@article{lin102391,
title = {Maternal Faecalibacterium pathobionts and low-fiber diets synergize to impact offspring health: implications for atopic dermatitis},
author = {Lee D, Park J, Park S, Hwang J, Kim S, Kee S, Kim H.},
journal = {Microbiome},
year = {2025},
}
@article{lin102397,
title = {The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice},
author = {Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.},
journal = {Microbiome Res Rep},
year = {2024},
}
@article{lin7571,
title = {Mechanism of inhibition of tannic acid and related compounds on the growth of intestinal bacteria.},
author = {Chung KT, Lu Z, Chou MW},
journal = {Food Chem Toxicol},
year = {1998},
doi = {10.1016/s0278-6915(98)00086-6},
pmid = {9862646}
}
@article{lin102362,
title = {Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa.},
author = {Haas KN, Blanchard JL.},
journal = {Int J Syst Evol Microbiol},
year = {2020},
doi = {10.1099/ijsem.0.003698},
pmid = {31782700}
}
@article{lin102359,
title = {Clostridium fessum sp. nov., isolated from human faeces.},
author = {Seo B, Jeon K, Baek I, Lee YM, Baek K, Ko G.},
journal = {Int J Syst Evol Microbiol},
year = {2021},
doi = {10.1099/ijsem.0.004579},
pmid = {33253079}
}
@article{lin102398,
title = {The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.},
author = {Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.},
journal = {Gut Microbes},
year = {2021},
doi = {10.1080/19490976.2020.1854008},
pmid = {33382950}
}
@article{lin102417,
title = {Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes.},
author = {Silamikele L, Silamikelis I, Ustinova M, Kalnina Z, Elbere I, Petrovska R, Kalnina I, Klovins J.},
journal = {Front Endocrinol (Lausanne)},
year = {2021},
doi = {10.3389/fendo.2021.626359},
pmid = {33815284}
}
@article{lin102407,
title = {Horizontal Transfer of Different erm(B)-Carrying Mobile Elements Among Streptococcus suis Strains With Different Serotypes.},
author = {Chen L, Huang J, Huang X, He Y, Sun J, Dai X, Wang X, Shafiq M, Wang L.},
journal = {Front Microbiol},
year = {2021},
doi = {10.3389/fmicb.2021.628740},
pmid = {33841355}
}
@article{lin102405,
title = {A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.},
author = {Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotna T, Ouattara DA, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A.},
journal = {Nat Commun},
year = {2021},
doi = {10.1038/s41467-021-26963-9},
pmid = {34795236}
}
@article{lin102410,
title = {In vitro interaction network of a synthetic gut bacterial community.},
author = {Weiss AS, Burrichter AG, Durai Raj AC, von Strempel A, Meng C, Kleigrewe K, Munch PC, Rossler L, Huber C, Eisenreich W, Jochum LM, Going S, Jung K, Lincetto C, Hubner J, Marinos G, Zimmermann J, Kaleta C, Sanchez A, Stecher B.},
journal = {ISME J},
year = {2022},
doi = {10.1038/s41396-021-01153-z},
pmid = {34857933}
}
@article{lin102401,
title = {Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.},
author = {Tourlousse DM, Narita K, Miura T, Ohashi A, Matsuda M, Ohyama Y, Shimamura M, Furukawa M, Kasahara K, Kameyama K, Saito S, Goto M, Shimizu R, Mishima R, Nakayama J, Hosomi K, Kunisawa J, Terauchi J, Sekiguchi Y, Kawasaki H.},
journal = {Microbiol Spectr},
year = {2022},
doi = {10.1128/spectrum.01915-21},
pmid = {35234490}
}
@article{lin102416,
title = {Distinct Functional Metagenomic Markers Predict the Responsiveness to Anti-PD-1 Therapy in Chinese Non-Small Cell Lung Cancer Patients.},
