2024
Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes
Peng X, Li S, Dou W, Li M, Gontcharov A, Peng Z, Qi B, Wang Q, Li Y. Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes. Microorganisms 2024, 12: 2540. PMID: 39770743, PMCID: PMC11677963, DOI: 10.3390/microorganisms12122540.Peer-Reviewed Original ResearchCommunity compositionMicrobial functional profilesHost-specific selectionMicrobial community compositionCharacteristics of microbiotaCulture-based studiesSpecies of bacteriaBacteria community compositionPhagocytosis of bacteriaFunctional traitsMetagenomic sequencingMyxomycete speciesAssociated microbiomeAmplicon sequencingFunctional redundancyMetagenomic insightsMicrobial communitiesMyxomycetesSpecies-specificBacteria speciesDominant bacteriaBacteriaFunctional roleFunctional analysisPlasmodiaComparative Analysis of Fecal Microbiota Between Adolescents with Early-Onset Psychosis and Adults with Schizophrenia
Nuncio-Mora L, Nicolini H, Lanzagorta N, García-Jaimes C, Sosa-Hernández F, González-Covarrubias V, Cabello-Rangel H, Sarmiento E, Glahn D, Genis-Mendoza A. Comparative Analysis of Fecal Microbiota Between Adolescents with Early-Onset Psychosis and Adults with Schizophrenia. Microorganisms 2024, 12: 2071. PMID: 39458380, PMCID: PMC11510430, DOI: 10.3390/microorganisms12102071.Peer-Reviewed Original ResearchEarly-onset psychosisPsychiatric disordersAtypical antipsychotic treatmentNon-psychotic individualsTreated with sertralineAntipsychotic treatmentSchizophrenia groupSchizophrenia patientsSchizophreniaGut-brain axisPsychosisGene orthology analysisPotential metabolic functionsAssociated with gut dysbiosisFunctional prediction analysisValproate treatmentPharmacological treatmentOscillospiraceae familiesOrthology analysisDecreased levelsFatty acid metabolismGut microbiomeExpressed genesMicrobial communitiesMicrobial compositionThe Association of the Oral Microbiota with Cognitive Functioning in Adolescence
Naumova O, Dobrynin P, Khafizova G, Grigorenko E. The Association of the Oral Microbiota with Cognitive Functioning in Adolescence. Genes 2024, 15: 1263. PMID: 39457387, PMCID: PMC11507344, DOI: 10.3390/genes15101263.Peer-Reviewed Original ResearchOral microbiotaKaufman Assessment Battery for Children IIHealthy oral microbiomeCognitive functionMetabolic pathwaysBacterial cell divisionAbundance of BacteroidetesAfrican-American originClinical phenotypeOral microbiomeAssociated with cognitive functionGut microbiomeMicrobiome diversityMicrobial communitiesBacterial speciesCell divisionGABA metabolismMicrobiomeMicrobiotaPopulation-based researchIndicators of general intelligenceMiddle-agedImprove cognitive healthAmerican originAssociationCommensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor
Tian K, Jing D, Lan J, Lv M, Wang T. Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor. Immunity Inflammation And Disease 2024, 12: e1316. PMID: 39023417, PMCID: PMC11256888, DOI: 10.1002/iid3.1316.Peer-Reviewed Original ResearchConceptsMucosal immune networkMucosal immune systemImmune systemMaintenance of intestinal healthSite of pathogen invasionPresence of commensal microbiotaImmune responsePattern recognition receptorsGut mucosal immune systemAntigen-presenting cellsMucosal immune cellsGastrointestinal mucosal immunityGut-associated lymphoid tissuePathogen invasionCommensal microbiotaGut homeostasisMicrobial communitiesProtective immune responsesAdaptive immune responsesNon-self antigensCommensal bacteriaCommensal microbiomeIntestinal healthInflammatory bowel diseaseRecognition receptorsImmunological and microbial shifts in the aging rhesus macaque lung during nontuberculous mycobacterial infection
