPI initiation, withdrawal/continuation patterns were analyzed between those with/without readmissions. Cross-sectional microbiota study: Cirrhotic outpatients and controls underwent stool microbiota analysis. Beneficial autochthonous and oral-origin taxa analysis vis-à-vis PPI use was performed. Longitudinal studies: Two cohorts of decompensated cirrhotic outpatients were enrolled. Patients on chronic unindicated PPI use were withdrawn for 14 days. Patients not on PPI were started on omeprazole for 14 days. Microbial analysis for oral-origin taxa was performed pre/post-intervention. RESULTS Readmissions study: 343 inpatients (151 on admission PPI) were enrolled. 21 were withdrawn and 45 were initiated on PPI resulting in a PPI use increase of 21%. PPIs were associated with higher 30 (p = 0.002) and 90-day readmissions (p = 0.008) independent of comorbidities, medications, MELD and age. Cross-sectional microbiota: 137 cirrhotics (59 on PPI) and 45 controls (17 on PPI) were included. PPI users regardless of cirrhosis had higher oral-origin microbiota while cirrhotics on PPI had lower autochthonous taxa compared to the rest. Longitudinal studies: Fifteen decompensated cirrhotics tolerated omeprazole initiation with an increase in oral-origin microbial taxa compared to baseline. PPIs were withdrawn from an additional 15 outpatients, which resulted in a significant reduction of oral-origin taxa compared to baseline. CONCLUSIONS PPIs modulate readmission risk and microbiota composition in cirrhosis, which responds to withdrawal. The systematic withdrawal and judicious use of PPIs is needed from a clinical and microbiological perspective in decompensated cirrhosis.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Melanie B White
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Douglas M Heuman
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Phillip B Hylemon
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Puneet Puri
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Mitchell L Schubert
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Arun J Sanyal
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Todd R Stravitz
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Mohammad S Siddiqui
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Velimir Luketic
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Masoumeh Sikaroodi
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
| | - Patrick M Gillevet
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA, USA. Microbiome Analysis Center, George Mason University, Manassas, VA, USA
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Bajaj JS, Idilman R, Mabudian L, Hood M, Fagan A, Turan D, White MB, Karakaya F, Wang J, Atalay R, Hylemon PB, Gavis EA, Brown R, Thacker LR, Acharya C, Heuman DM, Sikaroodi M, Gillevet PM. Diet affects gut microbiota and modulates hospitalization risk differentially in an international cirrhosis cohort. Hepatology 2018; 68:234-247. [PMID: 29350768 DOI: 10.1002/hep.29791] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/14/2017] [Accepted: 01/16/2018] [Indexed: 12/17/2022]
Abstract
UNLABELLED The relative ranking of cirrhosis-related deaths differs between high-/middle-income countries. Gut microbiome is affected in cirrhosis and is related to diet. Our aim was to determine the effect of differing dietary habits on gut microbiota and clinical outcomes. Outpatient compensated/decompensated patients with cirrhosis and controls from Turkey and the United States underwent dietary and stool microbiota analysis. Patients with cirrhosis were followed till 90-day hospitalizations. Shannon diversity and multivariable determinants (Cox and binary logistic) of microbial diversity and hospitalizations were studied within/between groups. Two hundred ninety-six subjects (157 U.S.: 48 controls, 59 compensated, 50 decompensated; 139 Turkey: 46 controls, 50 compensated, 43 decompensated) were included. Patients with cirrhosis between cohorts had similar Model for End-Stage Liver Disease (MELD) scores. American patients with cirrhosis had more men, greater rifaximin/lactulose use, and higher hepatitis C/alcohol etiologies. Coffee intake was higher in Americans whereas tea, fermented milk, and chocolate intake were higher in Turkey. The entire Turkish cohort had a significantly higher microbial diversity than Americans, which did not change between their controls and patients with cirrhosis. In contrast, microbial diversity changed in the U.S.-based cohort and was the lowest in decompensated patients. Coffee, tea, vegetable, chocolate, and fermented milk intake predicted a higher diversity whereas MELD score, lactulose use, and carbonated beverage use predicted a lower microbial diversity. The Turkish cohort had a lower risk of 90-day hospitalizations. On Cox and binary logistic regression, microbial diversity was protective against 90-day hospitalizations, along with coffee/tea, vegetable, and cereal intake. CONCLUSION In this study of patients with cirrhosis and healthy controls from the United States and Turkey, a diet rich in fermented milk, vegetables, cereals, coffee, and tea is associated with a higher microbial diversity. Microbial diversity was associated with an independently lower risk of 90-day hospitalizations. (Hepatology 2018;68:234-247).