author = {Fang C, Fang W, Xu L, Gao F, Hou Y, Zou H, Ma Y, Moll JM, Yang Y, Wang D, Huang Y, Ren H, Zhao H, Qin S, Zhong H, Li J, Liu S, Yang H, Wang J, Brix S, Kristiansen K, Zhang L.},
journal = {Front Oncol},
year = {2022},
doi = {10.3389/fonc.2022.837525},
pmid = {35530307}
}
@article{lin102411,
title = {Identification of bacterial lipopeptides as key players in IBS.},
author = {Petitfils C, Maurel S, Payros G, Hueber A, Agaiz B, Gazzo G, Marrocco R, Auvray F, Langevin G, Motta JP, Floch P, Tremblay-Franco M, Galano JM, Guy A, Durand T, Lachambre S, Durbec A, Hussein H, Decraecker L, Bertrand-Michel J, Saoudi A, Oswald E, Poisbeau P, Dietrich G, Melchior C, Boeckxstaens G, Serino M, Le Faouder P, Cenac N.},
journal = {Gut},
year = {2023},
doi = {10.1136/gutjnl-2022-328084},
pmid = {36241390}
}
@article{lin102419,
title = {Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.},
author = {Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T.},
journal = {ISME Commun},
year = {2021},
doi = {10.1038/s43705-021-00017-z},
pmid = {36732617}
}
@article{lin102367,
title = {Gut Bacteria Involved in Ellagic Acid Metabolism To Yield Human Urolithin Metabotypes Revealed.},
author = {Iglesias-Aguirre CE, Garcia-Villalba R, Beltran D, Frutos-Lison MD, Espin JC, Tomas-Barberan FA, Selma MV.},
journal = {J Agric Food Chem},
year = {2023},
doi = {10.1021/acs.jafc.2c08889},
pmid = {36840624}
}
@article{lin102404,
title = {Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.},
author = {Brochu E, Huletsky A, Boudreau DK, Raymond F, Berube E, Ouameur AA, Frenette J, Boissinot M, Corbeil J, Bergeron MG.},
journal = {JAC Antimicrob Resist},
year = {2023},
doi = {10.1093/jacamr/dlad026},
pmid = {36968950}
}
@article{lin102409,
title = {Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo.},
author = {Burckhardt JC, Chong DHY, Pett N, Tropini C.},
journal = {Microbiome},
year = {2023},
doi = {10.1186/s40168-023-01496-z},
pmid = {36991500}
}
@article{lin102342,
title = {Enterocloster alcoholdehydrogenati sp. nov., a Novel Bacterial Species Isolated from the Feces of a Patient with Alcoholism.},
author = {Oikawa D, Fukui K, Aoki Y, Waki T, Takahashi S, Shimoyama T, Nakayama T.},
journal = {Curr Microbiol},
year = {2023},
doi = {10.1007/s00284-023-03285-1},
pmid = {37074467}
}
@article{lin102414,
title = {Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria.},
author = {Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M.},
journal = {Microbiome},
year = {2023},
doi = {10.1186/s40168-023-01541-x},
pmid = {37208714}
}
@article{lin102370,
title = {Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME).},
author = {Liu L, Narrowe AB, Firrman JA, Mahalak KK, Bobokalonov JT, Lemons JMS, Bittinger K, Daniel S, Tanes C, Mattei L, Friedman ES, Soares JW, Kobori M, Zeng WB, Tomasula PM.},
journal = {Foods},
year = {2023},
doi = {10.3390/foods12112105},
pmid = {37297350}
}
@article{lin102358,
title = {Phage Targeting Neonatal Meningitis E. coli K1 In Vitro in the Intestinal Microbiota of Pregnant Donors and Impact on Bacterial Populations.},
author = {Antoine C, Laforet F, Goya-Jorge E, Gonza I, Lebrun S, Douny C, Duprez JN, Fall A, Taminiau B, Scippo ML, Daube G, Thiry D, Delcenserie V.},
journal = {Int J Mol Sci},
year = {2023},
doi = {10.3390/ijms241310580},
pmid = {37445758}
}
@article{lin102418,
title = {Infection, Dysbiosis and Inflammation Interplay in the COVID Era in Children.},
author = {Ailioaie LM, Ailioaie C, Litscher G.},
