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title = {Comparison of pH and bacterial communities in the rumen and reticulum during fattening of Japanese Black beef cattle},
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journal = {Animal Science Journal.},
year = {2020},
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title = {Extensive set of 16S rRNA-based probes for detection of bacteria in human feces.},
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title = {Quantification of uncultured Ruminococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes.},
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title = {In vitro model of colonization resistance by the enteric microbiota: effects of antimicrobial agents used in food-producing animals.},
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journal = {Antimicrob Agents Chemother},
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@article{lin417937,
title = {Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.},
author = {Ze X, Duncan SH, Louis P, Flint HJ.},
journal = {ISME J},
year = {2012},
doi = {10.1038/ismej.2012.4},
pmid = {22343308}
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@article{lin417947,
title = {Abilities of the mCP Agar method and CRENAME alpha toxin-specific real-time PCR assay to detect Clostridium perfringens spores in drinking water.},
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journal = {Appl Environ Microbiol},
year = {2013},
doi = {10.1128/aem.02791-13},
pmid = {24077714}
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@article{lin417945,
title = {Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection.},
author = {Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, Frank DN, McCarter MD, Wilson CC.},
journal = {Mucosal Immunol},
year = {2016},
doi = {10.1038/mi.2015.33},
pmid = {25921339}
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@article{lin417940,
title = {Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4.},
author = {Metzler-Zebeli BU, Schmitz-Esser S, Mann E, Grull D, Molnar T, Zebeli Q.},
journal = {Appl Environ Microbiol},
year = {2015},
doi = {10.1128/aem.02756-15},
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@article{lin54234,
title = {Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant.},
author = {Kim BC, Seung Jeon B, Kim S, Kim H, Um Y, Sang BI},
journal = {Int J Syst Evol Microbiol},
year = {2015},
doi = {10.1099/ijsem.0.000665},
pmid = {26474980}
}
@article{lin417936,
title = {Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association.},
author = {La Reau AJ, Meier-Kolthoff JP, Suen G.},
journal = {Microb Genom},
year = {2016},
doi = {10.1099/mgen.0.000099},
pmid = {28348838}
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@article{lin417941,
title = {Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation.},
author = {Laursen MF, Laursen RP, Larnkjaer A, Michaelsen KF, Bahl MI, Licht TR.},
journal = {BMC Microbiol},
year = {2017},
doi = {10.1186/s12866-017-1090-7},
pmid = {28818050}
}
@article{lin417948,
title = {Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.},
author = {de Muinck EJ, Lundin KEA, Trosvik P.},
journal = {mSystems},
year = {2017},
doi = {10.1128/msystems.00086-17},
pmid = {28904999}
}
@article{lin417939,
title = {In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media.},
author = {Wahlgren M, Axenstrand M, Hakansson A, Marefati A, Lomstein Pedersen B.},
journal = {Pharmaceutics},
year = {2019},
doi = {10.3390/pharmaceutics11020095},
pmid = {30813323}
}
@article{lin54236,
title = {Characterization of a novel extracellular alpha-amylase from Ruminococcus bromii ATCC 27255 with neopullulanase-like activity.},
author = {Jung JH, An YK, Son SY, Jeong SY, Seo DH, Kim MK, Park CS},
journal = {Int J Biol Macromol},
year = {2019},
doi = {10.1016/j.ijbiomac.2019.03.003},
pmid = {30836186}
}
@article{lin417943,
title = {Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection.},
author = {Hensley-McBain T, Wu MC, Manuzak JA, Cheu RK, Gustin A, Driscoll CB, Zevin AS, Miller CJ, Coronado E, Smith E, Chang J, Gale M, Somsouk M, Burgener AD, Hunt PW, Hope TJ, Collier AC, Klatt NR.},
