Refereed Publications, 2014

·       Lee, Z.M. and T.M. Schmidt (2014) Bacterial growth efficiencyvaries in soils under different land management practices. Soil Biology and Biochemistry. 69:282–290.


·       Blasiak, L.C.,  A.W. Schmidt, H. Andriamiarinoro, T. Mulaw, R. Rasolomampianina, W.L. Applequist, C. Birkinshaw, F. Rejo-Fienena, P.P. Lowry II, T.M. Schmidt, R.T. Hill (2014) Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity. PlosOne. In Press


·       Robertson, G. P., K. Gross, S. Hamilton, D. Landis, T.M. Schmidt, S. Snapp and S. Swinton (2014) Farming for Ecosystem Services: An Ecological Approach toProduction Agriculture. BioScience. In Press


·       Werling, B.P., T.L. Dickson, R. Isaacs, H. Gaines, C. Gratton, K.L. Gross, H. Liere, C.M. Malmstrom, T.D. Meehan, L. Ruan, B.A. Robertson, G.P. Robertson, T.M. Schmidt, A.C. Schrotenboer, T.K. Teal, J.K. Wilson, D.A. Landis (2014) Perennial grasslands increase multiple ecosystem services inbioenergy landscapes. PNAS In Press.


Refereed Publications, 2013

·       Theis, K.R., A. Venkataraman, J.A. Dycus, K.D. Koonter, E.N. Schmitt-Matzen, A.P. Wagner, K.E. Holekamp and T.M. Schmidt (2013) Symbiotic bacteria appear to mediate hyena social odors. PNAS 110:19832-19837.


·       Isapong, J., W. Sealy Hambright, A.G. Willis, A. Boonmee, S.J. Callister, K.E. Burnum, L. Paša-Tolić, C.D. Nicora, J.T. Wertz, T.M. Schmidt, J.L.M. Rodrigues (2013) Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a member of the termite hindgut VerrucomicrobiaThe ISME Journal, doi: 10.1038/ismej.2013.74.


·       Morris, RL and T.M. Schmidt. Shallow Breathing:  Bacterial Life at Low O2. (2013) Nature Microbiology Reviews. 11: 205 – 212.


·       Young, V.B., L.H. Raffals, S.W. Huse, M. Vital, D. Dai, P.D. Schloss, J.M. Brulc, D.A. Antonopoulos, R.L. Arrieta, J.H. Kwon, K.G. Reddy, N. Hubert, S.L. Grimm, J.H. Vineis, S. Dalal, H.G. Morrison, A.M. Eren, F. Meyer, T.M. Schmidt,  J.M. Tiedje, E.B. Chang and M.L. Sogin (2013) Multiphasic Analysis of the Temporal Development of the Distal Gut Microbiota in Patients Following Ileal Pouch Anal Anastomosis. Microbiome. Microbiome. 2013, 1:9 doi:10.1186/2049-2618-1-9


·       Vital, M. C.R. Penton, Q. Wang, V.B. Young, D.A. Antonopoulos, M.L. Sogin, H.G. Morrison, L.H. Raffals, E.B. Chang, G.B. Huffnagle, T.M. Schmidt, J.R. Cole, J.M. Tiedje (2013) A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome1:8


·       Morris, A., J.M. Beck, P. Schloss, T.B. Campbell, K. Crothers, J.L. Curtis, S.C. Flores, A.P. Fontenot, E. Ghedin, L. Huang, K. Jablonski, E. Kleerup, S.V. Lynch, E. Sodergren, H. Twigg, V.B. Young, A. Venkataraman, T.M. Schmidt and G. Weinstock (2013) Comparison of the respiratory microbiome in healthy non-smokers and smokersAm. J. Respir. Crit. Care Med. 187(10):1067-75.


·       Xue, K., L. Wu, Y. Deng, Z. He, J. Van Nostrand, R.P. Robertson, T.M. Schmidt and J. Zhou (2013) Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Applied and Environmental Microbiology 79:1284-92.

