Thomas M Schmidt

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. pmc rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
    Zarraz May Ping Lee
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Nucleic Acids Res 37:D489-93. 2009
  2. ncbi request reprint The maturing of microbial ecology
    Thomas M Schmidt
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824 4320, USA
    Int Microbiol 9:217-23. 2006
  3. pmc Performance of the translational apparatus varies with the ecological strategies of bacteria
    Les Dethlefsen
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 4320, USA
    J Bacteriol 189:3237-45. 2007
  4. pmc Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria
    Stephanie A Eichorst
    Michigan State University, Department of Microbiology and Molecular Genetics, 6180 Biomedical and Physical Sciences Building, East Lansing, MI 48824 4320, USA
    Appl Environ Microbiol 73:2708-17. 2007
  5. pmc Symbiotic bacteria appear to mediate hyena social odors
    Kevin R Theis
    Departments of Microbiology and Molecular Genetics and Zoology and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824
    Proc Natl Acad Sci U S A 110:19832-7. 2013
  6. pmc A systems approach to model natural variation in reactive properties of bacterial ribosomes
    Julius H Jackson
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    BMC Syst Biol 2:62. 2008
  7. pmc Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane
    Uri Y Levine
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    ISME J 5:1683-91. 2011
  8. doi request reprint Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea
    Ju Young Chang
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
    J Infect Dis 197:435-8. 2008
  9. pmc Modulation of host immune responses by the cytolethal distending toxin of Helicobacter hepaticus
    Jason S Pratt
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Infect Immun 74:4496-504. 2006
  10. pmc The effect of natural selection on the performance of maximum parsimony
    Dehua Hang
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    BMC Evol Biol 7:94. 2007

