Regulation of Immune Homeostasis, Inflammation, and HIV Persistence by the Microbiome, Short-Chain Fatty Acids, and Bile Acids

Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection

(2023) Flora Mikaeloff et al.   eLife

Defective humoral immunity disrupts bile acid homeostasis which promotes inflammatory disease of the small bowel

(2022) Ahmed Dawood Mohammed et al.   Nature Communications

Gut Microbiome and Bile Acid Metabolism Induced the Activation of CXCR5+ CD4+ T Follicular Helper Cells to Participate in Neuromyelitis Optica Spectrum Disorder Recurrence

(2022) Xi Cheng et al.   Frontiers in Immunology

IFNα-blockade during ART-treated SIV infection lowers tissue vDNA, rescues immune function, and improves overall health

(2022) Louise A. Swainson et al.   JCI Insight

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

(2022) Donggi Paik et al.   NATURE

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

(2022) et al.   SCIENCE

Butyrate administration is not sufficient to improve immune reconstitution in antiretroviral-treated SIV-infected macaques

(2022) Alexandra M. Ortiz et al.   Scientific Reports

Short-chain fatty acid acetate triggers antiviral response mediated by RIG-I in cells from infants with respiratory syncytial virus bronchiolitis

(2022) Krist H. Antunes et al.   EBioMedicine

Bile acids in immunity: Bidirectional mediators between the host and the microbiota

(2022) Urszula Godlewska et al.   Frontiers in Immunology

Bile acids and the gut microbiota: metabolic interactions and impacts on disease

(2022) Stephanie L. Collins et al.   NATURE REVIEWS MICROBIOLOGY

Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion

(2022) Jennifer A. Fulcher et al.   EBioMedicine

FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2

(2022) Teresa Brevini et al.   NATURE

Residual immune dysfunction under antiretroviral therapy

(2021) Catherine W. Cai et al.   SEMINARS IN IMMUNOLOGY

Bile Acids Impair Vaccine Response in Children With Biliary Atresia

(2021) Jinchuan Liu et al.   Frontiers in Immunology

Short chain fatty acids and its producing organisms: An overlooked therapy for IBD?

(2021) Sara Deleu et al.   EBioMedicine

Translocated microbiome composition determines immunological outcome in treated HIV infection

(2021) Krystelle Nganou-Makamdop et al.   CELL

A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1

(2021) Wei Li et al.   Cell Host & Microbe

Review: microbial transformations of human bile acids

(2021) Douglas V. Guzior et al.   Microbiome

HIV-Infected Individuals on ART With Impaired Immune Recovery Have Altered Plasma Metabolite Profiles

(2021) Sofia Nyström et al.   Open Forum Infectious Diseases

Therapeutic potential of indole derivatives as anti-HIV agents: A mini-review

(2021) Qingtai Chen et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease

(2020) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

B cell-intrinsic epigenetic modulation of antibody responses by dietary fiber-derived short-chain fatty acids

(2020) Helia N. Sanchez et al.   Nature Communications

Butyrate reprograms expression of specific interferon stimulated genes

(2020) Mahesh Chemudupati et al.   JOURNAL OF VIROLOGY

Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells

(2020) Clarissa Campbell et al.   NATURE

The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis

(2020) Emma S. Winkler et al.   CELL

Molecular Physiology of Bile Acid Signaling in Health, Disease and Aging

(2020) Alessia Perino et al.   PHYSIOLOGICAL REVIEWS

Microbiome definition re-visited: old concepts and new challenges

(2020) Gabriele Berg et al.   Microbiome

Short-Chain Fatty Acids and Their Association with Signalling Pathways in Inflammation, Glucose and Lipid Metabolism

(2020) Jin He et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gut microbiota, kynurenine pathway and mental disorders – Review

(2020) Magdalena Więdłocha et al.   PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY

Intestinal microbiota-derived short-chain fatty acids regulation of immune cell IL-22 production and gut immunity

(2020) Wenjing Yang et al.   Nature Communications

Gut microbiota-derived metabolites as central regulators in metabolic disorders

(2020) Allison Agus et al.   GUT

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism

(2020) Ryan K. Cheu et al.   PLoS Pathogens

Virus-induced accumulation of intracellular bile acids activates the TGR5-β-arrestin-SRC axis to enable innate antiviral immunity

(2019) Ming-Ming Hu et al.   CELL RESEARCH

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Secondary Bile Acids and Short Chain Fatty Acids in the Colon: A Focus on Colonic Microbiome, Cell Proliferation, Inflammation, and Cancer