Refereed Publications, 1985-2012

·       Shade, A., H. Peter, S.D. Allison, D. Baho, M. Berga, H. Bürgmann, D.H. Huber, S. Langenheder, J.T. Lennon, J.B.H. Martiny, K. Matulich, T.M. Schmidt and J. Handelsman (2012)  Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology. 3:417 doi: 10.3389/fmicb.2012.0041


·       Wertz, J.T., E. Kim, J.A. Breznak, T.M. Schmidt and J.L.M. Rodrigues (2012) Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colotermitum gen. nov., sp. nov. Reveals Microaerophily and Nitrogen Fixation Genes.  Applied and Environ. Microbiol. 78:1544-1555.


·       Evidence for a bacterial mechanism for group-specific social odors among hyenas (2012) Theis, K.R. T.M. Schmidt and K.E. Holekamp. Nature Scientific Reports 2:615. doi: 10.1038/srep00615


·       The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.


·       The Human Microbiome Project Consortium (2012) A framework for human microbiome research. Nature 486: 215-221.


·       Jangid, K., Williams, M.A., Franzluebbers, A.J., Schmidt, T.M., Coleman, D.C., Whitman, W.B. (2011) Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties. Soil Biology & Biochemistry. 43:2184-2193.


·       Young V.B., Kahn S.A., Schmidt T.M. and Chang E.B. (2011) Studying the enteric microbiome in inflammatory bowel diseases: getting through the growing pains and moving forward. Frontiers Microbiology 2:144. doi:10.3389/fmicb.2011.00144


·       Levine, U.Y., T.K. Teal, G.P. Robertson and T.M. Schmidt (2011) Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. The ISME Journal. 5:1683–1691.


·       Eichorst, S.A., C.R. Kuske and T.M. Schmidt (2011) Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria.  Applied and Environmental Microbiology. 77:586-596.


·       Gomez-AlvarezV., T.K. Teal and T.M. Schmidt (2009) Systematic artifacts in metagenomes from complex microbial communities.  The ISME Journal  3: 1314–1317.


·       Antonopoulos, D.A., S.M. Huse, H.G. Morrison, T.M. Schmidt, M.L. Sogin and V.B. Young (2009) Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.  Infect. Immun. 77:2367-2375.


·       Lee, Z. M-P., C. Bussema III and T.M. Schmidt (2009) rrnDB: Documenting the number of rRNA and tRNA genes in Bacteria and Archaea. Nucleic Acids Research. 37: D489–D493.


·       Rodrigues, J.L.M., M.A. Duffy, A.J. Tessier, D. Ebert, and T.M. Schmidt (2008) Phylogenetic characterization of Spirobacillus cienkowskii: a red-pigmented, spiral-shaped bacterial pathogen of freshwater populations of Daphnia. Applied and Environmental Microbiology 74: 1575-1582.


·       Jackson, J.H., T.M. Schmidt, and P.A. Herring (2008) A systems approach to model natural variation in reactive properties of bacterial ribosomes. BMC Systems Biology 2008, 2:62.


·       Chang, JY, D.A. Antonopoulos, A. Kalra, A. Tonelli, W.T. Khalife, T.M. Schmidt and V.B. Young (2008) Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. Journal of Infectious Diseases 197:435-438.


·       San I.G., W. Sheldon, T. M. Schmidt,…Michener, W.K. (2008) Defining linkages between the GSC and NSF’s LTER program:How the ecological metadata language (EML) relates to GCDML and other outcomes.  OMICS 12: 151-156.


·       Hang, D., E. Torng, C. Ofria and T.M. Schmidt (2007) The effect of natural selection on the performance of maximum parsimony. BMC Evolutionary Biology 7:94.


·       Eichorst, S.A. J. A. Breznak, T. M. Schmidt (2007) Taxonomy and ecology of newly isolated soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria.  Applied and Environmental Microbiology 70(8): 4748-4755.


·       Dethlefsen, L. and T.M. Schmidt (2007) Performance of the translational apparatus varies with the ecological strategies of bacteria.  Journal of Bacteriology 189:3237-3245.


·       Schmidt, T.M. (2006) The maturing of microbial ecology.  International Microbiology 9:217-223.


·       Dethlefsen, L. and T.M. Schmidt (2005) Differences in codon bias cannot explain differences in translational power among microbes.  BMC Bioinformatics 6:3 pp 1-20.


