Jeffrey I Gordon

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. ncbi request reprint A genomic view of our symbiosis with members of the gut microbiota
    Jeffrey I Gordon
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University, St Louis, Missouri, USA
    J Pediatr Gastroenterol Nutr 40:S28. 2005
  2. ncbi request reprint Response from Jeffrey I. Gordon et al.: Commensal bacteria make a difference
    Jeffrey I Gordon
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Trends Microbiol 11:150-1. 2003
  3. pmc Evolution of symbiotic bacteria in the distal human intestine
    Jian Xu
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Biol 5:e156. 2007
  4. ncbi request reprint Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches
    Marios Giannakis
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    J Biol Chem 281:11292-300. 2006
  5. pmc Mechanisms underlying the resistance to diet-induced obesity in germ-free mice
    Fredrik Backhed
    Center for Genome Sciences and Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:979-84. 2007
  6. ncbi request reprint Glycan foraging in vivo by an intestine-adapted bacterial symbiont
    Justin L Sonnenburg
    Center for Genome Sciences, Washington University, St Louis, MO 63108, USA
    Science 307:1955-9. 2005
  7. pmc A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism
    Erica D Sonnenburg
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:8834-9. 2006
  8. pmc Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells
    Marios Giannakis
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 105:4358-63. 2008
  9. pmc Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis
    Marios Giannakis
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    J Biol Chem 284:30383-94. 2009
  10. pmc Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection
    John F Rawls
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 127:423-33. 2006

Collaborators

Detail Information

Publications98

  1. ncbi request reprint A genomic view of our symbiosis with members of the gut microbiota
    Jeffrey I Gordon
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University, St Louis, Missouri, USA
    J Pediatr Gastroenterol Nutr 40:S28. 2005
  2. ncbi request reprint Response from Jeffrey I. Gordon et al.: Commensal bacteria make a difference
    Jeffrey I Gordon
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Trends Microbiol 11:150-1. 2003
    ....
  3. pmc Evolution of symbiotic bacteria in the distal human intestine
    Jian Xu
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Biol 5:e156. 2007
    ....
  4. ncbi request reprint Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches
    Marios Giannakis
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    J Biol Chem 281:11292-300. 2006
    ..The results reveal shared as well as distinctive features of adult gut stem cells when compared with other stem cell populations...
  5. pmc Mechanisms underlying the resistance to diet-induced obesity in germ-free mice
    Fredrik Backhed
    Center for Genome Sciences and Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:979-84. 2007
    ..Together, these findings support the notion that the gut microbiota can influence both sides of the energy balance equation, and underscore the importance of considering our metabolome in a supraorganismal context...
  6. ncbi request reprint Glycan foraging in vivo by an intestine-adapted bacterial symbiont
    Justin L Sonnenburg
    Center for Genome Sciences, Washington University, St Louis, MO 63108, USA
    Science 307:1955-9. 2005
    ..This flexible foraging behavior should contribute to ecosystem stability and functional diversity...
  7. pmc A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism
    Erica D Sonnenburg
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:8834-9. 2006
    ..An expanded repertoire of HTCS proteins with diversified sensor domains may be one reason for B. thetaiotaomicron's success in our intestinal ecosystem...
  8. pmc Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells
    Marios Giannakis
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 105:4358-63. 2008
    ..These results provide insights about how H. pylori may adapt to and influence stem cell biology and how its intracellular residency could contribute to gastric tumorigenesis...
  9. pmc Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis
    Marios Giannakis
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    J Biol Chem 284:30383-94. 2009
    ..This study illustrates an approach for identifying GEP responses specific to ChAG-associated H. Pylori strains and bacterial genes important for survival in a model of the ChAG gastric ecosystem...
  10. pmc Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection
    John F Rawls
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 127:423-33. 2006
    ....
  11. pmc Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
    Michael A Mahowald
    Center for Genome Sciences and Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 106:5859-64. 2009
    ....