Collaborators

Detail Information

Publications29

  1. pmc rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
    Zarraz May Ping Lee
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Nucleic Acids Res 37:D489-93. 2009
    ..The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes...
  2. ncbi request reprint The maturing of microbial ecology
    Thomas M Schmidt
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824 4320, USA
    Int Microbiol 9:217-23. 2006
    ....
  3. pmc Performance of the translational apparatus varies with the ecological strategies of bacteria
    Les Dethlefsen
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 4320, USA
    J Bacteriol 189:3237-45. 2007
    ....
  4. pmc Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria
    Stephanie A Eichorst
    Michigan State University, Department of Microbiology and Molecular Genetics, 6180 Biomedical and Physical Sciences Building, East Lansing, MI 48824 4320, USA
    Appl Environ Microbiol 73:2708-17. 2007
    ..The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil...
  5. pmc Symbiotic bacteria appear to mediate hyena social odors
    Kevin R Theis
    Departments of Microbiology and Molecular Genetics and Zoology and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824
    Proc Natl Acad Sci U S A 110:19832-7. 2013
    ..We anticipate that the fermentation hypothesis for chemical communication will prove broadly applicable among scent-marking mammals as others use the technical and analytical approaches used here...
  6. pmc A systems approach to model natural variation in reactive properties of bacterial ribosomes
    Julius H Jackson
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    BMC Syst Biol 2:62. 2008
    ....
  7. pmc Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane
    Uri Y Levine
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    ISME J 5:1683-91. 2011
    ..The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas...
  8. doi request reprint Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea
    Ju Young Chang
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
    J Infect Dis 197:435-8. 2008
    ..Preservation and restoration of the microbial diversity could represent novel strategies for prevention and treatment of recurrent CDAD, which is often recalcitrant to existing therapies...
  9. pmc Modulation of host immune responses by the cytolethal distending toxin of Helicobacter hepaticus
    Jason S Pratt
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Infect Immun 74:4496-504. 2006
    ..hepaticus. These results suggest that CDT plays a key immunomodulatory role that allows persistence of H. hepaticus and that in IL-10-/- mice this alteration of the host immune response results in the development of colitis...
  10. pmc The effect of natural selection on the performance of maximum parsimony
    Dehua Hang
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    BMC Evol Biol 7:94. 2007
    ..To gain insight into these issues, we study how well maximum parsimony performs with data generated by Avida, a digital life platform where populations of digital organisms evolve subject to natural selective pressures...
  11. pmc Life history implications of rRNA gene copy number in Escherichia coli
    Bradley S Stevenson
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48823 4320, USA
    Appl Environ Microbiol 70:6670-7. 2004
    ....
  12. pmc New strategies for cultivation and detection of previously uncultured microbes
    Bradley S Stevenson
    Department of Microbiology and Molecular Genetics, Michigan State University, 2209 Biomedical Physical Sciences, East Lansing, MI 48824 4320, USA
    Appl Environ Microbiol 70:4748-55. 2004
    ..Results illustrate the power of integrating culture methods with molecular techniques to isolate bacteria from phylogenetic groups underrepresented in culture...
  13. doi request reprint Overview of the gastrointestinal microbiota
    Vincent B Young
    Department of Medicine, Division of Infectious Diseases, The University of Michigan, Ann Arbor, Michigan 48109, USA
    Adv Exp Med Biol 635:29-40. 2008
    ..Following this discussion we will introduce methods that have been used to study the structure, function and dynamics of this community...
  14. pmc In vitro and in vivo characterization of Helicobacter hepaticus cytolethal distending toxin mutants
    Vincent B Young
    Department of Microbiology and Molecular Genetics, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA
    Infect Immun 72:2521-7. 2004
    ..However, a CDT-negative H. hepaticus mutant had a significantly diminished capacity to induce lesions in this murine model of inflammatory bowel disease...
  15. pmc Streptococcus intermedius causing infective endocarditis and abscesses: a report of three cases and review of the literature
    MaryAnn P Tran
    Department of Medicine, Infectious Diseases Division, Michigan State University, East Lansing, Michigan, USA
    BMC Infect Dis 8:154. 2008
    ..Identification of Streptococcus intermedius is difficult, leading to the development of molecular methods to more accurately identify and characterize this organism...
  16. ncbi request reprint Diversity and dynamics of microbial communities in soils from agro-ecosystems
    Daniel H Buckley
    Department of Microbiology and Molecular Genetics, Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Environ Microbiol 5:441-52. 2003
    ....
  17. pmc Differences in codon bias cannot explain differences in translational power among microbes
    Les Dethlefsen
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    BMC Bioinformatics 6:3. 2005
    ..coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias...
  18. pmc Phylogenetic characterization and prevalence of "Spirobacillus cienkowskii," a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species
    Jorge L M Rodrigues
    Department of Microbiology and Molecular Genetics, Biomedical and Physical Sciences Building, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 74:1575-82. 2008
    ..The broad geographic distribution, wide host range, and high virulence of S. cienkowskii suggest it plays an important role in the ecology and evolution of daphniids...
  19. doi request reprint Identifying and removing artificial replicates from 454 pyrosequencing data
    Tracy K Teal
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Cold Spring Harb Protoc 2010:pdb.prot5409. 2010
    ..g., in sequencing of amplified gene "tags." This protocol provides details on how to use the replicate filter and obtain a file of unique sequences for use in metagenomic or transcriptomic analyses...
  20. pmc Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains
    Katie E Hyma
    Microbial Evolution Laboratory, 165 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA
    J Bacteriol 187:619-28. 2005
    ..coli-like ancestor approximately 28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties...
  21. pmc Shallow breathing: bacterial life at low O(2)
    Rachel L Morris
    Department of Microbiology and Molecular Genetics, 6180 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824, USA
    Nat Rev Microbiol 11:205-12. 2013
    ..We explore the implications of these findings by highlighting the importance of microaerobic metabolism in host-associated bacteria related to health and disease...
  22. pmc Evidence for a bacterial mechanism for group-specific social odors among hyenas
    Kevin R Theis
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
    Sci Rep 2:615. 2012
    ....
  23. ncbi request reprint Systematic artifacts in metagenomes from complex microbial communities
    Vicente Gomez-Alvarez
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
    ISME J 3:1314-7. 2009
    ..Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts...
  24. pmc Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota
    Carole J Kuehl
    Department of Microbiology and Molecular Genetics, National Food Safety and Toxicology Center, Michigan State University, East Lansing, 48824, USA
    Infect Immun 73:6952-61. 2005
    ....
  25. pmc Inflammatory bowel disease causes reversible suppression of osteoblast and chondrocyte function in mice
    Laura Harris
    Department of Physiology, Michigan State University, East Lansing, Michigan, USA
    Am J Physiol Gastrointest Liver Physiol 296:G1020-9. 2009
    ..Changes in serum TNF-alpha (increased) and IGF-I (decreased) paralleled changes in bone parameters and returned to normal values with recovery, suggesting a potential role in the skeletal response...
  26. pmc Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes
    Ben P Werling
    Department of Entomology, Michigan State University, East Lansing, MI 48824
    Proc Natl Acad Sci U S A 111:1652-7. 2014
    ..Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services...
  27. pmc Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota
    Vincent B Young
    Department of Microbiology and Molecular Genetics, Infectious Diseases Unit, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA
    J Clin Microbiol 42:1203-6. 2004
    ....
  28. pmc Genetic diversity of Campylobacter sp. isolates from retail chicken products and humans with gastroenteritis in Central Michigan
    Brooke R Fitch
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    J Clin Microbiol 43:4221-4. 2005
    ..Campylobacter jejuni isolates from clinical sources had a greater diversity of flagellin alleles and a higher rate of quinolone resistance than isolates from retail chicken products...
  29. pmc Role of Rhodobacter sp. strain PS9, a purple non-sulfur photosynthetic bacterium isolated from an anaerobic swine waste lagoon, in odor remediation
    Young S Do
    Department of Microbiology, Iowa State University, 205 Science Building, Ames, IA 50011, USA
    Appl Environ Microbiol 69:1710-20. 2003
    ..In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride...

Research Grants4

  1. Cultivation and Characterization of Microaerobes from the Human Microbiome
    Vincent B Young; Fiscal Year: 2010
    ..To better understand their role in human health and disease, we proposed to cultivate these microbes in the laboratory to facilitate studies that will include the sequencing of their genomes. ..
  2. Cultivation and Characterization of Microaerobes from the Human Microbiome
    Thomas Schmidt; Fiscal Year: 2009
    ..To better understand their role in human health and disease, we proposed to cultivate these microbes in the laboratory to facilitate studies that will include the sequencing of their genomes. ..
  3. Cultivation and Characterization of Microaerobes from the Human Microbiome
    Thomas Schmidt; Fiscal Year: 2009
    ..To better understand their role in human health and disease, we proposed to cultivate these microbes in the laboratory to facilitate studies that will include the sequencing of their genomes. ..