·       Kuehl, C.J. H.D. Wood, T.L. Marsh, T.M. Schmidt and V.B. Young (2005) Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota. Infection and Immunity 73:6952–6961.


·       Lepp, P.W. and T.M. Schmidt (2004) Changes in Synechococcus population size and cellular ribosomal RNA content in response to predation and nutrient limitation. Microbial Ecology 48:1-9.

·       Stevenson, B.S, and T. M. Schmidt (2004) Life history implications of ribosomal RNA gene copy number in Escherichia coli. Applied and Environmental Microbiology 70:6670-6677.


·       Stevenson, B.S, S.A. Eichorst, J.T. Wertz, T. M. Schmidt and J.A. Breznak (2004) New strategies for cultivation and detection of previously uncultured microbes. Applied and Environmental Microbiology 70:4748-4755.


·       Young,V.B. and T. M. Schmidt (2004) Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. Journal of Clinical Microbiology 42:1203–1206.


·       Hang, D. C. Ofria, T.M. Schmidt and E. Torng (2003) The effect of natural selection on phylogeny reconstruction algorithms. Lecture Notes in Computer Science 2723:13–24.


        ·       Keough, B.P., T.M. Schmidt and R.E. Hicks (2003)  Archaeal        nucleic acids in picoplankton from Great Lakes of the World. Microbial Ecology 46:238-248.


·       Buckley, D.H. and T.M. Schmidt (2003) Diversity and dynamics of microbial communities in soils from agroecosystems. Environmental Microbiology 5:441-452.


      ·       Hashimoto, J.G., B. S. Stevenson and T.M. Schmidt (2003) Rates and consequences of recombination between ribosomal RNA operons. Journal of Bacteriology 185:966-972.


·       Do, Y.S., T.M. Schmidt, J.A Zahn, E.S. Boyd and A.A. Dispirito (2003) Role of Rhodobacter sp. PS9, a purple non-sulfur photosynthetic bacterium isolated from an anaerobic swine waste lagoon, in odor remediation . Applied and Environmental Microbiology 69:1710-1720.


·       Cole, J.R., B. Chai, T.L. Marsh, R.J. Farris, Q. Wang, S.A. Kulam, S. Chandra, D.M. McGarrell, T.M. Schmidt, G.M. Garrity, J.M. Tiedje (2003) The Ribosomal Database Project (RDP-II):  Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31:442-443.


·       Buckley, D.H. and T.M. Schmidt (2001) The structure of microbial communities in soil and the lasting impacts of cultivation. Microbial Ecology. 42:11-21.


·       Kappenbach, J.A., P.R. Saxman, J.R. Cole and T.M. Schmidt (2001) rrndb: The ribosomal RNA operon copy number database. Nucleic Acids Research 29:181-184.


·       Buckley, D.H. and T.M. Schmidt (2001) Environmental factors influencing the distribution of Verrucomicrobia in soil. FEMS Microbiology Ecology 35:105-112.


·       Urbance, J.W., B. J. Bratina, S. F. Stoddard and T. M. Schmidt (2001) Taxonomic characterization of Ketogulonigenium vulgare gen. nov. , sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid. International Journal of Systematic and Evolutionary Microbiology 51:1059-1070.


·       Maidak, B.L., J.R. Cole, T.G. Lilburn, C.T. Parker, P.R. Saxman, R.J. Farris, G.M. Garrity, G.J. Olsen, T.M. Schmidt, and J.M. Tiedje (2001) The RDP (Ribosomal Database Project) moves forward.  Nucleic Acids Research 29:173-174.


·       Klappenbach, J., J.M. Dunbar and T.M. Schmidt (2000) rRNA gene copy number predicts ecological strategies in bacteria. Applied and Environmental Microbiology 66:1328-1333.


·       Maidak, B.L., J.R. Cole, T.G. Lilburn, C.T. Parker, P.R. Saxman, J.M. Stredwick, G.M. Garrity, B. Li, G.J. Olsen, S. Pramanik, T.M. Schmidt, and J.M. Tiedje (2000) The RDP (Ribosomal Database Project) continues. Nucleic Acids Research 28:173-174.