  12. pmc Gut microbiota from twins discordant for obesity modulate metabolism in mice
    Vanessa K Ridaura
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 341:1241214. 2013
    ..These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions. ..
  13. pmc The impact of parietal cells on Helicobacter pylori tropism and host pathology: an analysis using gnotobiotic normal and transgenic mice
    Andrew J Syder
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 100:3467-72. 2003
    ..pylori within the gastric ecosystem, and emphasize the need to consider the evolution of pathology within a given host in a niche-specific context...
  14. pmc Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host
    Justin L Sonnenburg
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Biol 4:e413. 2006
    ....
  15. pmc Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 107:7503-8. 2010
    ..g., predicted cellulases, dockerins), and transcriptional activities. These results provide an expanded perspective about features that make each of us unique life forms and directions for future characterization of our gut ecosystems...
  16. pmc The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression
    Jung D Oh
    Center for Genome Sciences, Washington University School of Medicine, 4444 Forest Park, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:9999-10004. 2006
    ..pylori's adaptation to ChAG...
  17. ncbi request reprint Host-bacterial mutualism in the human intestine
    Fredrik Backhed
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 307:1915-20. 2005
    ..We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ...
  18. ncbi request reprint Functional genomic studies of the intestinal response to a foodborne enteropathogen in a humanized gnotobiotic mouse model
    Marc Lecuit
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 282:15065-72. 2007
    ..Together, these studies establish that hly, rather than bacterial invasion of the lamina propria mediated by InlA, is a dominant determinant of the intensity of the host response to L. monocytogenes infection via the oral route...
  19. pmc Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont
    Eric C Martens
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 284:18445-57. 2009
    ..This latter finding provides a new link in the dynamic interplay between complex glycan metabolism, microbial physiology, and host responses that occurs during colonization of the gut...
  20. pmc Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, MO 63108, USA
    Cell Host Microbe 3:213-23. 2008
    ..Our study illustrates how combining comparative metagenomics with gnotobiotic mouse models and specific dietary manipulations can disclose the niches of previously uncharacterized members of the gut microbiota...
  21. ncbi request reprint IgA response to symbiotic bacteria as a mediator of gut homeostasis
    Daniel A Peterson
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell Host Microbe 2:328-39. 2007
    ..Immunoselection of bacterial epitope expression may contribute to the remarkable strain-level diversity in this ecosystem...
  22. ncbi request reprint An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006
    ..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
  23. pmc The long-term stability of the human gut microbiota
    Jeremiah J Faith
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 341:1237439. 2013
    ..This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target. ..
  24. pmc The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Sci Transl Med 1:6ra14. 2009
    ..Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997...
  25. pmc Evolution of mammals and their gut microbes
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 320:1647-51. 2008
    ....
  26. ncbi request reprint Molecular characterization of mouse gastric zymogenic cells
    Jason C Mills
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Biol Chem 278:46138-45. 2003
    ..01). These results support an emerging theme that angiogenesis in the adult mouse gut is modulated by cross-talk between its epithelial lineages and the underlying mesenchyme...
  27. pmc Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm
    Eric C Martens
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 284:24673-7. 2009
    ..These systems provide insights into how gut, as well as terrestrial and aquatic, Bacteroidetes survive in highly competitive ecosystems...
  28. pmc Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
    Buck S Samuel
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:10643-8. 2007
    ..These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota...
  29. pmc Predicting a human gut microbiota's response to diet in gnotobiotic mice
    Jeremiah J Faith
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 333:101-4. 2011
    ..The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods...
  30. pmc Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells
    Thaddeus S Stappenbeck
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 99:15451-5. 2002
    ....
  31. pmc Metabolic niche of a prominent sulfate-reducing human gut bacterium
    Federico E Rey
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St Louis, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 110:13582-7. 2013
    ..Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it. ..