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Affiliation(s)
- Jasmohan S Bajaj
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Ramazan Idilman
- Ankara University School of Medicine, Department of Gastroenterology, Ankara, Turkey
| | - Leila Mabudian
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Matthew Hood
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Andrew Fagan
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Dilara Turan
- Ankara University School of Medicine, Department of Gastroenterology, Ankara, Turkey
| | - Melanie B White
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Fatih Karakaya
- Ankara University School of Medicine, Department of Gastroenterology, Ankara, Turkey
| | - Jessica Wang
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Rengül Atalay
- Bioinformatics Department, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Phillip B Hylemon
- Microbiology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Edith A Gavis
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Robert Brown
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Leroy R Thacker
- Biostatistics, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Chathur Acharya
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Douglas M Heuman
- Internal Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
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Bajaj JS, Liu EJ, Kheradman R, Fagan A, Heuman DM, White M, Gavis EA, Hylemon P, Sikaroodi M, Gillevet PM. Fungal dysbiosis in cirrhosis. Gut 2018; 67:1146-1154. [PMID: 28578302 DOI: 10.1136/gutjnl-2016-313170] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Cirrhotics have a high rate of infections, which are increasingly fungal or culture-negative in nature. While infected cirrhotics have bacterial dysbiosis, the role of fungi is unclear. We aimed to evaluate gut bacterial and fungal dysbiosis in cross-sectional and longitudinal analyses of outpatient and inpatient cirrhotics and prediction of hospitalisations. METHODS Cross-sectional: Age-matched controls, outpatients (with/without antibiotics) and hospitalised uninfected, culture-negative and culture-positive cirrhotics were included and followed for 90 days. Longitudinal: Three studies were conducted: (1) cirrhotics followed over 6 months, (2) outpatient cirrhotics administered antibiotics per standard of care for 5 days and (3) cirrhotics and controls administered omeprazole over 14 days. In all studies, stool bacterial/fungal profiles were analysed. RESULTS Cross-sectional: In 143 cirrhotics and 26 controls, bacterial and fungal diversities were significantly linked. Outpatients on antibiotics and patients with culture-positive infections had the lowest diversities. Bacterial and fungal correlations were complex in uninfected, outpatient and control groups but were markedly skewed in infected patients. 21% were admitted on 90-day follow-up. A lower Bacteroidetes/Ascomycota ratio was associated with lower hospitalisations. Longitudinal: Fungal and bacterial profiles were stable on follow-up (5 days and 6 months). After antibiotics, a significantly reduced bacterial and fungal diversity, higher Candida and lower autochthonous bacterial relative abundance were seen. After omeprazole, changes in bacterial diversity and composition were seen but fungal metrics remained stable. CONCLUSION There is a significant fungal dysbiosis in cirrhosis, which changes differentially with antibiotics and proton pump inhibitor use, but is otherwise stable over time. A combined bacterial-fungal dysbiosis metric, Bacteroidetes/Ascomycota ratio, can independently predict 90-day hospitalisations in patients with cirrhosis. CLINICAL TRIAL NUMBER NCT01458990.
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Affiliation(s)
- Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Eric J Liu
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Raffi Kheradman
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Andrew Fagan
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Douglas M Heuman
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Melanie White
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Edith A Gavis
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Phillip Hylemon
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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Bajaj JS, Kakiyama G, Cox IJ, Nittono H, Takei H, White M, Fagan A, Gavis EA, Heuman DM, Gilles HC, Hylemon P, Taylor-Robinson SD, Legido-Quigley C, Kim M, Xu J, Williams R, Sikaroodi M, Pandak WM, Patrick MG. Alterations in gut microbial function following liver transplant. Liver Transpl 2018; 24:752-761. [PMID: 29500907 PMCID: PMC5992060 DOI: 10.1002/lt.25046] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/16/2018] [Accepted: 02/25/2018] [Indexed: 12/12/2022]
Abstract
Liver transplantation (LT) improves daily function and ameliorates gut microbial composition. However, the effect of LT on microbial functionality, which can be related to overall patient benefit, is unclear and could affect the post-LT course. The aims were to determine the effect of LT on gut microbial functionality focusing on endotoxemia, bile acid (BA), ammonia metabolism, and lipidomics. We enrolled outpatient patients with cirrhosis on the LT list and followed them until 6 months after LT. Microbiota composition (Shannon diversity and individual taxa) and function analysis (serum endotoxin, urinary metabolomics and serum lipidomics, and stool BA profile) and cognitive tests were performed at both visits. We enrolled 40 patients (age, 56 ± 7 years; mean Model for End-Stage Liver Disease score, 22.6). They received LT 6 ± 3 months after enrollment and were re-evaluated 7 ± 3 months after LT with a stable course. A significant improvement in cognition with increase in microbial diversity, increase in autochthonous and decrease in potentially pathogenic taxa, and reduced endotoxemia were seen after LT compared with baseline. Stool BAs increased significantly after LT, and there was evidence of greater bacterial action (higher secondary, oxo and iso-BAs) after LT although the levels of conjugated BAs remained similar. There was a reduced serum ammonia and corresponding rise in urinary phenylacetylglutamine after LT. There was an increase in urinary trimethylamine-N-oxide, which was correlated with specific changes in serum lipids related to cell membrane products. The ultimate post-LT lipidomic profile appeared beneficial compared with the profile before LT. In conclusion, LT improves gut microbiota diversity and dysbiosis, which is accompanied by favorable changes in gut microbial functionality corresponding to BAs, ammonia, endotoxemia, lipidomic, and metabolomic profiles. Liver Transplantation 24 752-761 2018 AASLD.
