The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins

Science Translational Medicine

Volumn 3, Issue 106, 2011, Pages

  McNulty, Nathan P ^a   Yatsunenko, Tanya ^a   Hsiao, Ansel ^a   Faith, Jeremiah J ^a   Muegge, Brian D ^a   Goodman, Andrew L ^a,h   Henrissat, Bernard ^b   Oozeer, Raish ^c   Cools Portier, Stéphanie ^c   Gobert, Guillaume ^c   Chervaux, Christian ^c   Knights, Dan ^d   Lozupone, Catherine A ^e   Knight, Rob ^e   Duncan, Alexis E ^a,f   Bain, James R ^g   Muehlbauer, Michael J ^g   Newgard, Christopher B ^g   Heath, Andrew C ^a   Gordon, Jeffrey I ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CNRS   (France)

^c DANONE RESEARCH   (France)

^d UCB 450   (United States)

^e UNIVERSITY OF COLORADO   (United States)

^f WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^g DUKE UNIVERSITY MEDICAL CENTER   (United States)

^h YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; GLYCAN; TRANSCRIPTOME; UNCLASSIFIED DRUG; XYLOOLIGOSACCHARIDE; PROBIOTIC AGENT;

ADULT; ANIMAL EXPERIMENT; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BIFIDOBACTERIUM ANIMALIS; CARBOHYDRATE METABOLISM; CATABOLISM; CONTROLLED STUDY; FECES ANALYSIS; FEMALE; FERMENTED MILK PRODUCT; FERMENTED PRODUCT; FOOD COMPOSITION; FOOD INTAKE; FRUIT; GENETIC CODE; GNOTOBIOTICS; HUMAN; IN VIVO STUDY; INTESTINE FLORA; LACTOBACILLUS DELBRUECKII; LACTOCOCCUS LACTIS CREMORIS; METABOLITE; MICROBIAL CONSORTIUM; MICROBIOME; MONOZYGOTIC TWINS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; SEQUENCE ANALYSIS; STREPTOCOCCUS THERMOPHILUS; UPREGULATION; URINALYSIS; VEGETABLE; ANIMAL; BIFIDOBACTERIUM; C57BL MOUSE; DAIRY PRODUCT; GASTROINTESTINAL TRACT; GENETICS; GERMFREE ANIMAL; LACTOBACILLUS; MALE; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGY;

ANIMALS; BIFIDOBACTERIUM; CULTURED MILK PRODUCTS; FEMALE; GASTROINTESTINAL TRACT; GERM-FREE LIFE; HUMANS; LACTOBACILLUS; MALE; METAGENOME; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE DATA; PROBIOTICS; TWINS, MONOZYGOTIC;

EID: 80054960299     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.3002701     Document Type: Article

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35. Acknowledgments: We thank J. Manchester and J. Hoisington-López for assistance with DNA sequencing; M. Karlsson, D. O'Donnell, and S. Wagoner for help with gnotobiotic mouse husbandry; S. Deng for assistance in preparing Illumina DNA libraries; S. Marion and D. Hooper for their contributions to the human study; D. Carlsen for coordination of FMP production and logistics; S. Baumann and S. Fischer (Agilent Corp.) for providing the Fiehn GC/MS Metabolomics RTL library used for metabolomics analyses; members of the Gordon lab for valuable suggestions during the course of this work; and G. Denariaz for his continued support. We are also grateful to Integrated Genomics for generating the draft genome sequences of B. animalis subsp. lactis (CNCM I-2494) and S. thermophilus (CNCM I-1630). Funding: Supported by grants from the NIH (DK30292, DK70977, and DK078669) and Danone Research. Maintenance of the MOAFTS twin cohort is supported by NIH grants AA09022, AA11998, AA17915, and HD49024. Author contributions: N.P.M., T.Y., A.C.H., and J.I.G. designed the experiments; N.P.M., A.H., J.J.F., A.L.G., J.R.B., and M.J. M. performed experiments involving mice, whereas T.Y., J.J.F., R.O., S.C.-P., and G.G. conducted analyses of human biospecimens; N.P.M., T.Y., A.H., B.D.M., A.L.G., B.H., C.C., D.K., C.A.L., R.K., A.E.D., and C.B.N. analyzed the data; N.P.M., A.H., T.Y., and J.I.G. wrote the paper. Competing interests: The authors declare that they have no competing interests. Accession numbers: The complete genome sequence of Bifidobacterium animalis subsp. lactis (CNCM I-2494) has been deposited at GenBank under accession number CP002915. The Whole Genome Shotgun projects for Lactobacillus delbrueckii subsp. bulgaricus (CNCM I-1632, CNCM I-1519), Streptococcus thermophilis CNCM I-1630, and Lactococcus lactis subsp. cremoris CNCM I-1631 have been deposited at DDBJ/EMBL/GenBank under accession numbers AGFO00000000, AGHW00000000, AGFN00000000, and AGHX00000000, respectively. The version of each of these genomes described in this paper is the first version (CP002915.1, AGFO01000000, AGHW01000000, AGFN01000000, and AGHX01000000, respectively). COPRO-Seq and RNA-Seq data are deposited in the Gene Expression Omnibus (GEO) database (accession numbers GSE31943 and GSE31670, respectively), whereas 16S rRNA pyrosequencing reads and shotgun pyrosequencing reads of human fecal community DNA are deposited in MG-RAST (accession numbers qiime:803 and 4473933-4473980, respectively).