Cinco I, Napier E, Rhoades N, Davies M, Allison D, Kohama S, Bermudez L, Winthrop K, Fuss C, Spindel E, Messaoudi I. Immunological and microbial shifts in the aging rhesus macaque lung during nontuberculous mycobacterial infection. MBio 2024, 15: e00829-24. PMID: 38771046, PMCID: PMC11237422, DOI: 10.1128/mbio.00829-24.Peer-Reviewed Original ResearchConceptsNTM pulmonary diseaseIncreased disease severityNontuberculous mycobacteriaDisease severityBacterial DNAAged animalsAntigen-specific T cellsPulmonary diseaseAssociated with increased disease severityDysregulated macrophage responsePersistence of bacterial DNALack of animal modelsRhesus macaquesSingle-cell RNA sequencingNontuberculous mycobacterial infectionsImmune cell infiltrationRhesus macaque modelBacterial loadAged rhesus macaquesTesting novel therapeuticsRight caudal lobeLower respiratory microbiomeYears of ageMAH infectionMicrobial communitiesTlr9 deficiency in B cells leads to obesity by promoting inflammation and gut dysbiosis
Wang P, Yang X, Zhang L, Sha S, Huang J, Peng J, Gu J, Pearson J, Hu Y, Zhao H, Wong F, Wang Q, Wen L. Tlr9 deficiency in B cells leads to obesity by promoting inflammation and gut dysbiosis. Nature Communications 2024, 15: 4232. PMID: 38762479, PMCID: PMC11102548, DOI: 10.1038/s41467-024-48611-8.Peer-Reviewed Original ResearchConceptsToll-like receptor 9Gut microbiotaGut microbial communityTransferred to germ-free miceB cellsGerm-free miceTLR9 deficiencyKO miceGene sequencesGerminal center B cellsMicrobial communitiesMarginal zone B cellsGut dysbiosisFollicular helper cellsSelf-DNAMetabolic homeostasisAssociated with increased frequencyPro-inflammatory stateFat tissue inflammationGutHigh-fat dietMicrobiotaHelper cellsT cellsControl miceOuter membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly
Potapova A, Garvey W, Dahl P, Guo S, Chang Y, Schwechheimer C, Trebino M, Floyd K, Phinney B, Liu J, Malvankar N, Yildiz F. Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly. MBio 2024, 15: e03304-23. PMID: 38206049, PMCID: PMC10865864, DOI: 10.1128/mbio.03304-23.Peer-Reviewed Original ResearchConceptsBiofilm matrix assemblyOuter membrane proteinsOuter membrane protein OmpUOuter membrane vesiclesBiofilm formationBiofilm matrixMatrix assemblyMatrix proteinsBiofilm architectureExtracellular DNAPresence of outer membrane proteinsCausative agent of choleraMembrane vesiclesAgent of choleraBiofilm matrix proteinsBiofilm matrix componentsVibrio cholerae</i>Single-cell force spectroscopyCell surface adhesion forceMatrix proteomeVibrio cholerae</i>.OmpUHuman pathogensMicrobial communitiesEnvironmental survival
2023
New insight into the granule formation in the reactor for enhanced biological phosphorus removal
Pelevina A, Gruzdev E, Berestovskaya Y, Dorofeev A, Nikolaev Y, Kallistova A, Beletsky A, Ravin N, Pimenov N, Mardanov A. New insight into the granule formation in the reactor for enhanced biological phosphorus removal. Frontiers In Microbiology 2023, 14: 1297694. PMID: 38163067, PMCID: PMC10755871, DOI: 10.3389/fmicb.2023.1297694.Peer-Reviewed Original ResearchPhosphate-accumulating organismsSequencing batch reactorBiological phosphorus removalGlycogen accumulating organismsPhosphorus removalLaboratory sequencing batch reactorEfficiency of phosphorus removalProcess of granule formationActivated sludge flocsSludge flocsBatch reactorAggregate typeHigh efficiencyGranule formationReactorMicrobial taxonomic compositionPhysicochemical processesTaxonomic compositionMorphotype IIMetagenomic analysisSuccession of communitiesMorphotype IMicrobial communitiesBacterial cellsEBPRSpatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression
Huang K, Ma H, Chong R, Uchihara T, Lian B, Zhu F, Sheng T, Srivastava S, Tay S, Sundar R, Tan A, Ong X, Lee M, Ho S, Lesluyes T, Ashktorab H, Smoot D, Van Loo P, Chua J, Ramnarayanan K, Lau L, Gotoda T, Kim H, Ang T, Khor C, Lee J, Tsao S, Yang W, Teh M, Chung H, So J, Yeoh K, Tan P, Consortium S. Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression. Cancer Cell 2023, 41: 2019-2037.e8. PMID: 37890493, PMCID: PMC10729843, DOI: 10.1016/j.ccell.2023.10.004.Peer-Reviewed Original ResearchConceptsIntestinal metaplasiaProspective 10-year studyPre-malignant conditionChromatin regulationGastric cancer progressionMicrobial communitiesClinical-only modelClinical-genomic modelsCellular compartmentsIntestinal homeostasisMicrobial dysbiosisTranscriptome profilingDriver genesARID1A mutationsDiverse pathwaysIM patientsClonal dynamicsGenomic profilingSingle-cellEarly malignancyGC riskCell typesGastric cancerCancer progressionLineage heterogeneityDeconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination
Yitbarek S, Guittar J, Knutie S, Ogbunugafor C. Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination. IScience 2023, 26: 107875. PMID: 37860776, PMCID: PMC10583047, DOI: 10.1016/j.isci.2023.107875.Peer-Reviewed Original ResearchHost phenotypeGut-associated microbial communitiesHigher-order microbial interactionsEffects of higher-order interactionsHigher-order interactionsHost infection riskGut microbiotaMicrobial ecologyMicrobial interactionsMicrobial communitiesCommunity structureInsect hostsMicrobiotaEnvironmental contextParasite invasionHostPhenotypePairwise interactionsTaxaGutEcologyInteractionInvasionmbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundanceMoonlighting in the membrane
Hatzios S. Moonlighting in the membrane. Nature Chemical Biology 2023, 19: 1436-1437. PMID: 37349584, DOI: 10.1038/s41589-023-01369-4.Commentaries, Editorials and LettersCross-feeding in the gut microbiome: Ecology and mechanisms
Culp E, Goodman A. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host & Microbe 2023, 31: 485-499. PMID: 37054671, PMCID: PMC10125260, DOI: 10.1016/j.chom.2023.03.016.Peer-Reviewed Original ResearchConceptsHost healthHost-microbe interactionsSpecies fitnessMicrobe-microbeEvolutionary implicationsMicrobial inhabitantsGut communitiesTrophic networksMicrobial communitiesTrophic levelsMammalian gutPrimary fermentersMetabolic outputDifferent microbesAmino acidsGut commensalsCooperative interactionsGut microbiomeNegative interactionsFitnessMutualismEcologyMicrobesEmergent roleCofactorQuestioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy K, de Goffau M, Perez-Muñoz M, Arrieta M, Bäckhed F, Bork P, Braun T, Bushman F, Dore J, de Vos W, Earl A, Eisen J, Elovitz M, Ganal-Vonarburg S, Gänzle M, Garrett W, Hall L, Hornef M, Huttenhower C, Konnikova L, Lebeer S, Macpherson A, Massey R, McHardy A, Koren O, Lawley T, Ley R, O’Mahony L, O’Toole P, Pamer E, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda D, Smith G, Sokol H, Spector T, Surette M, Tannock G, Walker A, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023, 613: 639-649. PMID: 36697862, PMCID: PMC11333990, DOI: 10.1038/s41586-022-05546-8.Peer-Reviewed Original ResearchConceptsMicrobial populationsHuman immune developmentMicrobial ecologyReproductive biologyMicrobial communitiesLow biomass environmentsMicrobial signalsMicrobial studiesDNA sequencingMicrobiome studiesDNA extractionMicrobial analysisClinical microbiologyMechanistic conceptsCautionary exampleImmune developmentRecent studiesHuman fetusesFetal tissuesMammalsGnotobiologyEcologyMicrobiologyFetal microbiomeBiology
2022
Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection
Cen L, Chang Y, Bedree JK, Ma Y, Zhong Q, Utter DR, Dong PT, Lux R, Bor B, Liu J, McLean JS, Le S, He X. Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection. Journal Of Virology 2022, 96: e01063-22. PMID: 36000841, PMCID: PMC9472602, DOI: 10.1128/jvi.01063-22.Peer-Reviewed Original ResearchConceptsLytic transglycosylaseLytic phagesPhage receptorsOral phageRemarkable host specificityHuman oral microbiomeSimilar expression levelsPeptidoglycan remodelingWhole-genome sequencingMutant backgroundBacterial physiologyHost specificityMicrobial communitiesSurface-grown cellsPhage populationsSensitive phenotypeBacterial hostsOral microbiomePeptidoglycan structureWild typeMetagenomic analysisMutantsSpontaneous mutantsXH001Frameshift mutationDifferential richness inference for 16S rRNA marker gene surveys
Kumar M, Slud E, Hehnly C, Zhang L, Broach J, Irizarry R, Schiff S, Paulson J. Differential richness inference for 16S rRNA marker gene surveys. Genome Biology 2022, 23: 166. PMID: 35915508, PMCID: PMC9344657, DOI: 10.1186/s13059-022-02722-x.Peer-Reviewed Original ResearchConceptsMarker gene surveysRRNA marker gene surveysGene surveysMicrobial assemblagesSpecies discoveryMicrobial taxaMicrobial communitiesMicrobiome surveysRichness estimationSequencing readsDiversity measuresTaxaGenus abundanceMicrobiome dataR packageAbundanceRichnessDiscoveryDiversityReadsAssemblagesObserved numberExperimental evidenceAccumulationInferencephyloMDA: an R package for phylogeny-aware microbiome data analysis
Liu T, Zhou C, Wang H, Zhao H, Wang T. phyloMDA: an R package for phylogeny-aware microbiome data analysis. BMC Bioinformatics 2022, 23: 213. PMID: 35668363, PMCID: PMC9169257, DOI: 10.1186/s12859-022-04744-5.Peer-Reviewed Original ResearchConceptsHost-associated microbial communitiesShared evolutionary historyMicrobiome data analysisEvolutionary historyPhylogenetic informationPhylogenetic treeMicrobial communitiesR packageSequencing technologiesAbundance dataMicrobial compositionRelative abundanceMicrobiome dataSample sitesUser-friendly toolMultivariate abundance dataAbundanceUnique opportunityUnprecedented scaleDifferent patternsTreesMetagenome assembly of high-fidelity long reads with hifiasm-meta
Feng X, Cheng H, Portik D, Li H. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods 2022, 19: 671-674. PMID: 35534630, PMCID: PMC9343089, DOI: 10.1038/s41592-022-01478-3.Peer-Reviewed Original ResearchGut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam EE, Abellon-Ruiz J, Killinger BJ, Rosnow JJ, Wexler AG, Folta-Stogniew E, Wright AT, van den Berg B, Goodman AL. Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. MBio 2022, 13: e02845-21. PMID: 35227073, PMCID: PMC8941943, DOI: 10.1128/mbio.02845-21.Peer-Reviewed Original ResearchConceptsComplex microbial communitiesHuman gut commensalTerminal globular domainModel organismsGut microbiomeMicrobial communitiesCompetitive fitnessTransport systemStructural homologsAccessory proteinsNew proteinsAdditional proteinsTransport proteinsGlobular domainUnknown functionMultiple transport systemsSystem lociKey roleGut commensalsProteinDiverse repertoireRelated moleculesMajor groupsFitnessOrganismsNew Insight Into the Interspecies Shift of Anammox Bacteria Ca. “Brocadia” and Ca. “Jettenia” in Reactors Fed With Formate and Folate
Kallistova A, Nikolaev Y, Grachev V, Beletsky A, Gruzdev E, Kadnikov V, Dorofeev A, Berestovskaya J, Pelevina A, Zekker I, Ravin N, Pimenov N, Mardanov A. New Insight Into the Interspecies Shift of Anammox Bacteria Ca. “Brocadia” and Ca. “Jettenia” in Reactors Fed With Formate and Folate. Frontiers In Microbiology 2022, 12: 802201. PMID: 35185828, PMCID: PMC8851195, DOI: 10.3389/fmicb.2021.802201.Peer-Reviewed Original ResearchAnammox bacteriaNitrogen removal rateAnaerobic ammonium oxidationAnammox bacteria CaAnammox processBatch reactorAnammox speciesRemoval rateAnammoxAmmonium loadingEffect of formationAmmonium oxidationReactorComparative genome analysisRRNA gene profilingBacteria CaDissimilatory nitrate reductionGenomic analysisLow temperaturesMetagenomic analysisMicrobial communitiesEnvironmental fluctuationsGene profilesJetteniaBacteria
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