All Stories

  1. Influence of CUREs on STEM retention depends on demographic identities

    Article • Journal of Microbiology and Biology Education, December 2023, ASM Journals

    Professor Thomas M Schmidt

  2. Diversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residues

    Article • Ecological Applications, January 2023, Wiley

    Professor Thomas M Schmidt

  3. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes

    Article • mSystems, February 2022, ASM Journals

    Professor Thomas M Schmidt

  4. Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

    Article • mSphere, December 2021, ASM Journals

    Professor Thomas M Schmidt

  5. Organoid-derived adult human colonic epithelium responds to co-culture with a probiotic strain of Bifidobacterium longum

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Professor Thomas M Schmidt

  6. Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Professor Thomas M Schmidt

  7. Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD

    Article • Blood Advances, October 2019, American Society of Hematology

    Professor Thomas M Schmidt

  8. Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice

    Article • BMC Microbiology, June 2019, Springer Science + Business Media

    Professor Thomas M Schmidt

  9. Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers

    Article • mBio, February 2019, ASM Journals

    Professor Thomas M Schmidt

  10. Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Professor Thomas M Schmidt

  11. Biomass and biofuel crop effects on biodiversity and ecosystem services in the North Central US

    Article • Biomass and Bioenergy, July 2018, Elsevier

    Professor Thomas M Schmidt

  12. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

    Article • Nature Microbiology, September 2016, Springer Science + Business Media

    Professor Thomas M Schmidt

  13. Variable responses of human microbiomes to dietary supplementation with resistant starch

    Article • Microbiome, June 2016, Springer Science + Business Media

    Professor Thomas M Schmidt

  14. Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease

    Article • Nature Immunology, March 2016, Springer Science + Business Media

    Professor Thomas M Schmidt

  15. Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin

    Article • Frontiers in Microbiology, March 2016, Frontiers

    Professor Thomas M Schmidt

  16. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals

    Article • American Review of Respiratory Disease, December 2015, American Thoracic Society

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  17. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

    Article • Microbiome, April 2015, Springer Science + Business Media

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  18. Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

    Article • mBio, March 2015, ASM Journals

    Professor Thomas M Schmidt

  19. Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

    Article • mBio, January 2015, ASM Journals

    Professor Thomas M Schmidt

  20. The physiology and ecological implications of efficient growth

    Article • The ISME Journal, January 2015, Springer Science + Business Media

    Professor Thomas M Schmidt

  21. rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

    Article • Nucleic Acids Research, November 2014, Oxford University Press (OUP)

    Professor Thomas M Schmidt

  22. A Little O2 May Go a Long Way in Structuring the GI Microbiome

    Article • Gastroenterology, November 2014, Elsevier

    Professor Thomas M Schmidt

  23. Farming for Ecosystem Services: An Ecological Approach to Production Agriculture

    Article • BioScience, April 2014, Oxford University Press (OUP)

    Professor Thomas M Schmidt

  24. Bacterial growth efficiency varies in soils under different land management practices

    Article • Soil Biology and Biochemistry, February 2014, Elsevier

    Professor Thomas M Schmidt

  25. Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

    Article • PLoS ONE, January 2014, PLOS

    Professor Thomas M Schmidt

  26. Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes

    Article • Proceedings of the National Academy of Sciences, January 2014, Proceedings of the National Academy of Sciences

    Professor Thomas M Schmidt

  27. Symbiotic bacteria appear to mediate hyena social odors

    Article • Proceedings of the National Academy of Sciences, November 2013, Proceedings of the National Academy of Sciences

    Professor Thomas M Schmidt

  28. Methods for Characterizing Microbial Communities Associated with the Human Body

    Article • August 2013, Wiley

    Professor Thomas M Schmidt

  29. Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

    Article • American Journal of Respiratory and Critical Care Medicine, May 2013, American Thoracic Society

    Professor Elodie Ghedin, Professor Patrick D Schloss, Professor Thomas M Schmidt

  30. Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium

    Article • The ISME Journal, May 2013, Springer Science + Business Media

    Dr Jorge L Rodrigues, Professor Thomas M Schmidt

  31. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

    Article • Microbiome, March 2013, Springer Science + Business Media

    Professor Patrick D Schloss, Professor Thomas M Schmidt

  32. A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity

    Article • Microbiome, March 2013, Springer Science + Business Media

    Professor Thomas M Schmidt

  33. Shallow breathing: bacterial life at low O2

    Article • Nature Reviews Microbiology, February 2013, Springer Science + Business Media