  32. ncbi request reprint Functional genomic studies of uropathogenic Escherichia coli and host urothelial cells when intracellular bacterial communities are assembled
    Christopher S Reigstad
    Center for Genome Sciences and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 282:21259-67. 2007
    ..Together, these studies indicate that heme- and siderophore-associated iron play key roles in IBC development and provide a series of microbial and host biomarkers for comparing UPEC strains isolated from humans...
  33. pmc Linkage between cellular communications, energy utilization, and proliferation in metastatic neuroendocrine cancers
    Joseph E Ippolito
    Center for Genome Sciences, Washington University, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:12505-10. 2006
    ....
  34. pmc Postnatal lymphatic partitioning from the blood vasculature in the small intestine requires fasting-induced adipose factor
    Fredrik Backhed
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:606-11. 2007
    ..This organ-specific lymphovascular abnormality can be rescued by allowing embryonic Fiaf-/- intestinal isografts to develop in Fiaf+/+ recipients...
  35. pmc Dissecting the in vivo metabolic potential of two human gut acetogens
    Federico E Rey
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 285:22082-90. 2010
    ..These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest...
  36. pmc Viruses in the faecal microbiota of monozygotic twins and their mothers
    Alejandro Reyes
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 466:334-8. 2010
    ..These results indicate that a predatory viral-microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine...
  37. pmc Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41
    Buck S Samuel
    Center for Genome Sciences and Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 105:16767-72. 2008
    ..These results reveal that Gpr41 is a regulator of host energy balance through effects that are dependent upon the gut microbiota...
  38. pmc Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
    Brian D Muegge
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 332:970-4. 2011
    ..These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level...
  39. pmc In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut
    John F Rawls
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:7622-7. 2007
    ....
  40. pmc Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut
    Alejandro Reyes
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108
    Proc Natl Acad Sci U S A 110:20236-41. 2013
    ..cellulosilyticus prophage confers upon its host. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut. ..
  41. pmc Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts
    Eric C Martens
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS Biol 9:e1001221. 2011
    ....
  42. ncbi request reprint Message from a human gut symbiont: sensitivity is a prerequisite for sharing
    Jian Xu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Trends Microbiol 12:21-8. 2004
    ..This arrangement illustrates how a successful symbiont has evolved strategies for detecting and responding to conditions in its niche so that it can sustain beneficial relationships with its microbial and human partners...
  43. pmc A transgenic mouse model of metastatic carcinoma involving transdifferentiation of a gastric epithelial lineage progenitor to a neuroendocrine phenotype
    Andrew J Syder
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 101:4471-6. 2004
    ....
  44. pmc Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation
    Peter A Crawford
    Center for Genome Sciences and Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 106:11276-81. 2009
    ..Together, these results illustrate benefits provided by the gut microbiota during periods of nutrient deprivation, and emphasize the importance of further exploring the relationship between gut microbes and cardiovascular health...
  45. pmc Identifying genetic determinants needed to establish a human gut symbiont in its habitat
    Andrew L Goodman
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell Host Microbe 6:279-89. 2009
    ..INSeq provides a broadly applicable platform to explore microbial adaptation to the gut and other ecosystems...
  46. ncbi request reprint Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period
    Magnus K Bjursell
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    J Biol Chem 281:36269-79. 2006
    ....
  47. pmc Intracellular Helicobacter pylori in gastric epithelial progenitors
    Jung D Oh
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 102:5186-91. 2005
    ..The notion that adult mammalian epithelial progenitors can function as a repository for H. pylori broadens the view of host habitats available to this and perhaps other pathogens...
  48. pmc An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers
    Joseph E Ippolito
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 102:9901-6. 2005
    ..Transcriptional, metabolic, and electrophysiologic features of transformed mouse NE cells are also evident in neural progenitor cells...
  49. pmc Obesity alters gut microbial ecology
    Ruth E Ley
    Center for Genomes Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 102:11070-5. 2005
    ..The sequences reported in this paper have been deposited in the GenBank database [accession nos. DQ 014552--DQ 015671 (mothers) and AY 989911--AY 993908 (offspring)]...