·       Leadbetter, J.R., T.M. Schmidt, J.R. Graber and J. A. Breznak (1999) Acetogenesis from H2 plus CO2 by spirochetes from termite guts.  Science 283:686-689.


·       Lilburn, T.G., T.M. Schmidt and J.A. Breznak. (1999) Phylogenetic characterization of termite gut spirochetes. Environmental Microbiology 1:331-346.


·    Maidak, B.L., J.R. Cole, C.T. Parker, G.M. Garrity, N. Larsen, B. Li, T.G. Lilburn, M.J. McCaughery, G.J. Olsen, R. Overbeek, S. Pramanik, T.M. Schmidt, J.M. Tiedje, C.R. Woese (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Research 27:171-173.


·       Lopez, F.A., J. Manglicmot, T.M. Schmidt, C. Yeh, H.V. Smith, D.A. Relman (1999) Molecular characterization of Cyclospora-like organisms from baboons. Journal of Infectious Diseases    179:670-676.


·       Velicer, G., T.M. Schmidt and R.E. Lenski (1999) Application of traditional and phylogenetic comparative methods to test for a tradeoff in bacterial growth rates at low versus high substrate concentration.  Microbial Ecology 73:35-47.


·       Stevenson, B. and T.M. Schmidt (1998) Growth rate dependent accumulation of RNA from plasmid-borne ribosomal RNA operons. Journal of Bacteriology 180:1970-1972.


·       Lepp, P.W. and T.M. Schmidt (1998) Nucleic acid content of Synechococcus spp. during growth in continuous light and light:dark cycles. Archives of Microbiology 170:201-207.


·       Lenski, R.E., J.A. Mongold, P.D. Sniegowski, M. Travisano, F. Vasi, P.J. Gerrish, and T.M. Schmidt (1998) Evolution of competitive fitness in experimental populations of E. coli: What makes one genotype a better competitor than another?  Antonie van Leeuwenhoek 73:35-47.


·       Buckley, D.H., J.R. Graber and T.M. Schmidt (1998) Phylogenetic analysis of nonthermophilic Crenarchaeota and their diversity and abundance in soils. Applied and Environmental Microbiology 64: 3781-3787.


·       Button, D.K., B.R. Robertson, L. Pinto, P.W. Lepp and T.M. Schmidt (1998)  A high affinity, small, dilute, extinction-culture isolate having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Applied and Environmental Microbiology 64:4467-4476.


·       Bratina, B.J., B. Stevenson, W. J. Green and T.M. Schmidt (1998) Manganese reduction by microbes  from oxic regions of the Lake Vanda (Antarctica) water column. Applied and Environmental Microbiology 64: 3791-3797.


·       Bratina, B.J., M. Viebahn, and T.M. Schmidt. (1997) Achieving specificity in nucleic acid hybridizations using nuclease S1. Methods in Molecular and Cellular Biology 6:107-115.


·       Larsen, N., R. Overbeek, S. Pramanik, T.M. Schmidt, E.E. Selkov, O. Strunk, J.M. Tiedje, and J.W. Urbance  (1997) Towards microbial data integration.  Journal of Industrial Microbiology and Biotechnology 18:68-72.


·       Hogan, D.A., D.H. Buckley, C. Nakatsu, T.M. Schmidt and R.P. Hausinger (1997) Distribution of tfdA in soil isolates that do not degrade 2,4-dichlorophenoxyacetic acid (2,4-D). Microbial Ecology 34:90-96.


·       Yanni, Y.G., R.Y. Rizk, V. Corich, A. Squartini, K. Ninke, S. Philip-Hollingsworth, G. Orgambide, F.J. de Bruijn, J.Soltzfus, D. Buckley, T.M. Schmidt, P.F. Mateos, J.K. Ladha, and F.B. Dazzo (1997)  Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth.  Plant and Soil 194:99-114.


·       Lonergan, D.J., H.L. Jenter, J.D. Coates, E.J.P. Phillips, T.M. Schmidt and D.R. Lovely (1996) Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria.  Journal of Bacteriology        178:2402-2408.


·       Relman, D.A., T.M. Schmidt, A. Gajadhar, M. Sogin, J. Cross, K. Yoder, O. Sethabutr and P. Echeverria (1996)  Molecular phylogenetic analysis of the human intestinal pathogen, Cyclospora, suggests that it is closely related to Eimeria.  Journal of Infectious Diseases 173:440-445.