    Professor Thomas M Schmidt

  34. Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

    Article • Applied and Environmental Microbiology, December 2012, ASM Journals

    Kai Xue, Professor Thomas M Schmidt

  35. Evidence for a bacterial mechanism for group-specific social odors among hyenas

    Article • Scientific Reports, August 2012, Springer Science + Business Media

    Professor Thomas M Schmidt

  36. Structure, function and diversity of the healthy human microbiome

    Article • Nature, June 2012, Springer Science + Business Media

    Professor Patrick D Schloss, Dr Tatiana A Vishnivetskaya, Dr. Jacques Izard, Dr Nikos C Kyrpides, Professor Thomas M Schmidt

  37. A framework for human microbiome research

    Article • Nature, June 2012, Springer Science + Business Media

    Professor Patrick D Schloss, Dr Tatiana A Vishnivetskaya, Dr. Jacques Izard, Dr Nikos C Kyrpides, Professor Thomas M Schmidt

  38. Fundamentals of Microbial Community Resistance and Resilience

    Article • Frontiers in Microbiology, January 2012, Frontiers

    Professor Jay T Lennon, Professor Thomas M Schmidt

  39. Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

    Article • Applied and Environmental Microbiology, December 2011, ASM Journals

    Dr Jorge L Rodrigues, Professor Thomas M Schmidt

  40. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties

    Article • Soil Biology and Biochemistry, October 2011, Elsevier

    William Whitman, Professor Thomas M Schmidt

  41. Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane

    Article • The ISME Journal, April 2011, Springer Science + Business Media

    Professor Thomas M Schmidt

  42. Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward

    Article • Frontiers in Microbiology, January 2011, Frontiers

    Professor Thomas M Schmidt

  43. Influence of Plant Polymers on the Distribution and Cultivation of Bacteria in the PhylumAcidobacteria

    Article • Applied and Environmental Microbiology, November 2010, ASM Journals

    Professor Thomas M Schmidt

  44. Identifying and Removing Artificial Replicates from 454 Pyrosequencing Data

    Article • Cold Spring Harbor Protocols, April 2010, Cold Spring Harbor Laboratory Press

    Professor Thomas M Schmidt

  45. Systematic artifacts in metagenomes from complex microbial communities

    Article • The ISME Journal, July 2009, Springer Science + Business Media

    Professor Thomas M Schmidt

  46. Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

    Article • Infection and Immunity, March 2009, ASM Journals

    Professor Thomas M Schmidt

  47. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Professor Thomas M Schmidt

  48. A systems approach to model natural variation in reactive properties of bacterial ribosomes

    Article • BMC Systems Biology, July 2008, Springer Science + Business Media

    Professor Thomas M Schmidt

  49. Defining Linkages between the GSC and NSF's LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes

    Article • OMICS A Journal of Integrative Biology, June 2008, Mary Ann Liebert Inc

    Professor Thomas M Schmidt

  50. Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

    Article • The Journal of Infectious Diseases, February 2008, Oxford University Press (OUP)

    Professor Thomas M Schmidt

  51. Phylogenetic Characterization and Prevalence of “Spirobacillus cienkowskii,” a Red-Pigmented, Spiral-Shaped Bacterial Pathogen of Freshwater Daphnia Species

    Article • Applied and Environmental Microbiology, January 2008, ASM Journals

    Professor Thomas M Schmidt

  52. The effect of natural selection on the performance of maximum parsimony

    Article • BMC Evolutionary Biology, June 2007, Springer Science + Business Media

    Professor Thomas M Schmidt

  53. Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria

    Article • Applied and Environmental Microbiology, February 2007, ASM Journals

    Professor Thomas M Schmidt

  54. Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria

    Article • Journal of Bacteriology, February 2007, ASM Journals

    Professor Thomas M Schmidt

  55. Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota

    Article • Infection and Immunity, October 2005, ASM Journals

    Professor Thomas M Schmidt

  56. Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Professor Thomas M Schmidt

  57. Life History Implications of rRNA Gene Copy Number in Escherichia coli

    Article • Applied and Environmental Microbiology, November 2004, ASM Journals

    Professor Thomas M Schmidt

  58. New Strategies for Cultivation and Detection of Previously Uncultured Microbes

    Article • Applied and Environmental Microbiology, August 2004, ASM Journals

    Professor Thomas M Schmidt

  59. Changes in Synechococcus Population Size and Cellular Ribosomal RNA Content in Response to Predation and Nutrient Limitation