  50. pmc Positive selection identifies an in vivo role for FimH during urinary tract infection in addition to mannose binding
    Swaine L Chen
    Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 106:22439-44. 2009
    ....
  51. pmc Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition
    Vitas E Wagner
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63110, USA
    Sci Transl Med 8:366ra164. 2016
    ..These results illustrate how intraspecific (ETBF-NTBF) and interspecific interactions influence the effects of harboring B. fragilis...
  52. pmc Persistent gut microbiota immaturity in malnourished Bangladeshi children
    Sathish Subramanian
    Center for Genome Sciences and Systems Biology, Washington University in St Louis, St Louis, Missouri 63108, USA
    Nature 510:417-21. 2014
    ..More prolonged interventions with existing or new therapeutic foods and/or addition of gut microbes may be needed to achieve enduring repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes. ..
  53. pmc Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome
    Nathan P McNulty
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS Biol 11:e1001637. 2013
    ....
  54. pmc Microbial regulation of intestinal radiosensitivity
    Peter A Crawford
    Center for Genome Sciences and Department of Molecular Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 102:13254-9. 2005
    ..Together, these findings provide insights about the cellular and molecular targets involved in microbial regulation of intestinal radiosensitivity...
  55. ncbi request reprint Ecological and evolutionary forces shaping microbial diversity in the human intestine
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 124:837-48. 2006
    ..The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike...
  56. ncbi request reprint Interactions between gastric epithelial stem cells and Helicobacter pylori in the setting of chronic atrophic gastritis
    Jung D Oh
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63108, USA
    Curr Opin Microbiol 9:21-7. 2006
    ..pylori persistence in a gastric ecosystem that has lost its acid barrier to colonization by environmental, oral and intestinal microbes. One consequence to the host might be an increased risk of tumorigenesis...
  57. pmc Escherichia coli from urine of female patients with urinary tract infections is competent for intracellular bacterial community formation
    Corinne K Garofalo
    Department of Molecular Microbiology, Box 8230, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO 63110, USA
    Infect Immun 75:52-60. 2007
    ..Although UPEC isolates differ genetically in their virulence factors, the majority of UPEC isolates from different types of UTI proceed through the IBC pathway, confirming the generality of IBCs in UTI pathogenesis in mice...
  58. pmc Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota
    John F Rawls
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 101:4596-601. 2004
    ..Together, these studies establish gnotobiotic zebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract...
  59. pmc RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites
    Yan Hu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 101:5559-64. 2004
    ..through effects on cAMP), and enhances survival by inhibiting apoptosis. PNEC cell lines should be generally useful for genetic and/or pharmacologic studies of the regulation of NE cell proliferation, differentiation, and tumorigenesis...
  60. pmc Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont
    Eric C Martens
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell Host Microbe 4:447-57. 2008
    ..Thus, PUL-mediated glycan catabolism is an important component in gut colonization and may impact microbiota ecology...
  61. pmc A core gut microbiome in obese and lean twins
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 457:480-4. 2009
    ....
  62. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
  63. pmc Bacteria from diverse habitats colonize and compete in the mouse gut
    Henning Seedorf
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 159:253-66. 2014
    ..This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics...
  64. pmc Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection
    Swaine L Chen
    Center for Genome Sciences and Systems Biology, Washington University, St Louis, MO 63108, USA
    Sci Transl Med 5:184ra60. 2013
    ..Thus, UPEC appear capable of persisting in both the gut and urinary tract without a fitness trade-off, emphasizing the need to widen our consideration of potential reservoirs for strains causing recurrent UTI...
  65. pmc Gut microbiomes of Malawian twin pairs discordant for kwashiorkor
    Michelle I Smith
    Center for Genome Sciences and Systems Biology, Washington University in St Louis, St Louis, MO 63110, USA
    Science 339:548-54. 2013
    ..These findings implicate the gut microbiome as a causal factor in kwashiorkor...