journal = {Int J Mol Sci},
year = {2023},
doi = {10.3390/ijms241310874},
pmid = {37446047}
}
@article{lin102387,
title = {Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing.},
author = {Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M.},
journal = {Animals (Basel)},
year = {2023},
doi = {10.3390/ani13142303},
pmid = {37508080}
}
@article{lin102408,
title = {Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice.},
author = {von Strempel A, Weiss AS, Wittmann J, Salvado Silva M, Ring D, Wortmann E, Clavel T, Debarbieux L, Kleigrewe K, Stecher B.},
journal = {PLoS Pathog},
year = {2023},
doi = {10.1371/journal.ppat.1011600},
pmid = {37603558}
}
@article{lin102365,
title = {Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.},
author = {Park S, Li C, Wu X, Zhang T.},
journal = {Int J Mol Sci},
year = {2023},
doi = {10.3390/ijms241713329},
pmid = {37686135}
}
@article{lin102412,
title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.},
author = {Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A.},
journal = {Nat Commun},
year = {2023},
doi = {10.1038/s41467-023-41008-z},
pmid = {37723166}
}
@article{lin102402,
title = {Disease-specific loss of microbial cross-feeding interactions in the human gut.},
author = {Marcelino VR, Welsh C, Diener C, Gulliver EL, Rutten EL, Young RB, Giles EM, Gibbons SM, Greening C, Forster SC.},
journal = {Nat Commun},
year = {2023},
doi = {10.1038/s41467-023-42112-w},
pmid = {37863966}
}
@article{lin102364,
title = {Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.},
author = {Choi JY, Shim B, Park Y, Kang YA.},
journal = {Korean J Intern Med},
year = {2023},
doi = {10.3904/kjim.2023.097},
pmid = {37867139}
}
@article{lin102389,
title = {Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study.},
author = {Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R.},
journal = {Microorganisms},
year = {2023},
doi = {10.3390/microorganisms11102437},
pmid = {37894093}
}
@article{lin102399,
title = {Culture-dependent screening of endospore-forming clostridia in infant feces.},
author = {Ingribelli E, Modrackova N, Tejnecky V, Killer J, Schwab C, Neuzil-Bunesova V.},
journal = {BMC Microbiol},
year = {2023},
doi = {10.1186/s12866-023-03104-4},
pmid = {37978420}
}
@article{lin102374,
title = {Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis.},
author = {Mbaye B, Magdy Wasfy R, Borentain P, Tidjani Alou M, Mottola G, Bossi V, Caputo A, Gerolami R, Million M.},
journal = {Front Cell Infect Microbiol},
year = {2023},
doi = {10.3389/fcimb.2023.1279354},
pmid = {38035329}
}
@article{lin102385,
title = {High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome.},
author = {Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.},
journal = {Antibiotics (Basel)},
year = {2023},
doi = {10.3390/antibiotics12121667},
pmid = {38136701}
}
@article{lin102383,
title = {Experience with dalbavancin use in various gram-positive infections within Aberdeen Royal Infirmary OPAT service.},
author = {McSorley JC, Reyes D, Tonna I, Bateman V.},
journal = {Infection},
year = {2024},
doi = {10.1007/s15010-023-02152-2},
pmid = {38165594}
}
@article{lin102400,
title = {Contribution of bacterial and host factors to pathogen "blooming" in a gnotobiotic mouse model for Salmonella enterica serovar Typhimurium-induced enterocolitis.},
author = {Beutler M, Eberl C, Garzetti D, Herp S, Munch P, Ring D, Dolowschiak T, Brugiroux S, Schiller P, Hussain S, Basic M, Bleich A, Stecher B.},
