2025
The fungal microbiota modulate neonatal oxygen-induced lung injury
Martin I, Silverberg M, Abdelgawad A, Tanaka K, Halloran B, Nicola T, Myers E, Desai J, White C, Karabayir I, Akbilgic O, Tipton L, Gentle S, Ambalavanan N, Peters B, Vu L, Jain V, Lal C, Cormier S, Pierre J, Jilling T, Talati A, Willis K. The fungal microbiota modulate neonatal oxygen-induced lung injury. Microbiome 2025, 13: 24. PMID: 39871397, PMCID: PMC11773857, DOI: 10.1186/s40168-025-02032-x.Peer-Reviewed Original ResearchConceptsBronchopulmonary dysplasiaLung injury severityLung injuryDevelopment of bronchopulmonary dysplasiaSeverity of lung injuryAugmented lung injuryMorbidities of prematurityVery preterm infantsOxygen-induced lung injuryChronic lung diseaseIntestinal microbiomeMicrobiome of infantsPotential therapeutic strategyPreterm infantsNeonatal microbiomePremature infantsPremature neonatesInjury severityMurine modelNeonatal healthLung diseaseMouse modelTherapeutic strategiesLoss of function approachesFungal communitiesThe evolving understanding of systemic mechanisms in organ-specific IgA nephropathy: a focus on gut-kidney crosstalk
Wang X, Zhou X, Qiao X, Falchi M, Liu J, Zhang H. The evolving understanding of systemic mechanisms in organ-specific IgA nephropathy: a focus on gut-kidney crosstalk. Theranostics 2025, 15: 656-681. PMID: 39744688, PMCID: PMC11671385, DOI: 10.7150/thno.104631.Peer-Reviewed Original ResearchConceptsGut-kidney crosstalkExploration of gut microbiotaGut microbiotaKidney diseaseMechanism of IgANIntestinal microbiomeSignaling pathwayIgA nephropathyInter-organ crosstalkEfficient therapeutic strategiesPrognosis of patientsProgression of IgANElaborate mechanismsTherapeutic strategiesIgAN pathogenesisIgANCrosstalkMicrobiomeMicrobiotaMultiple organsKidneyProbioticsNephropathyDiseaseMechanism
2024
Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice
Chen H, Huang S, Zhao Y, Sun R, Wang J, Yao S, Huang J, Yu Z. Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice. Microbiology Spectrum 2024, 12: e03735-23. PMID: 38441977, PMCID: PMC10986500, DOI: 10.1128/spectrum.03735-23.Peer-Reviewed Original ResearchConceptsTaxonomic compositionGut microbiomeIntestinal microbiomeFunctional genesKEGG OrthologyMetagenomic analysisIntestinal microbiotaRegulatory mechanismsFunction of gut microbiomeComposition of gut microbiotaAbundance of functional genesMetagenomic sequencingGene functionGut microbiotaPotential regulatory mechanismSpecies levelIntervention of probioticsBacillus amyloliquefaciensMicrobiomeGenesMicrobiotaHost immune responseProbiotic interventionMetabolic reactionsSchistosoma japonicum</i>
2023
Bacillus amyloliquefaciens alleviates the pathological injuries in mice infected with Schistosoma japonicum by modulating intestinal microbiome
Chen H, Sun R, Wang J, Yao S, Batool S, Yu Z, Huang S, Huang J. Bacillus amyloliquefaciens alleviates the pathological injuries in mice infected with Schistosoma japonicum by modulating intestinal microbiome. Frontiers In Cellular And Infection Microbiology 2023, 13: 1172298. PMID: 37265494, PMCID: PMC10230073, DOI: 10.3389/fcimb.2023.1172298.Peer-Reviewed Original ResearchConceptsIntestinal microbiomeAbundances of potential pathogenic bacteriaRecovery of diversityRRNA gene sequencesPotential pathogenic bacteriaPathological organ damageEscherichia-ShigellaGene sequencesInteraction networkMammalian hostsBacillus amyloliquefaciensPathogenic bacteriaMicrobiomeIntestinal microenvironmentEffective therapeutic agentSchistosoma japonicum
2022
Intestinal microbiome associated with development of grade 3/4 adverse in patients with metastatic renal cell carcinoma (mRCC) treated with nivolumab plus ipilimumab (N/I) and probiotic support: Results from a phase Ib study.