  66. pmc Going viral: next-generation sequencing applied to phage populations in the human gut
    Alejandro Reyes
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nat Rev Microbiol 10:607-17. 2012
    ..Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes...
  67. pmc The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins
    Nathan P McNulty
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Sci Transl Med 3:106ra106. 2011
    ..These experiments illustrate a translational research pipeline for characterizing the effects of FMPs on the human gut microbiome...
  68. pmc Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins
    Elizabeth E Hansen
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 108:4599-606. 2011
    ....
  69. pmc Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
    Andrew L Goodman
    Center for Genome Science and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 108:6252-7. 2011
    ....
  70. pmc Molecular features of adult mouse small intestinal epithelial progenitors
    Thaddeus S Stappenbeck
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 100:1004-9. 2003
    ..This dataset, together with our recent analysis of gene expression in the gastric stem cell niche, discloses a set of molecular features shared by adult mouse gut epithelial progenitors...
  71. pmc A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism
    Buck S Samuel
    Center for Genome Sciences, Washington University School of Medicine, 4444 Forest Park, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:10011-6. 2006
    ..thetaiotaomicron-D. piger biassociated, animals. These findings demonstrate a link between this archaeon, prioritized bacterial utilization of polysaccharides commonly encountered in our modern diets, and host energy balance...
  72. pmc Honor thy symbionts
    Jian Xu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 100:10452-9. 2003
    ....
  73. pmc Worlds within worlds: evolution of the vertebrate gut microbiota
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nat Rev Microbiol 6:776-88. 2008
    ....
  74. pmc Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont
    Nicole Koropatkin
    Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA
    Biochemistry 48:1532-42. 2009
    ..The diversity in amino acid sequence level likely reflects early divergence from a common ancestor, while the unique and conserved alpha-helical fold the SusD family suggests a similar function in glycan uptake...
  75. ncbi request reprint Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations
    Thaddeus S Stappenbeck
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Methods Enzymol 356:167-96. 2002
  76. ncbi request reprint A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
    Jian Xu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Science 299:2074-6. 2003
    ..These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine...
  77. ncbi request reprint How host-microbial interactions shape the nutrient environment of the mammalian intestine
    Lora V Hooper
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Annu Rev Nutr 22:283-307. 2002
    ..These and other studies underscore the importance of understanding precisely how nutrient metabolism serves to establish and sustain symbiotic relationships between mammals and their bacterial partners...
  78. ncbi request reprint Improved magnetic resonance imaging detection of prostate cancer in a transgenic mouse model
    Sheng Kwei Song
    Biomedical MR Laboratory, Department of Chemistry, Washington University, St Louis, Missouri 63110, USA
    Cancer Res 62:1555-8. 2002
    ..00001). Clinical application of DWI may offer advantages over current T2-weighted magnetic resonance imaging methods...
  79. ncbi request reprint Genetic mosaic analysis indicates that the bulb region of coat hair follicles contains a resident population of several active multipotent epithelial lineage progenitors
    Raphael Kopan
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Dev Biol 242:44-57. 2002
    ..This latter feature resembles the behavior of hematopoietic stem cells after bone marrow transplantation, and raises the question of whether this property may be shared by stem cells in other self-renewing epithelia...
  80. pmc Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure
    Amanda L Lewis
    Glycobiology Research and Training Center, Departments of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 106:13552-7. 2009
    ..Together, these data indicate that some of the long-standing paradigms in Sia biology should be reconsidered in a wider evolutionary context of the extended family of NulO sugars...
  81. ncbi request reprint MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly
    Jian Xu
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 21:1265-6. 2005
    ..Using the locations of sequence markers on the physical map, MapLinker generates a tentative sequence map of the genome that serves to verify the map and to guide genome-wide finishing...
  82. ncbi request reprint Genetic mosaic analysis reveals that GATA-4 is required for proper differentiation of mouse gastric epithelium
    Christina M Jacobsen
    Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Dev Biol 241:34-46. 2002
    ....