journal = {Infect Immun},
year = {2024},
doi = {10.1128/iai.00318-23},
pmid = {38189339}
}
@article{lin102347,
title = {A case of bacteremia caused by Dialister micraerophilus with Enterocloster clostridioformis and Eggerthella lenta in a patient with pyometra.},
author = {Kitagawa H, Tadera K, Omori K, Nomura T, Shigemoto N, Ohge H.},
journal = {BMC Infect Dis},
year = {2024},
doi = {10.1186/s12879-024-08999-6},
pmid = {38267864}
}
@article{lin102403,
title = {Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.},
author = {Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.},
journal = {Sci Rep},
year = {2024},
doi = {10.1038/s41598-024-53784-9},
pmid = {38336892}
}
@article{lin102382,
title = {The Use of Fecal Microbiota Transplant in Overcoming and Modulating Resistance to Anti-PD-1 Therapy in Patients with Skin Cancer.},
author = {Vongsavath T, Rahmani R, Tun KM, Manne V.},
journal = {Cancers (Basel)},
year = {2024},
doi = {10.3390/cancers16030499},
pmid = {38339251}
}
@article{lin102393,
title = {Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury.},
author = {Li J, Barnes S, Lefkowitz E, Yarar-Fisher C.},
journal = {Physiol Genomics},
year = {2024},
doi = {10.1152/physiolgenomics.00107.2023},
pmid = {38344780}
}
@article{lin102380,
title = {Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.},
author = {Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligne B, Titecat M.},
journal = {Int J Mol Sci},
year = {2024},
doi = {10.3390/ijms25042164},
pmid = {38396840}
}
@article{lin102415,
title = {Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation.},
author = {Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.},
journal = {Sci Rep},
year = {2024},
doi = {10.1038/s41598-024-56242-8},
pmid = {38448687}
}
@article{lin102348,
title = {Age and aging process alter the gut microbes.},
author = {Zhanbo Q, Jing Z, Shugao H, Yinhang W, Jian C, Xiang Y, Feimin Z, Jian L, Xinyue W, Wei W, Shuwen H.},
journal = {Aging (Albany NY)},
year = {2024},
doi = {10.18632/aging.205728},
pmid = {38613799}
}
@article{lin102394,
title = {Role of the gut microbiota in tumorigenesis and treatment.},
author = {Liu Q, Yang Y, Pan M, Yang F, Yu Y, Qian Z.},
journal = {Theranostics},
year = {2024},
doi = {10.7150/thno.91700},
pmid = {38646653}
}
@article{lin102413,
title = {Single-cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a proinflammatory metabolic signature in male mice at late adulthood.},
author = {Lim JJ, Goedken M, Jin Y, Gu H, Cui JY.},
journal = {Toxicol Sci},
year = {2024},
doi = {10.1093/toxsci/kfae047},
pmid = {38648751}
}
@article{lin102363,
title = {Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging-oriented single-cell sequencing.},
author = {Gao J, Sun D, Li B, Yang C, Wang W.},
journal = {mLife},
year = {2022},
doi = {10.1002/mlf2.12041},
pmid = {38818223}
}
@article{lin102388,
title = {Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.},
author = {Tamburini FB, Tripathi A, Gold MP, Yang JC, Biancalani T, McBride JM, Keir ME, Gardenia Study Group.},
journal = {J Crohns Colitis},
year = {2024},
doi = {10.1093/ecco-jcc/jjae084},
pmid = {38836628}
}
@article{lin102378,
title = {Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae.},
author = {Lin X, Hu T, Wu Z, Li L, Wang Y, Wen D, Liu X, Li W, Liang H, Jin X, Xu X, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y.},
journal = {Imeta},
year = {2024},
doi = {10.1002/imt2.174},
pmid = {38882499}
}
@article{lin102406,