(2019) Huawei Zeng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

(2019) Julie Schulthess et al.   IMMUNITY

Fungal Translocation is Associated with Immune Activation and Systemic Inflammation in Treated HIV

(2019) Lukasz Weiner et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Altered differentiation is central to HIV-specific CD4+ T cell dysfunction in progressive disease

(2019) Antigoni Morou et al.   NATURE IMMUNOLOGY

Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response

(2019) Krist Helen Antunes et al.   Nature Communications

The Role of the Microbiome in Drug Response

(2019) Rosina Pryor et al.   Annual Review of Pharmacology and Toxicology

Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans

(2019) Thomas Hagan et al.   CELL

Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome

(2019) Ornella Sortino et al.   Open Forum Infectious Diseases

Differentiation into an Effector Memory Phenotype Potentiates HIV-1 Latency Reversal in CD4+ T Cells

(2019) Deanna A. Kulpa et al.   JOURNAL OF VIROLOGY

Bile acid metabolites control TH17 and Treg cell differentiation

(2019) Saiyu Hang et al.   NATURE

Exacerbation of Chikungunya Virus Rheumatic Immunopathology by a High Fiber Diet and Butyrate

(2019) Natalie A. Prow et al.   Frontiers in Immunology

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

(2019) Xinyang Song et al.   NATURE

The microbial metabolite trimethylamine-N-oxide in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages

(2018) Catharina Missailidis et al.   AIDS

Dietary Fiber Confers Protection against Flu by Shaping Ly6c − Patrolling Monocyte Hematopoiesis and CD8 + T Cell Metabolism

(2018) Aurélien Trompette et al.   IMMUNITY

Gut Microbial-related Choline Metabolite Trimethylamine-N-oxide is Associated with Progression of Carotid Artery Atherosclerosis in HIV Infection

(2018) Zhilei Shan et al.   JOURNAL OF INFECTIOUS DISEASES

Role of Bile Acids in Metabolic Control

(2018) Antonio Molinaro et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The microbiome and HIV persistence

(2018) Wei Li A. Koay et al.   Current Opinion in HIV and AIDS

Reprogramming of pro-inflammatory human macrophages to an anti-inflammatory phenotype by bile acids

(2018) Marianne Wammers et al.   Scientific Reports

Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells

(2018) Camille Martin-Gallausiaux et al.   Scientific Reports

Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients

(2018) Wei Lu et al.   Frontiers in Microbiology

Regulatory T Cells As Potential Targets for HIV Cure Research

(2018) Adam J. Kleinman et al.   Frontiers in Immunology

Regulation of the effector function of CD8+ T cells by gut microbiota-derived metabolite butyrate

(2018) Maik Luu et al.   Scientific Reports

Enrichment of gut-derived Fusobacterium is associated with suboptimal immune recovery in HIV-infected individuals

(2018) Soo Ching Lee et al.   Scientific Reports

Bile Acids Activated Receptors Regulate Innate Immunity

(2018) Stefano Fiorucci et al.   Frontiers in Immunology

Gut Microbiome, Short-Chain Fatty Acids, and Mucosa Injury in Young Adults with Human Immunodeficiency Virus Infection

(2018) Yong Qing et al.   DIGESTIVE DISEASES AND SCIENCES

Metabolite-Sensing G Protein Coupled Receptor TGR5 Protects Host From Viral Infection Through Amplifying Type I Interferon Responses

(2018) Qingqing Xiong et al.   Frontiers in Immunology

The role of the microbiota in infectious diseases

(2018) Josie Libertucci et al.   Nature Microbiology

Farnesoid X receptor induces Takeda G-protein receptor 5 cross-talk to regulate bile acid synthesis and hepatic metabolism

(2017) Preeti Pathak et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lithocholic acid controls adaptive immune responses by inhibition of Th1 activation through the Vitamin D receptor

(2017) Thijs W. H. Pols et al.   PLoS One

Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells

(2017) Claudia Nastasi et al.   Scientific Reports

Butyrate Conditions Human Dendritic Cells to Prime Type 1 Regulatory T Cells via both Histone Deacetylase Inhibition and G Protein-Coupled Receptor 109A Signaling