journal = {PLoS Pathog},
year = {2019},
doi = {10.1371/journal.ppat.1007672},
pmid = {30973942}
}
@article{lin417935,
title = {Commensal and Pathogenic Bacteria Indirectly Induce IL-22 but Not IFNgamma Production From Human Colonic ILC3s via Multiple Mechanisms.},
author = {Castleman MJ, Dillon SM, Purba CM, Cogswell AC, Kibbie JJ, McCarter MD, Santiago ML, Barker E, Wilson CC.},
journal = {Front Immunol},
year = {2019},
doi = {10.3389/fimmu.2019.00649},
pmid = {30984202}
}
@article{lin417934,
title = {Enteric bacteria induce IFNgamma and Granzyme B from human colonic Group 1 Innate Lymphoid Cells.},
author = {Castleman MJ, Dillon SM, Purba C, Cogswell AC, McCarter M, Barker E, Wilson C.},
journal = {Gut Microbes},
year = {2020},
doi = {10.1080/19490976.2019.1667723},
pmid = {31583949}
}
@article{lin417942,
title = {Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening.},
author = {Ogata T, Makino H, Ishizuka N, Iwamoto E, Masaki T, Ikuta K, Kim YH, Sato S.},
journal = {PLoS One},
year = {2019},
doi = {10.1371/journal.pone.0225448},
pmid = {31770419}
}
@article{lin417918,
title = {Characterization of variations within the rumen metaproteome of Holstein dairy cattle relative to morning feed offering.},
author = {Honan MC, Greenwood SL.},
journal = {Sci Rep},
year = {2020},
doi = {10.1038/s41598-020-59974-5},
pmid = {32081893}
}
@article{lin54233,
title = {Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens.},
author = {Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R, Bengelsdorf FR},
journal = {Int J Syst Evol Microbiol},
year = {2020},
doi = {10.1099/ijsem.0.004283},
pmid = {32584751}
}
@article{lin54235,
title = {Comparison of pH and bacterial communities in the rumen and reticulum during fattening of Japanese Black beef cattle.},
author = {Ogata T, Kim YH, Iwamoto E, Masaki T, Ikuta K, Sato S},
journal = {Anim Sci J},
year = {2020},
doi = {10.1111/asj.13487},
pmid = {33368874}
}
@article{lin417921,
title = {In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition.},
author = {Teichmann J, Cockburn DW.},
journal = {Front Microbiol},
year = {2021},
doi = {10.3389/fmicb.2021.640253},
pmid = {33995299}
}
@article{lin417919,
title = {Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement.},
author = {Brereton NJB, Pitre FE, Gonzalez E.},
journal = {Comput Struct Biotechnol J},
year = {2021},
doi = {10.1016/j.csbj.2021.03.040},
pmid = {33995915}
}
@article{lin417929,
title = {Gut Bacteria Induce Granzyme B Expression in Human Colonic ILC3s In Vitro in an IL-15-Dependent Manner.},
author = {Castleman MJ, Dillon SM, Thompson TA, Santiago ML, McCarter MD, Barker E, Wilson CC.},
journal = {J Immunol},
year = {2021},
doi = {10.4049/jimmunol.2000239},
pmid = {34117105}
}
@article{lin417927,
title = {Resistant starch, microbiome, and precision modulation.},
author = {Dobranowski PA, Stintzi A.},
journal = {Gut Microbes},
year = {2021},
doi = {10.1080/19490976.2021.1926842},
pmid = {34275431}
}
@article{lin417931,
title = {A Natural Polyphenol Exerts Antitumor Activity and Circumvents Anti-PD-1 Resistance through Effects on the Gut Microbiota.},
author = {Messaoudene M, Pidgeon R, Richard C, Ponce M, Diop K, Benlaifaoui M, Nolin-Lapalme A, Cauchois F, Malo J, Belkaid W, Isnard S, Fradet Y, Dridi L, Velin D, Oster P, Raoult D, Ghiringhelli F, Boidot R, Chevrier S, Kysela DT, Brun YV, Falcone EL, Pilon G, Onate FP, Gitton-Quent O, Le Chatelier E, Durand S, Kroemer G, Elkrief A, Marette A, Castagner B, Routy B.},
journal = {Cancer Discov},
year = {2022},
doi = {10.1158/2159-8290.cd-21-0808},
pmid = {35031549}
}
@article{lin417915,
title = {Human gut commensal bacterium Ruminococcus species FMB-CY1 completely degrades the granules of resistant starch.},
author = {Hong YS, Jung DH, Chung WH, Nam YD, Kim YJ, Seo DH, Park CS.},
journal = {Food Sci Biotechnol},
year = {2022},
doi = {10.1007/s10068-021-01027-2},
pmid = {35186353}
}
@article{lin417932,
title = {TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data.},
author = {Yan D, Cao L, Zhou M, Mohimani H.},
journal = {Metabolites},
year = {2022},