title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.},
author = {Xu SY, Feng XR, Zhao W, Bi YL, Diao QY, Tu Y.},
journal = {Microbiome},
year = {2024},
doi = {10.1186/s40168-024-01844-7},
pmid = {39030599}
}
@article{lin102390,
title = {Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes.},
author = {Kardos G, Laczko L, Kaszab E, Timmer B, Szarka K, Prepost E, Banyai K.},
journal = {Antibiotics (Basel)},
year = {2024},
doi = {10.3390/antibiotics13070573},
pmid = {39061255}
}
@article{lin102381,
title = {Genomic characterization of prophage elements in Clostridium clostridioforme: an understudied component of the intestinal microbiome.},
author = {Humphrey S, Marouli A, Thummler K, Mullin M, Pritchard L, Wall DM.},
journal = {Microbiology (Reading)},
year = {2024},
doi = {10.1099/mic.0.001486},
pmid = {39132742}
}
@article{lin102372,
title = {Comparison of gnotobiotic communities reveals milk-adapted metabolic functions and unexpected amino acid metabolism by the pre-weaning microbiome.},
author = {Lubin JB, Silverman MA, Planet PJ.},
journal = {Gut Microbes},
year = {2024},
doi = {10.1080/19490976.2024.2387875},
pmid = {39133869}
}
@article{lin102386,
title = {Gut resistome of NSCLC patients treated with immunotherapy.},
author = {Iwan E, Grenda A, Bomba A, Bielinska K, Wasyl D, Kieszko R, Rolska-Kopinska A, Chmielewska I, Krawczyk P, Rybczynska-Tkaczyk K, Olejnik M, Milanowski J.},
journal = {Front Genet},
year = {2024},
doi = {10.3389/fgene.2024.1378900},
pmid = {39170692}
}
@article{lin102369,
title = {Spaceflight alters host-gut microbiota interactions.},
author = {Gonzalez E, Lee MD, Tierney BT, Lipieta N, Flores P, Mishra M, Beckett L, Finkelstein A, Mo A, Walton P, Karouia F, Barker R, Jansen RJ, Green SJ, Weging S, Kelliher J, Singh NK, Bezdan D, Galazska J, Brereton NJB.},
journal = {NPJ Biofilms Microbiomes},
year = {2024},
doi = {10.1038/s41522-024-00545-1},
pmid = {39209868}
}
@article{lin102361,
title = {Disease-associated microbiome signature species in the gut.},
author = {Li J, Li J, O'Toole PW.},
journal = {PNAS Nexus},
year = {2024},
doi = {10.1093/pnasnexus/pgae352},
pmid = {39228810}
}
@article{lin102384,
title = {Colorectal cancer-specific microbiome in peripheral circulation and cancer tissues.},
author = {Yan S, Liu T, Zhao H, Zhao C, Zhu Y, Dai W, Sun W, Wang H, Sun J, Zhao L, Xu D.},
journal = {Front Microbiol},
year = {2024},
doi = {10.3389/fmicb.2024.1422536},
pmid = {39234556}
}
@article{lin102379,
title = {Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo.},
author = {Deyaert S, Poppe J, Dai Vu L, Baudot A, Bubeck S, Bayne T, Krishnan K, Giusto M, Moltz S, Van den Abbeele P.},
journal = {Metabolites},
year = {2024},
doi = {10.3390/metabo14090497},
pmid = {39330504}
}
@article{lin102371,
title = {The gut microbiome is associated with susceptibility to febrile malaria in Malian children.},
author = {Van Den Ham KM, Bower LK, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW.},
journal = {Nat Commun},
year = {2024},
doi = {10.1038/s41467-024-52953-8},
pmid = {39500866}
}
@article{lin102396,
title = {Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.},
author = {Holman DB, Gzyl KE, Kommadath A.},
journal = {mSystems},
year = {2024},
doi = {10.1128/msystems.01250-24},
pmid = {39584815}
}
@article{lin102377,
title = {Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection.},
author = {Bi Y, Wang Y, Li W, Chen Y, Qin J, Zheng H.},
journal = {BMC Microbiol},
year = {2025},
