2 Metagenome Analysis
67
Markowitz VM, Ivanova NN, Szeto E et al (2008) IMG/M: a data management and analysis system
for metagenomes. Nucleic Acids Res 36:D534–D538
Markowitz VM, Korzeniewski F, Palaniappan K et al (2006) The integrated microbial genomes
(IMG) system. Nucleic Acids Res 34:D344–D348
Martin HG, Ivanova N, Kunin V et al (2006) Metagenomic analysis of two enhanced biological
phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24:1263–1269
Martín-Cuadrado AB, López-García P, Alba JC et al (2007) Metagenomics of the deep
Mediterranean, a warm bathypelagic habitat. PLoS One 2:e914
Mavromatis K, Ivanova N, Barry K et al (2007) Use of simulated data sets to evaluate the fidelity
of metagenomic processing methods. Nat Methods 4:495–500
McHardy AC, Goesmann A, Pühler A et al (2004) Development of joint application strategies for
two microbial gene finders. Bioinformatics 20:1622–1631
McHardy AC, Martin HG, Tsirigos A et al (2007) Accurate phylogenetic classification of variablelength DNA fragments. Nat Methods 4:63–72
McHardy AC, Rigoutsos I (2007) What’s in the mix: phylogenetic classification of metagenome
sequence samples. Curr Opin Microbiol 10:499–503
Meyer F, Goesmann A, McHardy AC et al (2003) GenDB – an open source genome annotation
system for prokaryote genomes. Nucleic Acids Res 31:2187–2195
Meyerdierks A, Kube M, Lombardot T et al (2005) Insights into the genomes of archaea mediating
the anaerobic oxidation of methane. Environ Microbiol 7:1937–1951
Monaco AP, Larin Z (1994) YACs, BACs, PACs and MACs – artificial chromosomes as research
tools. Trends Biotechnol 12:280–286
Mou XZ, Sun SL, Edwards RA et al (2008) Bacterial carbon processing by generalist species in
the coastal ocean. Nature 451:708–U711
Mulder NJ, Apweiler R, Attwood TK et al (2003) The InterPro Database, 2003 brings increased
coverage and new features. Nucleic Acids Res 31:315–318
Mussmann M, Hu FZ, Richter M et al (2007) Insights into the genome of large sulfur bacteria
revealed by analysis of single filaments. PLoS Biol 5:1923–1937
Mußmann M, Richter M, Lombardot T et al (2005) Clustered genes related to sulfate respiration in
uncultured prokaryotes support the theory of their concomitant horizontal transfer. J Bacteriol
187:7126–7137
Nelson JR, Cai YC, Giesler TL et al (2002) TempliPhi, phi 29 DNA polymerase based rolling
circle amplification of templates for DNA sequencing. Biotechniques, 44–47
Neufeld JD, Chen Y, Dumont MG et al (2008) Marine methylotrophs revealed by stable-isotope
probing, multiple displacement amplification and metagenomics. Environ Microbiol 10:
1526–1535
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental
genome shotgun sequences. Nucleic Acids Res 34:5623–5630
Olsen GJ, Lane DJ, Giovannoni SJ et al (1986) Microbial ecology and evolution – a ribosomalRNA Approach. Ann Review of Microbiol 40:337–365
Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change – breathing new life
into microbiology. J Bacteriol 176:1–6
Osoegawa K, Tateno M, Woon PY et al (2000) Bacterial artificial chromosome libraries for mouse
sequencing and functional analysis. Genome Res 10:116–128
Osoegawa K, Woon PY, Zhao B et al (1998) An improved approach for construction of bacterial
artificial chromosome libraries. Genomics 52:1–8
Ottesen EA, Hong JW, Quake SR et al (2006) Microfluidic digital PCR enables multigene analysis
of individual environmental bacteria. Science 314:1464–1467
Overbeek R, Begley T, Butler RM et al (2005) The subsystems approach to genome annotation
and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702
Overbeek R, Fonstein M, D’Souza M et al (1999) The use of gene clusters to infer functional