doi = {10.3390/metabo12020119},
pmid = {35208194}
}
@article{lin417930,
title = {Granzyme B+ CD4 T cells accumulate in the colon during chronic HIV-1 infection.},
author = {Dillon SM, Mickens KL, Thompson TA, Cooper EH, Nesladek S, Christians AJ, Castleman M, Guo K, Wood C, Frank DN, Kechris K, Santiago ML, Wilson CC.},
journal = {Gut Microbes},
year = {2022},
doi = {10.1080/19490976.2022.2045852},
pmid = {35258402}
}
@article{lin417944,
title = {Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.},
author = {El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crepin A.},
journal = {Front Microbiol},
year = {2022},
doi = {10.3389/fmicb.2022.828359},
pmid = {35495704}
}
@article{lin417926,
title = {Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties.},
author = {Shetty SA, Kostopoulos I, Geerlings SY, Smidt H, de Vos WM, Belzer C.},
journal = {ISME J},
year = {2022},
doi = {10.1038/s41396-022-01255-2},
pmid = {35717467}
}
@article{lin417928,
title = {Discovery of a New Microbial Origin Cold-Active Neopullulanase Capable for Effective Conversion of Pullulan to Panose.},
author = {Wang M, Hu H, Zhang B, Zheng Y, Wu P, Lu Z, Zhang G.},
journal = {Int J Mol Sci},
year = {2022},
doi = {10.3390/ijms23136928},
pmid = {35805929}
}
@article{lin417933,
title = {Design, construction, and in vivo augmentation of a complex gut microbiome.},
author = {Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.},
journal = {Cell},
year = {2022},
doi = {10.1016/j.cell.2022.08.003},
pmid = {36070752}
}
@article{lin417917,
title = {Characterizing the Effect of Amylase Inhibitors on Maltodextrin Metabolism by Gut Bacteria Using Fluorescent Glycan Labeling.},
author = {Lui O, Dridi L, Gonzalez E, Yasmine S, Kubinski R, Billings H, Bohlmann J, Withers SG, Maurice C, Castagner B.},
journal = {ACS Chem Biol},
year = {2023},
doi = {10.1021/acschembio.2c00791},
pmid = {36728836}
}
@article{lin417925,
title = {Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting.},
author = {Beauchemin ET, Hunter C, Maurice CF.},
journal = {Gut Microbes},
year = {2023},
doi = {10.1080/19490976.2023.2180317},
pmid = {36823031}
}
@article{lin417924,
title = {Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.},
author = {Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.},
journal = {Cell},
year = {2023},
doi = {10.1016/j.cell.2023.05.037},
pmid = {37352836}
}
@article{lin417922,
title = {Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.},
author = {Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.},
journal = {Front Cell Infect Microbiol},
year = {2023},
doi = {10.3389/fcimb.2023.1056866},
pmid = {37520440}
}
@article{lin417938,
title = {Commensal bacteria signal through TLR5 and AhR to improve barrier integrity and prevent allergic responses to food.},
author = {Kemter AM, Patry RT, Arnold J, Hesser LA, Campbell E, Ionescu E, Mimee M, Wang S, Nagler CR.},
journal = {Cell Rep},
year = {2023},
doi = {10.1016/j.celrep.2023.113153},
pmid = {37742185}
}
@article{lin417923,
title = {A synbiotic of Anaerostipes caccae and lactulose prevents and treats food allergy in mice.},
author = {Hesser LA, Puente AA, Arnold J, Ionescu E, Mirmira A, Talasani N, Lopez J, Maccio-Maretto L, Mimee M, Nagler CR.},
journal = {Cell Host Microbe},
year = {2024},
doi = {10.1016/j.chom.2024.05.019},
pmid = {38906158}
}
@article{lin417914,
title = {Community metabolic modeling of host-microbiota interactions through multi-objective optimization.},
author = {Lambert A, Budinich M, Mahe M, Chaffron S, Eveillard D.},
journal = {iScience},
year = {2024},
doi = {10.1016/j.isci.2024.110092},
pmid = {38952683}
}
@article{lin417913,
title = {Important roles of Ruminococcaceae in the human intestine for resistant starch utilization.},
author = {Kim YJ, Jung DH, Park CS.},
journal = {Food Sci Biotechnol},
year = {2024},
doi = {10.1007/s10068-024-01621-0},
pmid = {39130658}
}
@article{lin417920,
title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.},
author = {Arnoldini M, Sharma R, Moresi C, Chure G, Chabbey J, Slack E, Cremer J.},
journal = {Cell},
year = {2025},
doi = {10.1016/j.cell.2025.07.005},
pmid = {40744013}
}