(2017) Maria M. M. Kaisar et al.   Frontiers in Immunology

Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys

(2016) Dan H. Barouch et al.   CELL

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination

(2016) Scott A. Handley et al.   Cell Host & Microbe

Gut Microbial Metabolites Fuel Host Antibody Responses

(2016) Myunghoo Kim et al.   Cell Host & Microbe

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Bile Acids Control Inflammation and Metabolic Disorder through Inhibition of NLRP3 Inflammasome

(2016) Chuansheng Guo et al.   IMMUNITY

Kynurenine Reduces Memory CD4 T-Cell Survival by Interfering with Interleukin-2 Signaling Early during HIV-1 Infection

(2016) Xavier Dagenais-Lussier et al.   JOURNAL OF VIROLOGY

Pharmacology of bile acid receptors: Evolution of bile acids from simple detergents to complex signaling molecules

(2016) Bryan L. Copple et al.   PHARMACOLOGICAL RESEARCH

Residual inflammation and viral reservoirs

(2016) Marta Massanella et al.   Current Opinion in HIV and AIDS

Conjugated bile acid-activated S1P receptor 2 is a key regulator of sphingosine kinase 2 and hepatic gene expression

(2015) Masayuki Nagahashi et al.   HEPATOLOGY

Lactate and short chain fatty acids produced by microbial fermentation downregulate proinflammatory responses in intestinal epithelial cells and myeloid cells

(2015) Carolina Iraporda et al.   IMMUNOBIOLOGY

Factors Associated With Plasma IL-6 Levels During HIV Infection

(2015) Álvaro H. Borges et al.   JOURNAL OF INFECTIOUS DISEASES

A Novel Assay to Measure the Magnitude of the Inducible Viral Reservoir in HIV-infected Individuals

(2015) Francesco Andrea Procopio et al.   EBioMedicine

Probiotics Reduce Inflammation in Antiretroviral Treated, HIV-Infected Individuals: Results of the “Probio-HIV” Clinical Trial

(2015) Gabriella d’Ettorre et al.   PLoS One

The effect of short-chain fatty acids on human monocyte-derived dendritic cells

(2015) Claudia Nastasi et al.   Scientific Reports

Bile acids and the gut microbiome

(2014) Jason M. Ridlon et al.   CURRENT OPINION IN GASTROENTEROLOGY

β-hydroxybutyrate: Much more than a metabolite

(2014) John C. Newman et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia

(2014) S M Dillon et al.   Mucosal Immunology

Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR–S6K pathway

(2014) J Park et al.   Mucosal Immunology

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression

(2014) Netanya G. Sandler et al.   NATURE

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

(2014) Pamela V. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

(2014) Ece A. Mutlu et al.   PLoS Pathogens

Gut Microbiota-Derived Short-Chain Fatty Acids, T Cells, and Inflammation

(2014) Chang H. Kim et al.   Immune Network

Alterations in the Gut Microbiota Associated with HIV-1 Infection

(2013) Catherine A. Lozupone et al.   Cell Host & Microbe

Bile acids PKA-dependently induce a switch of the IL-10/IL-12 ratio and reduce proinflammatory capability of human macrophages

(2013) Katrin Haselow et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Bile acid receptors as targets for drug development

(2013) Frank G. Schaap et al.   Nature Reviews Gastroenterology & Hepatology

The Bile Acid Sensor FXR Is Required for Immune-Regulatory Activities of TLR-9 in Intestinal Inflammation

(2013) Barbara Renga et al.   PLoS One

Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation

(2013) Jennifer L. Pluznick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

(2013) Ivan Vujkovic-Cvijin et al.   Science Translational Medicine

HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

(2013) Ian H McHardy et al.   Microbiome

Butyrate increases IL-23 production by stimulated dendritic cells

(2012) Bradford E. Berndt et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Butyrate interferes with the differentiation and function of human monocyte-derived dendritic cells

(2012) Lu Liu et al.   CELLULAR IMMUNOLOGY

α5β1-integrins are sensors for tauroursodeoxycholic acid in hepatocytes

(2012) Holger Gohlke et al.   HEPATOLOGY

Bile acids induce monocyte differentiation toward interleukin-12 hypo-producing dendritic cells via a TGR5-dependent pathway

(2012) Riko Ichikawa et al.   IMMUNOLOGY

A role for mucosal IL-22 production and Th22 cells in HIV-associated mucosal immunopathogenesis

(2012) C J Kim et al.   Mucosal Immunology

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial translocation in HIV infection: causes, consequences and treatment opportunities