    Article • Microbial Ecology, May 2004, Springer Science + Business Media

    Professor Thomas M Schmidt

  60. Antibiotic-Associated Diarrhea Accompanied by Large-Scale Alterations in the Composition of the Fecal Microbiota

    Article • Journal of Clinical Microbiology, March 2004, ASM Journals

    Professor Thomas M Schmidt

  61. Archaeal nucleic acids in picoplankton from great lakes on three continents

    Article • Microbial Ecology, August 2003, Springer Science + Business Media

    Professor Thomas M Schmidt

  62. Diversity and dynamics of microbial communities in soils from agro‐ecosystems

    Article • Environmental Microbiology, May 2003, Wiley

    Professor Thomas M Schmidt

  63. Role of Rhodobacter sp. Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation

    Article • Applied and Environmental Microbiology, March 2003, ASM Journals

    Professor Thomas M Schmidt

  64. Rates and Consequences of Recombination between rRNA Operons

    Article • Journal of Bacteriology, February 2003, ASM Journals

    Professor Thomas M Schmidt

  65. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

    Article • Nucleic Acids Research, January 2003, Oxford University Press (OUP)

    Prof George M Garrity, Professor Thomas M Schmidt

  66. rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria

    Article • Applied and Environmental Microbiology, April 2000, ASM Journals

    Professor Thomas M Schmidt

  67. Molecular Characterization ofCyclospora‐like Organisms from Baboons

    Article • The Journal of Infectious Diseases, March 1999, Oxford University Press (OUP)

    Professor Thomas M Schmidt

  68. Acetogenesis from H 2 Plus CO 2 by Spirochetes from Termite Guts

    Article • Science, January 1999, American Association for the Advancement of Science

    Professor Thomas M Schmidt

  69. A new version of the RDP (Ribosomal Database Project)

    Article • Nucleic Acids Research, January 1999, Oxford University Press (OUP)

    Prof George M Garrity, Professor Thomas M Schmidt

  70. Application of Traditional and Phylogenetically Based Comparative Methods to Test for a Trade-off in Bacterial Growth Rate at Low versus High Substrate Concentration

    Article • Microbial Ecology, January 1999, Springer Science + Business Media

    Professor Thomas M Schmidt

  71. Nucleic acid content of Synechococcus spp. during growth in continuous light and light/dark cycles

    Article • Archives of Microbiology, August 1998, Springer Science + Business Media

    Professor Thomas M Schmidt

  72. Article • Antonie van Leeuwenhoek, January 1998, Springer Science + Business Media

    Professor Thomas M Schmidt

  73. Distribution of the tfdA Gene in Soil Bacteria That Do Not Degrade 2,4-Dichlorophenoxyacetic Acid (2,4-D)

    Article • Microbial Ecology, September 1997, Springer Science + Business Media

    Robert Hausinger, Professor Thomas M Schmidt

  74. Vitamin A or Zymosan Pretreatment Attenuates α-Naphthylisothiocyanate-Induced Liver Injury

    Article • Toxicology and Applied Pharmacology, September 1995, Elsevier

    Professor Thomas M Schmidt

  75. [16] Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences

    Article • January 1994, Elsevier

    Professor Thomas M Schmidt

  76. Identification of the Whipple's Disease Bacillus

    Article • New England Journal of Medicine, January 1993, New England Journal of Medicine (NEJM/MMS)

    Professor Thomas M Schmidt

  77. Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis, and other alpha‐proteobacteria

    Article • Molecular Microbiology, July 1992, Wiley

    Professor Thomas M Schmidt

  78. The first cellular bioenergetic process: Primitive generation of a proton-motive force

    Article • Journal of Molecular Evolution, October 1991, Springer Science + Business Media

    Professor Thomas M Schmidt

  79. The Agent of Bacillary Angiomatosis

    Article • New England Journal of Medicine, December 1990, New England Journal of Medicine (NEJM/MMS)

    Professor Thomas M Schmidt

  80. Spectral characterization of c-type cytochromes purified from Beggiatoa alba

    Article • Archives of Microbiology, October 1990, Springer Science + Business Media

    Professor Alan A DiSpirito, Professor Thomas M Schmidt

  81. Electron transport and respiration in Beggiatoa and Vitreoscilla

    Article • Archives of Microbiology, June 1986, Springer Science + Business Media

    Professor Thomas M Schmidt

  82. Protein synthesis by Beggiatoa alba B18LD in the presence and absence of sulfide

    Article • Archives of Microbiology, March 1986, Springer Science + Business Media

    Professor Thomas M Schmidt

  83. Overview of the Gastrointestinal Microbiota

    Article • Springer Science + Business Media

    Professor Thomas M Schmidt