70
A. Meyerdierks and F.O. Glöckner
Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured
marine bacteria, one cell at a time. Proc Natl Acad Sci U S A 104:9052–9057
Stoffels M, Ludwig W, Schleifer KH (1999) rRNA probe-based cell fishing of bacteria. Environ
Microbiol 1:259–271
Stothard P, Wishart DS (2006) Automated bacterial genome analysis and annotation. Curr Opin
Microbiol 9:505–510
Strous M, Pelletier E, Mangenot S et al (2006) Deciphering the evolution and metabolism of an
anammox bacterium from a community genome. Nature 440:790–794
Tao Q, Zhang HB (1998) Cloning and stable maintenance of DNA fragments over 300 kb in
Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res 26:4901–4909
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science
278:631–637
Teeling H, Meyerdierks A, Bauer M et al (2004) Application of tetranucleotide frequencies for the
assignment of genomic fragments. Environ Microbiol 6:938–947
Telenius H, Carter NP, Bebb CE et al (1992) Degenerate oligonucleotide-primed PCR – General
amplification of target DNA by a single degenerate primer. Genomics 13:718–725
Thornhill DJ, Wiley AA, Campbell AL et al (2008) Endosymbionts of Siboglinum fiordicum and
the phylogeny of bacterial endosymbionts in Siboglinidae (Annelida). Biol Bull 214:135–144
Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ
Microbiol 56:782–787
Treusch AH, Kletzin A, Raddatz G et al (2004) Characterization of large-insert DNA libraries from
soil for environmental genomic studies of Archaea. Environ Microbiol 6:970–980
Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev
Genet 6:805–814
Tringe SG, von Mering C, Kobayashi A et al (2005) Comparative metagenomics of microbial
communities. Science 308:554–557
Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with
increased capacity for energy harvest. Nature 444:1027–1031
Tyson GW, Chapman J, Hugenholtz P et al (2004) Community structure and metabolism through
reconstruction of microbial genomes from the environment. Nature 428:37–43
Uchiyama T, Abe T, Ikemura T et al (2005) Substrate-induced gene-expression screening of
environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93
Urbach E, Vergin KL, Giovannoni SJ (1999) Immunochemical detection and isolation of DNA
from metabolically active bacteria. Appl Environ Microbiol 65:1207–1213
Vallenet D, Labarre L, Rouy Z et al (2006) MaGe: a microbial genome annotation system supported
by synteny results. Nucleic Acids Res 34:53–65
Van Domselaar GH, Stothard P, Shrivastava S et al (2005) BASys: a web server for automated
bacterial genome annotation. Nucleic Acids Res 33:W455–W459
Venter JC, Remington K, Heidelberg JF et al (2004) Environmental genome shotgun sequencing
of the Sargasso Sea. Science 304:66–74
von Mering C, Hugenholtz P, Raes J et al (2007) Quantitative phylogenetic assessment of microbial
communities in diverse environments. Science 315:1126–1130
Ward DM, Weller R, Bateson MM (1990) 16s ribosomal-RNA sequences reveal numerous
uncultured microorganisms in a natural community. Nature 345:63–65
Warnecke F, Luginbuhl P, Ivanova N et al (2007) Metagenomic and functional analysis of hindgut
microbiota of a wood-feeding higher termite. Nature 450:U560–U565
Watabe K, Leusch M, Ito J (1984) Replication of bacteriophage phi-29 DNA in vitro – the roles of
terminal protein and DNA-polymerase. Proc Natl Acad Sci USA-Biol Sci 81:5374–5378
Webster G, Newberry CJ, Fry JC et al (2003) Assessment of bacterial community structure in
the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J Microbiol
Meth 55:155–164
Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by
massively parallel DNA sequencing. Nature 452:U872–U875
A. Meyerdierks and F.O. Glöckner
Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured
marine bacteria, one cell at a time. Proc Natl Acad Sci U S A 104:9052–9057
Stoffels M, Ludwig W, Schleifer KH (1999) rRNA probe-based cell fishing of bacteria. Environ
Microbiol 1:259–271
Stothard P, Wishart DS (2006) Automated bacterial genome analysis and annotation. Curr Opin
Microbiol 9:505–510
Strous M, Pelletier E, Mangenot S et al (2006) Deciphering the evolution and metabolism of an
anammox bacterium from a community genome. Nature 440:790–794
Tao Q, Zhang HB (1998) Cloning and stable maintenance of DNA fragments over 300 kb in
Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res 26:4901–4909
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science
278:631–637
Teeling H, Meyerdierks A, Bauer M et al (2004) Application of tetranucleotide frequencies for the
assignment of genomic fragments. Environ Microbiol 6:938–947
Telenius H, Carter NP, Bebb CE et al (1992) Degenerate oligonucleotide-primed PCR – General
amplification of target DNA by a single degenerate primer. Genomics 13:718–725
Thornhill DJ, Wiley AA, Campbell AL et al (2008) Endosymbionts of Siboglinum fiordicum and
the phylogeny of bacterial endosymbionts in Siboglinidae (Annelida). Biol Bull 214:135–144
Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ
Microbiol 56:782–787
Treusch AH, Kletzin A, Raddatz G et al (2004) Characterization of large-insert DNA libraries from
soil for environmental genomic studies of Archaea. Environ Microbiol 6:970–980
Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev
Genet 6:805–814
Tringe SG, von Mering C, Kobayashi A et al (2005) Comparative metagenomics of microbial
communities. Science 308:554–557
Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with
increased capacity for energy harvest. Nature 444:1027–1031
Tyson GW, Chapman J, Hugenholtz P et al (2004) Community structure and metabolism through
reconstruction of microbial genomes from the environment. Nature 428:37–43
Uchiyama T, Abe T, Ikemura T et al (2005) Substrate-induced gene-expression screening of
environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93
Urbach E, Vergin KL, Giovannoni SJ (1999) Immunochemical detection and isolation of DNA
from metabolically active bacteria. Appl Environ Microbiol 65:1207–1213
Vallenet D, Labarre L, Rouy Z et al (2006) MaGe: a microbial genome annotation system supported
by synteny results. Nucleic Acids Res 34:53–65
Van Domselaar GH, Stothard P, Shrivastava S et al (2005) BASys: a web server for automated
bacterial genome annotation. Nucleic Acids Res 33:W455–W459
Venter JC, Remington K, Heidelberg JF et al (2004) Environmental genome shotgun sequencing
of the Sargasso Sea. Science 304:66–74
von Mering C, Hugenholtz P, Raes J et al (2007) Quantitative phylogenetic assessment of microbial
communities in diverse environments. Science 315:1126–1130
Ward DM, Weller R, Bateson MM (1990) 16s ribosomal-RNA sequences reveal numerous
uncultured microorganisms in a natural community. Nature 345:63–65
Warnecke F, Luginbuhl P, Ivanova N et al (2007) Metagenomic and functional analysis of hindgut
microbiota of a wood-feeding higher termite. Nature 450:U560–U565
Watabe K, Leusch M, Ito J (1984) Replication of bacteriophage phi-29 DNA in vitro – the roles of
terminal protein and DNA-polymerase. Proc Natl Acad Sci USA-Biol Sci 81:5374–5378
Webster G, Newberry CJ, Fry JC et al (2003) Assessment of bacterial community structure in
the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J Microbiol
Meth 55:155–164
Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by
massively parallel DNA sequencing. Nature 452:U872–U875