(2012) Netanya G. Sandler et al.   NATURE REVIEWS MICROBIOLOGY

Bile Acids Specifically Increase Hepatitis C Virus RNA-Replication

(2012) Patrick Chhatwal et al.   PLoS One

Bile Acids Induce Inflammatory Genes in Hepatocytes

(2011) Katryn Allen et al.   AMERICAN JOURNAL OF PATHOLOGY

Short-Chain Fatty Acids Induce Pro-Inflammatory Cytokine Production Alone and in Combination with Toll-Like Receptor Ligands

(2011) Paria Mirmonsef et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Molecular Control of Systemic Bile Acid Homeostasis by the Liver Glucocorticoid Receptor

(2011) Adam J. Rose et al.   Cell Metabolism

The G-Protein-coupled bile acid receptor, Gpbar1 (TGR5), negatively regulates hepatic inflammatory response through antagonizing nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) in mice

(2011) Yan-Dong Wang et al.   HEPATOLOGY

Bile Acids Promote HCV Replication through the EGFR/ERK Pathway in Replicon-Harboring Cells

(2011) John B. Patton et al.   INTERVIROLOGY

SCFAs Induce Mouse Neutrophil Chemotaxis through the GPR43 Receptor

(2011) Marco A. R. Vinolo et al.   PLoS One

Balancing acts: the role of TGF-β in the mucosal immune system

(2011) Joanne E. Konkel et al.   TRENDS IN MOLECULAR MEDICINE

Inhibition of interferon-α-induced signaling by hyperosmolarity and hydrophobic bile acids

(2010) Dirk Graf et al.   BIOLOGICAL CHEMISTRY

Butyrate in vitro immune-modulatory effects might be mediated through a proliferation-related induction of apoptosis

(2010) Elvira Bailón et al.   IMMUNOBIOLOGY

Dissecting thein VivoMetabolic Potential of Two Human Gut Acetogens

(2010) Federico E. Rey et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antiretroviral therapy and management of HIV infection

(2010) Paul A Volberding et al.   LANCET

Compromised gastrointestinal integrity in pigtail macaques is associated with increased microbial translocation, immune activation and IL-17 production in the absence of SIV infection

(2010) N R Klatt et al.   Mucosal Immunology

Damaged Intestinal Epithelial Integrity Linked to Microbial Translocation in Pathogenic Simian Immunodeficiency Virus Infections

(2010) Jacob D. Estes et al.   PLoS Pathogens

GPR109A Is a G-protein-Coupled Receptor for the Bacterial Fermentation Product Butyrate and Functions as a Tumor Suppressor in Colon

(2009) M. Thangaraju et al.   CANCER RESEARCH

Incomplete Peripheral CD4+Cell Count Restoration in HIV‐Infected Patients Receiving Long‐Term Antiretroviral Treatment

(2009) Colleen F. Kelley et al.   CLINICAL INFECTIOUS DISEASES

Plasma Levels of Bacterial DNA Correlate with Immune Activation and the Magnitude of Immune Restoration in Persons with Antiretroviral‐Treated HIV Infection

(2009) Wei Jiang et al.   JOURNAL OF INFECTIOUS DISEASES

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Plasma Bile Acid Concentrations in Patients with Human Immunodeficiency Virus Infection Receiving Protease Inhibitor Therapy: Possible Implications for Hepatotoxicity

(2009) MaryPeace McRae et al.   PHARMACOTHERAPY

The role of HIV in serious diseases other than AIDS

(2008) Andrew N Phillips et al.   AIDS

Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections

(2008) J. M. Brenchley et al.   BLOOD

Effects of short chain fatty acids on effector mechanisms of neutrophils

(2008) Marco A. R. Vinolo et al.   CELL BIOCHEMISTRY AND FUNCTION

Persistence of HIV in Gut‐Associated Lymphoid Tissue despite Long‐Term Antiretroviral Therapy

(2008) Tae‐Wook Chun et al.   JOURNAL OF INFECTIOUS DISEASES

Transactivation of the Hepatitis B Virus Core Promoter by the Nuclear Receptor FXR 

(2008) C. Ramiere et al.   JOURNAL OF VIROLOGY

Transcription factor FOXO3a controls the persistence of memory CD4+ T cells during HIV infection

(2008) Julien van Grevenynghe et al.   NATURE MEDICINE

Enhancement of genotype 1 hepatitis C virus replication by bile acids through FXR

(2007) Caroline Scholtes et al.   JOURNAL OF HEPATOLOGY