·       Schmidt, T.M. (1994) Fingerprinting bacterial genomes using ribosomal RNA genes and operons. Methods in Molecular and Cellular Biology 5:3-12.


·       Schmidt, T.M. and D.A. Relman (1994) Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences.  Methods in Enzymology 235: 205-222.


·       Garrad, R., T.M. Schmidt and J.K. Bhattacharjee (1994) Molecular and functional analysis of the LYS1 gene of Candida albicans. Infection and Immunity 62:5027-5031.


·       Stevenson, B.S., A.A. DiSpirito and T.M. Schmidt (1994) Reduction of enzyme adsorption to polypropylene surfaces in the presence of a nonionic detergent. Biotechniques 17:1048-1050.


·       Govindaswami, M., T.M. Schmidt, D.C. White and J.C. Loper (1993) Population analysis of a bacterial aerobic degrader of azo dyes.  Journal of Bacteriology 175:6062-6066.


·       Relman, D.A., P.W. Lepp, K.N. Sadler and T.M. Schmidt (1992) Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis and other alpha-proteobacteria.  Molecular Microbiology 6:1801-1807.


·       Relman, D.A., T.M. Schmidt, R.P. MacDermott and S. Falkow (1992) Identification of the uncultured bacillus of Whipple’s disease.  New England Journal of Medicine 327:293-301.


·       Schmidt, T.M., E.F. Delong and N.R. Pace (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.  Journal of Bacteriology 173:4371-4378.


·       Schmidt, T.M., B. Pace and N.R. Pace (1991) Contamination in Taq polymerase. Biotechniques        11:176-178.


·       Eden, P.E., T.M. Schmidt, R.P. Blakemore and N.R. Pace (1991) Phylogenetic analysis of Aquaspirillum magnetotacticum using PCR-amplified 16S ribosomal RNA-specific DNA.  International Journal of Systematic Bacteriology 41:324-325.


·       Koch, A.L. and T.M. Schmidt (1991) The first cellular bioenergetic process:Primitive generation of a protonmotive force. Journal of Molecular Evolution 33:297-304.


·       Relman, D.A., J.S. Loutit, T.M. Schmidt, S. Falkow and L.S. Tompkins (1990) An approach to the identification of uncultured pathogens: the causative agent of bacillary angiomatosis. New England Journal of Medicine 323:1573-1580.


·       Schmidt, T.M. and A.A. Dispirito (1990) Spectral characterization of c-type cytochromes purified from Beggiatoa alba. Archives of Microbiology 154:453-458.


·       Giovannoni, S.J., E.F. DeLong, T.M. Schmidt and N.R. Pace (1990)  Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Applied and Environmental Microbiology 56:2572-2575.


·       Schmidt, T.M., K. Kopecky and K.H. Nealson (1989) Bioluminescence of the insect pathogen Xenorhabdus luminescens. Applied and Environmental Microbiology 55:2607-2612.


·       Schmidt, T.M., B. Bleakley and K.H. Nealson (1988) Characterization of an extracellular protease from the insect pathogen Xenorhabdus luminescens. Applied and Environmental Microbiol. 54:2793-2797.


·       Richardson, W.H., T.M. Schmidt and K.H. Nealson (1988) Identification of an anthraquinone pigment and a hydroxystilbene antibiotic from Xenorhabdus luminescens. Applied and Environmental Microbiology 54:1602-1605.


·       Schmidt, T.M., B. Arieli, Y. Cohen, E. Padan and W.R. Strohl (1987) Sulfur metabolism in Beggiatoa alba. Journal of Bacteriology 169:5466-5472.


·       Stahl, D.A., D.J. Lane, G.J. Olsen, D.J. Heller, T.M. Schmidt and N.R. Pace (1987) Phylogenetic analysis of certain sulfide-oxidizing and related morphologically conspicuous bacteria by 5S ribosomal ribonucleic acid sequences. International Journal of Systematic Bacteriology 37:116-122.


·       Schmidt, T.M., V.A. Vinci and W.R. Strohl (1986) Protein synthesis by Beggiatoa alba B18LD in the presence and absence of sulfide. Archives of Microbiology 144:158-162.