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Affiliation(s)
- Jasmohan S. Bajaj
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Genta Kakiyama
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - I. Jane Cox
- Institute of Hepatology, London, Foundation for Liver Research, London UK
| | | | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Tokyo, Japan
| | - Melanie White
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Andrew Fagan
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Edith A. Gavis
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Douglas M. Heuman
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Ho Chong Gilles
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - Phillip Hylemon
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | | | | | - Min Kim
- Faculty of Life Sciences & Medicine, Kings College, London, UK
| | - Jin Xu
- Faculty of Life Sciences & Medicine, Kings College, London, UK
| | - Roger Williams
- Institute of Hepatology, London, Foundation for Liver Research, London UK
| | | | - William M. Pandak
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
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Solano-Aguilar GI, Lakshman S, Jang S, Beshah E, Xie Y, Sikaroodi M, Gupta R, Vinyard B, Molokin A, Urban JF, Gillevet P, Davis CD. The Effect of Feeding Cocoa Powder and Lactobacillus rhamnosus on the Composition and Function of Pig Intestinal Microbiome. Curr Dev Nutr 2018; 2:nzy011. [PMID: 30019034 PMCID: PMC6041806 DOI: 10.1093/cdn/nzy011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/15/2017] [Accepted: 01/30/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Dietary habits have been linked with variability of gut microbiota composition and disease risk. OBJECTIVE The aim of this study was to evaluate the effect of feeding a cocoa powder with or without a probiotic on the composition and function of the fecal microbiome of pigs. METHODS Four groups of 8 pigs each were fed a standard growth diet supplemented with cocoa powder, Lactobacillus rhamnosus (LGG), cocoa powder + LGG, or an equal amount of fiber similar to that found in cocoa powder (control group). Fecal samples were collected prior to and 4 wk after initiation of the dietary intervention. Microbiota composition was determined after amplification of the first 2 variable regions of the 16S ribosomal DNA (rDNA). Predictions of metagenomic function were calculated using 16S rDNA sequence data through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). RESULTS After 4 wk of treatment, bacterial abundance analysis demonstrated a prebiotic effect of cocoa powder on endogenous Bifidobacteriaceae and Lactobacillaceae and increased abundance of saccharolytic butyrate-producing bacteria like Roseburia. An increased bacterial evenness, Shannon diversity index, and diverse metabolic profile were detected in microbiomes of pigs fed the cocoa powder + LGG (P < 0.05) but not in pigs in the other 3 groups. CONCLUSION The data generated from this work demonstrated that 4-wk dietary treatment with cocoa powder alone or in combination with LGG probiotic had an impact on the composition and function of the fecal microbiota of healthy pigs.
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Affiliation(s)
- Gloria I Solano-Aguilar
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Sukla Lakshman
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Saebyeol Jang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Ethiopia Beshah
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | | | - Richi Gupta
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Bryan Vinyard
- Biometrical Consulting Services, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Aleksey Molokin
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Joseph F Urban
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Patrick Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Cindy D Davis
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD
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48
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Keshteli AH, Tso R, Dieleman LA, Park H, Kroeker KI, Jovel J, Gillevet PM, Sikaroodi M, Mandal R, Fedorak RN, Madsen KL. A Distinctive Urinary Metabolomic Fingerprint Is Linked With Endoscopic Postoperative Disease Recurrence in Crohn's Disease Patients. Inflamm Bowel Dis 2018; 24:861-870. [PMID: 29562272 DOI: 10.1093/ibd/izx070] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Crohn's disease (CD) patients who undergo ileocolonic resection frequently have disease recurrence. The aim of this preliminary study was to identify urinary metabolomic profiles associated with disease recurrence in order to identify underlying mechanisms of recurrence and possible disease biomarkers. METHODS Biopsies from the neoterminal ileum were collected from CD patients (n = 38) after ileocolonic resection in order to assess mucosa-associated microbiota using 16S rRNA multitag pyrosequencing. Urine samples were collected, and metabolomic profiling was done using high-resolution nuclear magnetic resolution spectroscopy and a combined direct infusion liquid chromatography tandem mass spectrometry. The Rutgeerts scoring system was used to assess endoscopic postoperative recurrence of CD. RESULTS There were 28 (73.7%) patients with endoscopic CD recurrence. CD patients who were in endoscopic remission had a higher abundance of Bacteroidetes and lower abundance of Fusobacteria and Proteobacteria in comparison with CD patients who had endoscopic recurrence. In addition, metabolomic profiling could also discriminate between these 2 groups of patients. Endoscopic recurrence was associated with increased concentration of urinary levoglucosan. Rutgeerts score was positively correlated with levoglucosan and propylene glycol levels. CONCLUSIONS CD patients who present with endoscopic disease recurrence after surgery have a unique urinary metabolomic fingerprint that can differentiate them from CD patients who are in endoscopic remission after ileocolonic resection. In addition, mucosal-associated microbiota in CD patients with or without disease recurrence after surgery differs and correlates with some urinary metabolites.