doi = {10.1186/s12866-024-03709-3},
pmid = {39755613}
}
@article{lin102350,
title = {Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut.},
author = {Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B.},
journal = {Nat Commun},
year = {2025},
doi = {10.1038/s41467-025-56332-9},
pmid = {39875389}
}
@article{lin102395,
title = {A metagenome-wide study of the gut virome in chronic kidney disease.},
author = {Zhang P, Guo R, Ma S, Jiang H, Yan Q, Li S, Wang K, Deng J, Zhang Y, Zhang Y, Wang G, Chen L, Li L, Guo X, Zhao G, Yang L, Wang Y, Kang J, Sha S, Fan S, Cheng L, Meng J, Yu H, Chen F, He D, Wang J, Liu S, Shi H.},
journal = {Theranostics},
year = {2025},
doi = {10.7150/thno.101601},
pmid = {39897560}
}
@article{lin102357,
title = {Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression.},
author = {Jacobsen GE, Gonzalez EE, Mendygral P, Faust KM, Hazime H, Fernandez I, Santander AM, Quintero MA, Jiang C, Damas OM, Deshpande AR, Kerman DH, Proksell S, Sendzischew Shane M, Sussman DA, Ghaddar B, Cickovsk T, Abreu MT.},
journal = {Inflamm Bowel Dis},
year = {2025},
doi = {10.1093/ibd/izae316},
pmid = {39951038}
}
@article{lin102349,
title = {Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function.},
author = {Beresford-Jones BS, Suyama S, Clare S, Soderholm A, Xia W, Sardar P, Lee J, Harcourt K, Lawley TD, Pedicord VA.},
journal = {Microbiome},
year = {2025},
doi = {10.1186/s40168-025-02050-9},
pmid = {40022210}
}
@article{lin102392,
title = {Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.},
author = {Zhang C, Liu Z, Yu H, Shen Y, Lu L, Kong F, Sun W, Wei X, Jin L, Ge L, Zeng B.},
journal = {Front Microbiol},
year = {2025},
doi = {10.3389/fmicb.2025.1537286},
pmid = {40078542}
}
@article{lin102352,
title = {The effect of culturing temperature on the growth of the most dominant bacterial species of human gut microbiota and harmful bacterial species.},
author = {Shimokawa H, Sakakibara H, Ami Y, Hirano R, Kurihara S.},
journal = {Biosci Microbiota Food Health},
year = {2025},
doi = {10.12938/bmfh.2024-087},
pmid = {40171389}
}
@article{lin102343,
title = {Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.},
author = {Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.},
journal = {Cell},
year = {2025},
doi = {10.1016/j.cell.2025.02.029},
pmid = {40239649}
}
@article{lin102351,
title = {Co-Colonization of Non-difficile Clostridial Species in Antibiotic-Associated Diarrhea Caused by Clostridioides difficile.},
author = {Salas-Trevino D, Flores-Trevino S, Cisneros-Rendon C, Dominguez-Rivera CV, Camacho-Ortiz A.},
journal = {Antibiotics (Basel)},
year = {2025},
doi = {10.3390/antibiotics14040397},
pmid = {40298552}
}
@article{lin102368,
title = {Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.},
author = {Guedon G, Charron-Bourgoin F, Lacroix T, Hamadouche T, Soler N, Douzi B, Chiapello H, Leblond-Bourget N.},
journal = {Sci Rep},
year = {2025},
doi = {10.1038/s41598-025-99981-y},
pmid = {40379875}
}
@article{lin102345,
title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.},
author = {Duong JT, Hayden HS, Verster AJ, Pope CE, Miller C, Kelsi Penewit, Salipante SJ, Rowe SM, Solomon GM, Nichols D, Kelly A, Schwarzenberg SJ, Freedman SD, Hoffman LR.},
journal = {J Cyst Fibros},
year = {2025},
doi = {10.1016/j.jcf.2025.05.006},
pmid = {40483244}
}
@article{lin102344,
title = {Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing.},
author = {Hosoda T, Suzuki M, Matsuno T, Matsui K, Ohyama K, Doi Y.},