·       Strohl, W.R., T.M. Schmidt, V.A. Vinci and J.M. Larkin (1986) Electron transport and respiration in Beggiatoa  and Vitreoscilla. Archives of Microbiology 145:71-75.


·       Strohl, W.R., T.M. Schmidt, H.N. Lawry, M.J. Mezzino and J.M. Larkin (1986) Characterization of Vitreoscilla beggiatoides and V. filiformis sp. nov., nom. rev., and a comparison to V. stercoraria and Beggiatoa. International Journal of Systematic Bacteriology 36:302-313.


·       Guerrero, R., C. Pedros-Alio, T.M. Schmidt and J. Mas. (1985) A survey of buoyant densities of microorganisms in pure cultures and natural samples.  Microbiologica 1:53-65. 

Book Chapters, Reviews and Commentaries

·       Schmidt, T.M. and C. Waldron (2013) Microbial Diversity in Soils of Agricultural Landscapes and its Relation to Ecosystem Functions.  In: The Ecology of Agricultural Ecosystems: Research on the Path to Sustainability. S.K. Hamilton, G.P. Robertson and J.E. Doll, eds. Oxford University Press, Inc.

Accepted for publication.


·       Bassis, C., T.M. Schmidt and V.B. Young (2013) Methods for characterizing microbial communities associated with the human body.  In: The Human Microbiota: How Microbial Communities Affect Health and Disease. Fredricks, D.N. ed.  John Wiley and Sons Ltd.


·     Schmidt, T.M. (2012) Bacteria Battling for Survival.  In "Microbes and Evolution: The World That Darwin Never Saw". S. Maloy R. Kolter and eds. ASM Press, Washington, D.C.


·       T.K. Teal and T.M. Schmidt (2010) Identifying and removing artificial replicates from 454 pyrosequencing data. Cold Spring Harb. Protoc.; 2010; doi:10.1101/pdb.prot5409


·       Young, V.B., R.A. Britton and T.M. Schmidt (2009) The Human Microbiome and Infectious Diseases: Beyond Koch. Interdisciplinary Perspectives on Infectious Diseases doi:10.1155/2008/296873


·       Schmidt, T.M. and A.E. Konopka (2009) Physiological and ecological adaptations of slow-growing, heterotrophic microbes and consequences for cultivation. Uncultivated Microorganisms, S. Epstein (Editor). Series: Microbiology Monographs. Springer Publishing Co.


·       Antonopoulos, D. and T.M. Schmidt (2008) Sequence-Based Characterization of Microbes and Microbial Communities. Prospects and Applications for Plant-Associated Microbes. A Laboratory Manual, Part A: Bacteria. S. Sorvari and A.M. Pirttila, eds. BioBien Innovations, Finland.


·       Young, V.B. and T.M. Schmidt (2008) Overview of the gastrointestinal microbiota. In GI Microbiota and Regulation of the Immune System. G. Huffnagle and M. Noverr eds., Landes Bioscience. Springer.


·       Schmidt, T.M. (2007) Life in the really hard places. Science 318:1727


·       Buckley, D.H. and T.M. Schmidt (2007) Measurement of ribosomal RNA abundance by hybridization with oligodeoxynucleotide probes.  In Methods in General and Molecular Microbiology, 3rd Edition.  A. Reddy, T.J. Beveridge, J.A. Breznak, G.A. Marzluf, T.M. Schmidt and L.R. Snyder eds. ASM Press.


·       Schmidt, T.M.  Bacteria and Archaea (2002) In Encyclopedia of Evolution. M. Pagel, Ed. Oxford University Press, New York, NY.


·       Buckley, D.H. and T.M. Schmidt (2002) Exploring the biodiversity of soil - a microbial rainforest.  In Biodiversity of Microbial Life.  J.T. Staley and A.-L Reysenbach, eds. Wiley-Liss, Inc.


·       Bratina, B.J., W. J.  Green and T.M. Schmidt (1998) Microbially mediated transformations of manganese in Lake Vanda.   Antarctic Journal of the U.S. - 1996 Mini-Review. 31: 213-214.