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Affiliation(s)
- Ammar Hassanzadeh Keshteli
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Robert Tso
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Levinus A Dieleman
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Heekuk Park
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Karen I Kroeker
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Juan Jovel
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | | | | | - Rupasri Mandal
- Department of Biological Science, University of Alberta, Edmonton, AB, Canada
| | - Richard N Fedorak
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, AB, Canada
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49
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Bajaj JS, Thacker LR, Fagan A, White MB, Gavis EA, Hylemon PB, Brown R, Acharya C, Heuman DM, Fuchs M, Dalmet S, Sikaroodi M, Gillevet PM. Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis. JCI Insight 2018. [PMID: 29515036 DOI: 10.1172/jci.insight.98019] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cirrhosis is associated with gut microbial changes, but current 16S rDNA techniques sequence both dead and live bacteria. We aimed to determine the rRNA content compared with DNA from the same stool sample to evaluate cirrhosis progression and predict hospitalizations. METHODS Cirrhotics and controls provided stool for RNA and DNA analysis. Comparisons were made between cirrhotics/controls and within cirrhosis (compensated/decompensated, infected/uninfected, renal dysfunction/not, rifaximin use/not) with respect to DNA and RNA bacterial content using linear discriminant analysis. A separate group was treated with omeprazole for 14 days with longitudinal microbiota evaluation. Patients were followed for 90 days for hospitalizations. Multivariable models for hospitalizations with clinical data with and without DNA and RNA microbial data were created. RESULTS Twenty-six controls and 154 cirrhotics (54 infected, 62 decompensated, 20 renal dysfunction, 18 rifaximin) were included. RNA and DNA analysis showed differing potentially pathogenic taxa but similar autochthonous taxa composition. Thirty subjects underwent the omeprazole study, which demonstrated differences between RNA and DNA changes. Thirty-six patients were hospitalized within 90 days. In the RNA model, MELD score and Enterococcus were independently predictive of hospitalizations, while in the DNA model MELD was predictive and Roseburia protective. In both models, adding microbiota significantly added to the MELD score in predicting hospitalizations. CONCLUSION DNA and RNA analysis of the same stool sample demonstrated differing microbiota composition, which independently predicts the hospitalization risk in cirrhosis. RNA and DNA content of gut microbiota in cirrhosis are modulated differentially with disease severity, infections, and omeprazole use. TRIAL REGISTRATION NCT01458990. FUNDING VA Merit I0CX001076.
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Affiliation(s)
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition
| | | | - Edith A Gavis
- Division of Gastroenterology, Hepatology and Nutrition
| | - Phillip B Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Robert Brown
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | | | | | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition
| | - Swati Dalmet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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50
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Laffin M, Perry T, Park H, Gillevet P, Sikaroodi M, Kaplan GG, Fedorak R, Kroeker KI, Dieleman LA, Dicken B, Madsen K. A83 THE MUCOSA-ASSOCIATED-MICROBIOTA IS ASSOCIATED WITH RELAPSE IN CROHN’S DISEASE PATIENTS UNDERGOING ILEOCECAL RESECTION. J Can Assoc Gastroenterol 2018. [DOI: 10.1093/jcag/gwy008.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M Laffin
- University of Alberta, Edmonton, AB, Canada
| | - T Perry
- University of Alberta, Edmonton, AB, Canada
| | - H Park
- University of Alberta, Edmonton, AB, Canada
| | | | | | - G G Kaplan
- Medicine and Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - R Fedorak
- University of Alberta, Edmonton, AB, Canada
| | | | | | - B Dicken
- University of Alberta, Edmonton, AB, Canada
| | - K Madsen
- University of Alberta, Edmonton, AB, Canada
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