Group Director

Todd Taylor, Ph.D.

Our main area of research is the analysis of and development of tools for metagenomic sequence data derived from various human health- and environmental-related microbial communities. We are developing a robust system, called iMetaSys, for high-throughput analysis and storage of metagenomic sequence data. We will use this system to establish a knowledgebase for comprehensive comparative analysis and annotation of all metagenomic data which is deposited in the public databases. Some other metagenomic-related projects include: a tool (MetaBioME) for identifying potential new enzymes of industrial importance from metagenomic datasets; a program which attempts to assign functional information to the mass of unannotated genes from both metagenomic and non-metagenomic datasets; and protocols for phylogenetic binning and assembly of metagenomic sequence data. We are also involved in the assembly, analysis, and annotation of several individual bacterial, protist, and other genomes. The ultimate goal of our research will be to model and predict the behavior and interactions of whole environments of organisms.

Research Topics

• Metagenomic analysis of human gut and other environments
  
• Development of high-throughput open-source tools and databases
  
• Analysis of bacterial and other genome sequences

Publication

• Sharma VK, Kumar N, Prakash T, Taylor TD.
  "Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin."
  PLoS ONE 7(3):e34030. (April 4, 2012) PMID 22496776
• Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J.
  "Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping."
  Open Biology pending:doi:10.1098/rsob.120043. (April, 2012)
• Toh H, Sharma VK, Oshima K, Kondo S, Hattori M, Ward FB, Free A, Taylor TD.
  "Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell."
  J Bacteriol 193(22):6411-6412. (November, 2011) PMID 22038970
• Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M.
  "Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation."
  Cell Host & Microbe 10(3):273-284. (September 15, 2011) PMID 21925114
• Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Mégraud F, Ahmed N.
  "Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient."
  J Bacteriol 193(13):3385-3386. (July, 2011) PMID 21515762
• Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., Tobe T., Clarke J.M., Topping D.L., Suzuki T., Taylor T.D., Itoh K., Kikuchi J., Morita H., Hattori M., Ohno H.:
  "Bifidobacteria can protect from enteropathogenic infection through production of acetate."
  Nature 469 (7331), 543-547 (2011).
  
• Prakash T., Sharma V.K., Adati N., Ozawa R., Kumar N., Nishida Y., Fujikake T., Takeda T., Taylor T.D.:
  "Expression of conjoined genes: another mechanism for gene regulation in eukaryotes."
  PLoS ONE 5 (10), 1-9 e13284 (2010).
  
• Devi S.H., Taylor T.D., Avasthi T.S., Kondo S., Suzuki Y., Megraud F., Ahmed N.:
  "The genome of Helicobacter pylori strain 908."
  J. Bacteriol. 192 (24), 6488-6489 (2010).
  
• Toh H., Oshima K., Toyoda A., Ogura Y., Ooka T., Sasamoto H., Park S.H., Iyoda S., Kurokawa K., Morita H., Itoh K., Taylor T.D., Hayashi T., Hattori M.:
  "Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2."
  J. Bacteriol. 192 (4), 1165-1166 (2010).
  
• Sharma V.K., Kumar N., Prakash T., Taylor T.D.:
  "MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets."
  Nucleic Acids Research 38 (Database), D468-D472 (2009).