Meza L, Dizman N, Bergerot P, Dorff T, Lyou Y, Frankel P, Llamas M, Hsu J, Zengin Z, Salgia N, Malhotra J, Chawla N, Gillece J, Reining L, Trent J, Takahashi M, Oka K, Higashi S, Highlander S, Pal S. Intestinal microbiome associated with development of grade 3/4 adverse in patients with metastatic renal cell carcinoma (mRCC) treated with nivolumab plus ipilimumab (N/I) and probiotic support: Results from a phase Ib study. Journal Of Clinical Oncology 2022, 40: 374-374. DOI: 10.1200/jco.2022.40.6_suppl.374.Peer-Reviewed Original ResearchMetastatic renal cell carcinomaSetting of mRCCStool microbiome compositionPhase Ib studyWeeks of therapyFirst-line treatmentLung cancer patientsRenal cell carcinomaMicrobiome compositionDevelopment of treatmentsB. thetaiotamicronMedian followMRCC patientsAdverse eventsData cutoffOverall cohortIntervention armLine treatmentCell carcinomaCancer patientsTRAEsStool samplesStool specimensIntestinal microbiomeLarge cohort
2021
Obeticholic Acid Decreases Intestinal Content of Enterococcus in Rats With Cirrhosis and Ascites
Yan K, Hung A, Parmer C, Yang H, Jain D, Lim B, Goodman AL, Garcia‐Tsao G. Obeticholic Acid Decreases Intestinal Content of Enterococcus in Rats With Cirrhosis and Ascites. Hepatology Communications 2021, 5: 1507-1517. PMID: 34510838, PMCID: PMC8435275, DOI: 10.1002/hep4.1740.Peer-Reviewed Original ResearchHigher serum albuminBacterial translocationObeticholic acidEnd of studyAspartate aminotransferaseLymph nodesIntestinal microbiomeIntestinal contentsSemisynthetic bile acidMesenteric lymph nodesEnd of treatmentCarbon tetrachloride inhalationExtra-intestinal sitesLower aspartate aminotransferaseFurther decompensationLiver injuryLiver functionPolymerase chain reactionExperimental cirrhosisPathogenic bacteriaCirrhosisHepatocyte deathDay 1Bile acidsPlaceboMulti-Omics Analysis on Neurodevelopment in Preterm Neonates
Casavant S, Chen J, Xu W, Lainwala S, Matson A, Chen M, Starkweather A, Maas K, Cong X. Multi-Omics Analysis on Neurodevelopment in Preterm Neonates. Nursing Research 2021, 70: 462-468. PMID: 34380978, PMCID: PMC8563389, DOI: 10.1097/nnr.0000000000000548.Peer-Reviewed Original ResearchConceptsPreterm infantsIntensive care unitNecrotizing enterocolitisFeeding intoleranceNeurodevelopmental impairmentNeonatal intensive care unit periodAdverse outcomesHost genetic variationIntestinal microbiomePreterm infants born <Care unitNeonatal intensive care unitInfants born <Weeks gestational ageGut microbiomeIntensive care unit periodFollow-up visitRegulation of intestinal healthPreterm neonatesGestational agePotential adverse outcomesNeurodevelopmental outcomesPain sensitivityPretermMulti-omics analysisButyrate and the Intestinal Epithelium: Modulation of Proliferation and Inflammation in Homeostasis and Disease
Salvi PS, Cowles RA. Butyrate and the Intestinal Epithelium: Modulation of Proliferation and Inflammation in Homeostasis and Disease. Cells 2021, 10: 1775. PMID: 34359944, PMCID: PMC8304699, DOI: 10.3390/cells10071775.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsAnti-proliferative effectsIntestinal stem cellsTolerogenic dendritic cellsAnti-inflammatory cytokinesEpithelial cellsInflammatory bowel diseaseMicrobial metabolite butyrateStem cellsApparent protective effectButyrate-producing bacteriaCellular fuelRole of butyrateCrypt base stem cellsModulation of proliferationButyrate paradoxMalabsorptive statesBowel diseaseDendritic cellsEpithelial inflammationColonic neoplasiaIntestinal microbiomeProtective effectIntestinal neoplasiaIntestinal lumenEpithelial proliferationThe Microbiome and p-Inulin in Hemodialysis: A Feasibility Study.
