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About Microbe Research LLC and this website

Microbe Research LLC is an independent research laboratory located near Ann Arbor, Michigan and the University of Michigan. The goal of the lab is to investigate questions of a basic nature in the field of microbiology and publish the findings. Most projects will involve bacteria that have a history of use in industrial fermentations. Some of these have not been well studied outside of their industrial context, leaving certain questions of general interest open for investigation. A secondary goal is to make this website interesting and useful by publishing items of historical interest or technical utility.

The lab is equipped for most operations involving basic microbiological techniques with non-hazardous microorganisms. Microbe Research has the facilities and the know-how to isolate and cultivate obligately anaerobic bacteria and their bacteriophages.

My name is Steve Stoddard.

Please direct inquires to info@microberesearch.com

Formal Training and Experience

Image: Steve Stoddard Microbe Research LLCMy first full-time research training was in the field of platelet physiology, conducting experiments under the direction of Dr. Jonathan Gerrard in the Department of Pediatric Oncology, University of Minnesota. After this I earned a bachelors degree in Microbiology from the same institution. My doctorate was earned at the University of Wisconsin-Madison, where I studied bacteriophage Mu with Dr. Martha Howe. I pursued postdoctoral studies at the University of Illinois at Urbana-Champaign, studying the pyruvate carboxylase enzyme of a thermophilic methanogen with Dr. Ralph Wolfe. In industry I held a string of positions focusing on the manufacture of amino acids, vitamins and biofuels by fermentation, technical management, and bioinformatics for the Archer Daniels Midland Company. Following that I joined a venture-funded biotech startup, Tetravitae Bioscience, where the goal was to re-commercialize the butanol-acetone fermentation. I retired from the University of Michigan at Ann Arbor, where I studied bacteriophages of Clostridium beijerinckii, developed database-driven bioinformatics resources, and studied a symbiotic human gut anaerobe working with Dr. Thomas M. Schmidt.

In 1986 I attended the MBL Microbial Diversity summer course at the Marine Biological Laboratory in Woods Hole, directed by Drs. Ralph Wolfe and E. Peter Greenberg. In 1999 I attended "Perl Programing for Bioinformatics" (now called Programming for Biology) at Cold Spring Harbor Laboratory, directed by Drs. Lincoln Stein and Steve Rozen. Later I attended courses in SQL and relational data modeling, and Oracle SQL taught by Blue Star Training (San Diego) and Oracle.

Publications

  • Roller, B.R., Stoddard, S.F. and T.M. Schmidt (2016). Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat. Microbiol. 1:16160.
  • Stoddard, S.F., Smith, B.J., Hein, R., Roller, B.R.K. and T.M. Schmidt (2015). rrnDB: Improved tools for interpreting rRNA gene abundance in Bacteria and Archaea and a new foundation for future development. Nucleic Acids Res. 43 (Database issue):D593-8.
  • Copeland, A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S., Sims,D., Brettin,T., Bruce,D., Tapia,R., Brainard,J., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Bennet,G., Cann,I., Chen,J.-S., Contreras,A.L., Jones,D., Kashket,E., Mitchell,W., Stoddard,S., Schwarz,W., Qureshi,N., Young,M., Shi,Z., Ezeji,T., White,B., Blaschek,H. and Richardson,P (2007). Clostridium beijerinckii NCIMB 8052, complete genome. GenBank Locus CP000721.
  • Urbance, J.W., Bratina, B.J., Stoddard, S.F. 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. Int. J. Syst. Evol. Microbiol. 51:1059-70.
  • Mukhopadhyay, B., S.F. Stoddard, and R.S. Wolfe (1998). Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain deltaH. J. Biol. Chem. 273:5155-5166.
  • Stoddard, S.F., and M.M. Howe (1990). Characterization of the C gene operon of bacteriophage Mu. J. Bacteriol. 172:361-371.
  • Stoddard, S.F., (1989). Localization of bacteriophage Mu promoters and characterization of the C operon. Ph.D. Thesis. University of Wisconsin-Madison.
  • Stoddard, S.F., and M.M. Howe (1989). Localization and regulation of bacteriophage Mu promoters. J. Bacteriol. 171:3440-3448.
  • Stoddard, S.F., and M.M. Howe (1987). DNA sequence within the Mu C operon. Nucl. Acids Res. 15:7198-7198.
  • Shapiro, R.S., J.M. Gerrard, N.K.C. Ramsay, M.E. Nesbit, P.F. Coccia, S.F. Stoddard, E.F. Plow, J.G. White, and W. Krivit (1980). Selective deficiency in collagen induced platelet aggregation during L-asparaginase therapy. Am. J. Pediatr. Hematol. Oncol. 2(3):207-212.
  • Bulter, A.M., J.M. Gerrard, J. Peller, S.F. Stoddard, G.H.R. Rao, and J.G. White (1979). Vitamin E inhibits the release of calcium from a platelet membrane fraction in vitro. Prostaglandins Med. 2:203-216.
  • Gerrard, J.M., A.M. Butler, G. Graff, S.F. Stoddard, and J.G. White (1978). Prostaglandin endoperoxides promote calcium release from platelet membrane fraction. Prostaglandins Med. 1:373-385.
  • Gerrard, J.M., S.F. Stoddard, R.S. Shapiro, P.F. Coccia, N.K.C. Ramsay, M.E. Nesbit, G.H.R. Rao, W. Krivit, and J.G. White (1978). Platelet storage pool deficiency and prostaglandin synthesis in chronic granulocytic leukemia. Br. J. Haematol. 40:597-607.
  • Gerrard, J.M., D. Townsend, S.F. Stoddard, C.J. Witkop, and J.G. White (1977). The influence of prostaglandin G2 on platelet ultrastructure and platelet secretion. American J. Pathol. 86:99-116.


Issued U.S. Patents

  • 9,267,106 - Method for incorporation of recombinant DNA.
  • 9,080,187 - Methods and compositions for producing solvents.
  • 7,247,458 - Enzymatic decarboxylation of 2-keto-L-gulonic acid to produce xylose.
  • 7,053,197 - Ketogulonigenium endogenous plasmids.
  • 7,053,196 - Ketogulonigenium endogenous plasmids.
  • 7,030,233 - Ketogulonigenium endogenous plasmids.
  • 6,562,584 - Bacterial strains for the production of 2-keto-L-gulonic acid.
  • 6,541,239 - Bacterial strains and use thereof in fermentation processes for 2-keto-L-gulonic acid production.
  • 6,511,820 - Bacterial strains for the production of Pyrroloquinoline Quinone.
  • 6,506,583 - Bacterial strains for the production of 2-keto-L-gulonic acid.
    (claims disclose production of non-toxic bacterial LPS by Ketogulonicigenium)
  • 6,503,748 - Endogenous Ketogulonigenium plasmid.
  • 6,316,231 - Bacterial strains for the production of 2-keto-L-gulonic acid.
  • 5,834,231 - Bacterial strains and use thereof in fermentation process for 2-keto-L-gulonic acid production.

Website Logo Image

The image in the upper right corner of these web pages is a transmission electron micrograph of bacteriophage TMS-P25 particles after negative staining with 1% uranyl acetate. The phage was isolated in the lab of Thomas M. Schmidt (University of Michigan) and propagated in agar overlays seeded with Clostridium beijerinckii strain NCIMB 8052 as the host. The capsid diameter is about 60 nanometers. The image is displayed with Dr. Schmidt's permission.

Other

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