·       Schmidt, T.M. (1997) Multiplicity of Ribosomal RNA Operons in Prokaryotes. In Bacterial Genomes: Physical Structure and Analysis. F.J. DeBruijn, J.R. Lupiski, and G. Weinstock (eds) Chapman and Hall. pp. 221-229.


·       Tiedje, J., J. Urbance, N. Larsen, T. Schmidt, O. Strunk, S. Pramanik, R. Ovebeek, R. Martin and J. Holt (1996) Towards an Integrated Microbial Database.  In Culture Collections to Improve the Quality of Life. R. A. Samson,  J.A. Stalpers, D. van der Mei, and A. H. Stouthamer (eds) CBS Publishing, Baarn,  Netherlands. pp. 63-68.


·       Lepp, P.W. and T.M. Schmidt (1996) Assessing the influence of predation and resource limitation on microbial populations.  In Biotechnology Risk Assessment: Proceedings of the Biotechnology Risk Assessment Symposium. University of Maryland Press. pp. 317-327.


·       Bratina, B.J., W.J. Green and T.M. Schmidt (1995) Microbial interactions with manganese cycling in Lake Vanda.  Antarctic Journal of the U.S. 30:312-313


·       Pace, N.R., E.A. Angert, E.F. DeLong, T.M. Schmidt and G.S. Wickham (1993) New perspective on the natural microbial world.  In Industrial Microorganisms: Basic and Applied Molecular Genetics.  R.H. Baltz, G.D. Hegeman and P.L. Skatrud (eds) Am. Society for Microbiology Press, Washington, DC


·       Nealson, K.H., J. Baross, M. Carr, R. Pepin, T. M. Schmidt, J. Shann, J.R. Vestal, D.C. White and R. Young (1992) Biological Contamination of Mars: Issues and Recommendation.  National Academy Press, Washington, DC.


·       Schmidt, T.M., E.F. DeLong and N.R. Pace (1991) Phylogenetic identification of uncultivated microorganisms in natural habitats. In Rapid Methods and Automation in Microbiology and Immunology. A. Vaheri, R.C. Tilton and A. Balows (eds)  Springer-Verlag, Berlin. pp. 37-46.


·       Nealson, K.H., T.M Schmidt and B. Bleakley (1990) Biochemistry and physiology of Xenorhabdus. In Entomopathogenic nematodes in Biological Control. R. Gaugler and H.K. Kaya (eds) CRC Press.  Boca Raton, FL. pp 271-282.


·       DeLong, E.F., T.M. Schmidt and N.R. Pace (1989) Analysis of single cells and oligotrophic picoplankton populations using 16S ribosomal RNA sequences. In Proceedings of the 5th International Symposium on Microbial Ecology. pp. 697-701.


·       Nealson, K.H., T.M. Schmidt and B. Bleakley (1988) Luminescent bacteria: symbionts of nematodes and pathogens of insects.  In Cell to Cell Signals in Plant, Animal and Microbial Symbioses. S. Scannerini and D. White (eds) Springer-Verlag, Berlin. pp. 101-114.


·       Strohl, W.R. and T.M. Schmidt (1984) Mixotrophy of the colorless, sulfide-oxidizing gliding bacteria Beggiatoa  and Thiothrix. In Microbial Chemoautotrophy, W.R. Strohl and O.H. Tuovinen (eds) The Ohio State University Press; Columbus, OH. pp. 79-95.

Books and Patents

·       Topics in Ecological and Environmental Microbiology (2012) T.M. Schmidt and M. Schaechter, eds. Academic Press, Elsevier. ISBN: 9780-0-12-383878-0


·       Encyclopedia of Microbiology (2009) Environmental Microbiology and Ecology, T.M. Schmidt, section editor. M. Schaechter, Editor-in-Chief. Elsevier Inc.


·       Methods for General and Molecular Microbiology, 3rd Edition (2007) C.A. Reddy, T.J. Beveridge, J.A. Breznak, G.A. Marzluf, T.M. Schmidt and L.R. Snyder, Editors.  ASM Press.

 ·       Schmidt, T.M. and S.F. Stoddard (2002). Endogenous ketogulonigenium plasmid.  United States Patent 6,503,748 B2