Raj D, Sohn M, Charytan D, Himmelfarb J, Ikizler T, Mehrotra R, Ramezani A, Regunathan-Shenk R, Hsu J, Landis J, Li H, Kimmel P, Kliger A, Dember L. The Microbiome and p-Inulin in Hemodialysis: A Feasibility Study. Kidney360 2021, 2: 445-455. PMID: 35369018, PMCID: PMC8786005, DOI: 10.34067/kid.0006132020.Peer-Reviewed Original ResearchConceptsGut microbiomeStool samplesMicrobiome compositionMetabolomic profilesCLINICAL TRIAL REGISTRY NAMEWeighted UniFrac distancesStudy of patientsTRIAL REGISTRY NAMEUniFrac distancesMicrobiome diversityPretreatment to post-treatmentMaintenance hemodialysisUremic toxicityClinical trialsIntestinal microbiomeMicrobiomePost-treatmentREGISTRY NAMEGutPatientsHemodialysisMetabolome compositionFrequent sample collectionRegistration numberESKDThe fermented soy beverage Q-CAN® plus induces beneficial changes in the oral and intestinal microbiome
Dioletis E, Paiva RS, Kaffe E, Secor ER, Weiss TR, Fields MR, Ouyang X, Ali A. The fermented soy beverage Q-CAN® plus induces beneficial changes in the oral and intestinal microbiome. BMC Nutrition 2021, 7: 6. PMID: 33658080, PMCID: PMC7931600, DOI: 10.1186/s40795-021-00408-4.Peer-Reviewed Original ResearchObese participantsIntestinal microbiomeOral microbiomeBeneficial health consequencesHuman intestinal microbiomePositive health benefitsMethodsProspective studyObese populationLean populationStool samplesStool microbiomeHealth consequencesFecal microbiomeHealth benefitsBeneficial changesSignificant increaseBlautiaTrialsWeeksMicrobiomeSignificant changesSalivaBifidobacteriaFamily VeillonellaceaeVeillonellaceae
2020
In utero human intestine harbors unique metabolomic features including bacterial metabolites
Li Y, Toothaker JM, Ben-Simon S, Ozeri L, Schweitzer R, McCourt BT, McCourt CC, Werner L, Snapper SB, Shouval DS, Khatib S, Koren O, Agnihorti S, Tseng G, Konnikova L. In utero human intestine harbors unique metabolomic features including bacterial metabolites. JCI Insight 2020, 5: e138751. PMID: 33001863, PMCID: PMC7710283, DOI: 10.1172/jci.insight.138751.Peer-Reviewed Original ResearchConceptsFetal immune systemIntestinal barrier integrityMicrobial-associated metabolitesHost-derived metabolitesBacterial DNAIntestinal immunityMaternal microbiomeIntestinal functionImmune regulationGastrointestinal tractIntestinal microbiomeFetal intestineBarrier integrityImmune systemHuman intestinal samplesIntestinal samplesIntestinal profileMicrobial encountersMetabolomic featuresBacterial metabolitesUteroNutrient metabolismMetabolitesRecent studiesMicrobiome
2019
The Fermented Soy Beverage Q-CAN® Plus Induces Changes in the Oral and Intestinal Microbiome (P20-018-19)
Mehal W, Dioletis E, Paiva R, Secor E, Weiss T, Fields M, Ali A. The Fermented Soy Beverage Q-CAN® Plus Induces Changes in the Oral and Intestinal Microbiome (P20-018-19). Current Developments In Nutrition 2019, 3: nzz040.p20-018-19. PMCID: PMC6574065, DOI: 10.1093/cdn/nzz040.p20-018-19.Peer-Reviewed Original ResearchObese groupSoy consumptionObese subjectsLean groupLeast square meansGut microbiomeMethods Prospective studyVisit 7Clinic visitsProspective studyVisit 3Obese body typeObese individualsVisit 8High prevalenceStool samplesBacteroidetes ratioHealthy subjectsIntestinal microbiomeOral microbiomeBeneficial effectsHealth benefitsMetabolic phenotypeSignificant decreaseGroup differences
2017
Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury
Bertacco A, Dehner CA, Caturegli G, D'Amico F, Morotti R, Rodriguez MI, Mulligan DC, Kriegel MA, Geibel JP. Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury. Frontiers In Physiology 2017, 8: 1064. PMID: 29311987, PMCID: PMC5742259, DOI: 10.3389/fphys.2017.01064.Peer-Reviewed Original ResearchIschemic injuryIntestinal ischemiaProtective effectIntestinal ischemic injuryLight-level microscopyEosin-stained sectionsLactate administrationAntibiotic treatmentIschemic protectionIntestinal barrierLactate perfusionRat modelIntestinal microbiomeIntestinal preservationIntestinal segmentsIschemic cellsSmall intestineInert sugarsInjuryIschemiaPerfusionEpithelium morphologySecretionPerfusion deviceFITC-inulinCurrent and future pharmacologic treatment of nonalcoholic steatohepatitis
Banini BA, Sanyal AJ. Current and future pharmacologic treatment of nonalcoholic steatohepatitis. Current Opinion In Gastroenterology 2017, 33: 134-141. PMID: 28346237, PMCID: PMC5491795, DOI: 10.1097/mog.0000000000000356.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNonalcoholic fatty liver diseaseEnd-stage liver diseaseNonalcoholic steatohepatitisLiver diseaseTrend of NAFLDChemokine receptor type 2Future pharmacologic treatmentsCornerstone of therapyStage liver diseaseFatty liver diseasePeroxisome proliferator activator receptorProgression of fibrosisAnti-inflammatory agentsDietary caloric restrictionGlucagon-like peptide 1 pathwayReceptor type 2Liver histologyMetabolic endotoxemiaPharmacologic treatmentTherapeutic optionsHepatocellular cancerAntifibrotic agentsIntestinal microbiomeAggressive formPharmacologic target
2014
Navigating the Pediatric Microbiome: Emerging Evidence and Clinical Implications
Kassam Z, Murray T. Navigating the Pediatric Microbiome: Emerging Evidence and Clinical Implications. Current Pediatrics Reports 2014, 2: 93-101. DOI: 10.1007/s40124-014-0040-1.Peer-Reviewed Original ResearchPediatric microbiomeInflammatory bowel diseaseFecal microbiota transplantLong-term healthAtopic diseasesBowel diseaseMicrobiota transplantNovel therapiesPediatric diseasesIntestinal microbiomeFuture careClinical implicationsDiseaseEarly lifeMicrobiomeResident microbesChildrenCollective genomesHost functionsCurrent understandingObesityTransplantInfantsTherapyPediatrics
2013
Low Incidence of Spontaneous Type 1 Diabetes in Non-Obese Diabetic Mice Raised on Gluten-Free Diets Is Associated with Changes in the Intestinal Microbiome
Marietta E, Gomez A, Yeoman C, Tilahun A, Clark C, Luckey D, Murray J, White B, Kudva Y, Rajagopalan G. Low Incidence of Spontaneous Type 1 Diabetes in Non-Obese Diabetic Mice Raised on Gluten-Free Diets Is Associated with Changes in the Intestinal Microbiome. PLOS ONE 2013, 8: e78687. PMID: 24236037, PMCID: PMC3827256, DOI: 10.1371/journal.pone.0078687.Peer-Reviewed Original ResearchConceptsGluten-free dietNon-obese diabetic (NOD) miceAnti-diabetogenic effectsIncidence of hyperglycemiaNOD miceType 1 diabetesIntestinal microbiomeDietary glutenDiabetic miceSpontaneous type 1 diabetesAkkermansia speciesIncidence of diabetesIncidence of T1DIncidence of T1D.Blood glucose levelsIntestinal microbiome compositionLower incidenceGlucose levelsHigh incidenceAnimal studiesGut microfloraGut microbiomeHyperglycemiaIncidenceMiceIntestinal microbiome and digoxin inactivation: meal plan for digoxin users?
Lu L, Wu Y, Zuo L, Luo X, Large PJ. Intestinal microbiome and digoxin inactivation: meal plan for digoxin users? World Journal Of Microbiology And Biotechnology 2013, 30: 791-799. PMID: 24105082, DOI: 10.1007/s11274-013-1507-x.Peer-Reviewed Original ResearchConceptsDigoxin inactivationIntestinal microbiomeDigoxin usersArginine supplementsInactivation of digoxinBioavailability of digoxinHeart diseaseEpidemiological dataAnimal modelsMeal planTherapeutic agentsMetabolism of argininePotential interventionsDigoxinDiseaseDigoxin activityHuman diseasesRecent studiesMicrobiomeSupplementsBioavailabilityInactivationAgents
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