journal = {Microbiol Spectr},
year = {2025},
doi = {10.1128/spectrum.01014-25},
pmid = {40503827}
}
@article{lin102366,
title = {Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.},
author = {Serrano-Gomez G, Yanez F, Soler Z, Pons-Tarin M, Mayorga L, Herrera-deGuise C, Borruel N, Rodriguez-Sinovas A, Consegal M, Manjon I, Vega-Abellaneda S, Manichanh C.},
journal = {Biomark Res},
year = {2025},
doi = {10.1186/s40364-025-00802-1},
pmid = {40524271}
}
@article{lin102356,
title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.},
author = {Dike CR, Duan Q, Ahmed F, Denson LA, Haslam D, Minar P, Ollberding NJ, Papachristou GI, Setchell KDR, Thompson T, Vitale DS, Zhao X, Abu-El-Haija M.},
journal = {J Pediatr Gastroenterol Nutr},
year = {2025},
doi = {10.1002/jpn3.70135},
pmid = {40600350}
}
@article{lin102355,
title = {Clinical Utility of Plasma Microbial Cell-Free DNA Surveillance in Neutropenic Patients with Acute Myeloid Leukemia Undergoing Outpatient Chemotherapy: A Case Series.},
author = {Lampou M, Trull EC, Warren HM, Ghebremichael MS, Nakka R, Floyd DJ, Fathi AT, Brunner AM, Mansour MK.},
journal = {Diagnostics (Basel)},
year = {2025},
doi = {10.3390/diagnostics15131715},
pmid = {40647714}
}
@article{lin102375,
title = {Isolation, Characterization, and Epizootiology of Clostridioides cuniculi from Immunodeficient Mice with Enteric Disease.},
author = {Funk A, Crawford A, Nickerson K, Janke L, Stringer T, Sun Y, Marsh A, Inoue M, Savage C, Emmons J, Henderson K, Tang L, Pisharath H.},
journal = {J Am Assoc Lab Anim Sci},
year = {2025},
doi = {10.30802/aalas-jaalas-25-030},
pmid = {40683644}
}
@article{lin102373,
title = {The role of the gut microbiota in chemotherapy response, efficacy and toxicity: a systematic review.},
author = {Bohm D, Russ E, Guchelaar HJ, Ziemons J, Penders J, Smidt ML, van Best N, Deenen MJ.},
journal = {NPJ Precis Oncol},
year = {2025},
doi = {10.1038/s41698-025-01034-0},
pmid = {40738965}
}
@article{lin102346,
title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.},
author = {Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M, Aichinger G, Hausmann B, Berry D, Richter A, Marko D, Mussmann M, Schleheck D, Stecher B, Loy A.},
journal = {Microbiome},
year = {2025},
doi = {10.1186/s40168-025-02175-x},
pmid = {40775374}
}
@article{lin102353,
title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.},
author = {Bryson S, Sisson Z, Nelson B, Grove J, Reister E, Liachko I, Auch B, Graiziger C, Khoruts A.},
journal = {Gut Microbes},
year = {2025},
doi = {10.1080/19490976.2025.2559019},
pmid = {40948444}
}
@article{lin102376,
title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.},
author = {Park R, Chevalier C, Kieser S, Marizzoni M, Paquis A, Armand S, Scheffler M, Allali G, Assal F, Momjian S, Frisoni GB.},
journal = {PLoS One},
year = {2025},
doi = {10.1371/journal.pone.0330251},
pmid = {40953029}
}
@article{lin102354,
title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.},
author = {Qie J, Cao M, Xu M, Zhang Y, Luo L, Sun C, Ke D, Yuan S, Jia W, Qiu T, Li T, Du X, Xiao C, Hong Z, Zhang B.},
journal = {mSystems},
year = {2025},
doi = {10.1128/msystems.01091-25},
pmid = {40960303}
}
@article{lin102360,
title = {Microbial succession at weaning is guided by microbial metabolism of host glycans.},
author = {Lubin JB, Planet PJ, Silverman MA.},
journal = {Microbiome},
year = {2025},
doi = {10.1186/s40168-025-02193-9},
pmid = {41152947}
}