  83. ncbi request reprint Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systems
    Britta M Björkholm
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, 660 S Euclid Avenue, St Louis, MO 63110, USA
    J Biol Chem 277:34191-7. 2002
    ..This suggests that the functions of these HsdS homologs may include control of expression of microbial determinants that affect the extent of gastric responses to this potentially virulent pathogen...
  84. pmc The gut microbiota as an environmental factor that regulates fat storage
    Fredrik Backhed
    Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 101:15718-23. 2004
    ..Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY 667702--AY 668946)...
  85. ncbi request reprint Microbial ecology: human gut microbes associated with obesity
    Ruth E Ley
    Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 444:1022-3. 2006
    ..Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications...
  86. ncbi request reprint Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?
    Justin L Sonnenburg
    Department of Molecular Biology and Pharmacology and Center for Genome Sciences, Washington University, St Louis, Missouri 63110, USA
    Nat Immunol 5:569-73. 2004
    ..Here we propose that the mucus gel layer overlying the intestinal epithelium is a key contributor to the structural and functional stability of this microbiota and its tolerance by the host...
  87. ncbi request reprint Selection of multipotent stem cells during morphogenesis of small intestinal crypts of Lieberkuhn is perturbed by stimulation of Lef-1/beta-catenin signaling
    Melissa H Wong
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Biol Chem 277:15843-50. 2002
    ..These results indicate that developmental changes in beta-catenin-mediated signaling can play an important role in establishing a stem cell hierarchy during crypt morphogenesis...
  88. pmc Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
    Swaine L Chen
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:5977-82. 2006
    ..coli isolates from patients with UTI. These studies outline a computational approach that may be broadly applicable for studying strain-specific adaptation and pathogenesis in other bacteria...
  89. ncbi request reprint A gnotobiotic transgenic mouse model for studying interactions between small intestinal enterocytes and intraepithelial lymphocytes
    Indira U Mysorekar
    Department of Molecular Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Biol Chem 277:37811-9. 2002
    ..Together, these findings demonstrate that changes in the proliferative status of the intestinal epithelium affects maturation of gammadelta TCR(+) IELs and produces an influx of alphabeta TCR(+) IELs even in the absence of a microflora...
  90. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  91. pmc Host-bacterial coevolution and the search for new drug targets
    Jesse Zaneveld
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, United States
    Curr Opin Chem Biol 12:109-14. 2008
    ..Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities...
  92. ncbi request reprint Molecular characterization of a metastatic neuroendocrine cell cancer arising in the prostates of transgenic mice
    Yan Hu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Biol Chem 277:44462-74. 2002
    ..These results underscore the value of CR2-TAg mice for characterizing normal NE cell biology and tumorigenesis...
  93. pmc Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases
    Daniel A Peterson
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell Host Microbe 3:417-27. 2008
    ....
  94. ncbi request reprint Fibroblast growth factor receptor signalling is crucial for liver homeostasis and regeneration
    Heike Steiling
    Institute of Cell Biology, ETH Zurich, Honggerberg, CH 8093 Zurich, Switzerland
    Oncogene 22:4380-8. 2003
    ..These data demonstrate a key role of FGFR signalling in repair after liver injury...
  95. pmc Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird
    Filipa Godoy-Vitorino
    Department of Biology, University of Puerto Rico, San Juan, Puerto Rico 00931 3360
    Appl Environ Microbiol 74:5905-12. 2008
    ..1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the "species" level and thus likely include novel cellulolytic lineages...
  96. pmc The convergence of carbohydrate active gene repertoires in human gut microbes
    Catherine A Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 105:15076-81. 2008
    ....
  97. pmc Innate immunity and intestinal microbiota in the development of Type 1 diabetes
    Li Wen
    Section of Endocrinology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nature 455:1109-13. 2008
    ..Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition...
  98. pmc Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices
    Nicole M Koropatkin
    Donald Danforth Plant Science Center, St Louis, MO 63132, USA
    Structure 16:1105-15. 2008
    ....