coupling. Proc Natl Acad Sci U S A 96:2896–2901
67
Markowitz VM, Ivanova NN, Szeto E et al (2008) IMG/M: a data management and analysis system
for metagenomes. Nucleic Acids Res 36:D534–D538
Markowitz VM, Korzeniewski F, Palaniappan K et al (2006) The integrated microbial genomes
(IMG) system. Nucleic Acids Res 34:D344–D348
Martin HG, Ivanova N, Kunin V et al (2006) Metagenomic analysis of two enhanced biological
phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24:1263–1269
Martín-Cuadrado AB, López-García P, Alba JC et al (2007) Metagenomics of the deep
Mediterranean, a warm bathypelagic habitat. PLoS One 2:e914
Mavromatis K, Ivanova N, Barry K et al (2007) Use of simulated data sets to evaluate the fidelity
of metagenomic processing methods. Nat Methods 4:495–500
McHardy AC, Goesmann A, Pühler A et al (2004) Development of joint application strategies for
two microbial gene finders. Bioinformatics 20:1622–1631
McHardy AC, Martin HG, Tsirigos A et al (2007) Accurate phylogenetic classification of variablelength DNA fragments. Nat Methods 4:63–72
McHardy AC, Rigoutsos I (2007) What’s in the mix: phylogenetic classification of metagenome
sequence samples. Curr Opin Microbiol 10:499–503
Meyer F, Goesmann A, McHardy AC et al (2003) GenDB – an open source genome annotation
system for prokaryote genomes. Nucleic Acids Res 31:2187–2195
Meyerdierks A, Kube M, Lombardot T et al (2005) Insights into the genomes of archaea mediating
the anaerobic oxidation of methane. Environ Microbiol 7:1937–1951
Monaco AP, Larin Z (1994) YACs, BACs, PACs and MACs – artificial chromosomes as research
tools. Trends Biotechnol 12:280–286
Mou XZ, Sun SL, Edwards RA et al (2008) Bacterial carbon processing by generalist species in
the coastal ocean. Nature 451:708–U711
Mulder NJ, Apweiler R, Attwood TK et al (2003) The InterPro Database, 2003 brings increased
coverage and new features. Nucleic Acids Res 31:315–318
Mussmann M, Hu FZ, Richter M et al (2007) Insights into the genome of large sulfur bacteria
revealed by analysis of single filaments. PLoS Biol 5:1923–1937
Mußmann M, Richter M, Lombardot T et al (2005) Clustered genes related to sulfate respiration in
uncultured prokaryotes support the theory of their concomitant horizontal transfer. J Bacteriol
187:7126–7137
Nelson JR, Cai YC, Giesler TL et al (2002) TempliPhi, phi 29 DNA polymerase based rolling
circle amplification of templates for DNA sequencing. Biotechniques, 44–47
Neufeld JD, Chen Y, Dumont MG et al (2008) Marine methylotrophs revealed by stable-isotope
probing, multiple displacement amplification and metagenomics. Environ Microbiol 10:
1526–1535
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental
genome shotgun sequences. Nucleic Acids Res 34:5623–5630
Olsen GJ, Lane DJ, Giovannoni SJ et al (1986) Microbial ecology and evolution – a ribosomalRNA Approach. Ann Review of Microbiol 40:337–365
Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change – breathing new life
into microbiology. J Bacteriol 176:1–6
Osoegawa K, Tateno M, Woon PY et al (2000) Bacterial artificial chromosome libraries for mouse
sequencing and functional analysis. Genome Res 10:116–128
Osoegawa K, Woon PY, Zhao B et al (1998) An improved approach for construction of bacterial
artificial chromosome libraries. Genomics 52:1–8
Ottesen EA, Hong JW, Quake SR et al (2006) Microfluidic digital PCR enables multigene analysis
of individual environmental bacteria. Science 314:1464–1467
Overbeek R, Begley T, Butler RM et al (2005) The subsystems approach to genome annotation
and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702
Overbeek R, Fonstein M, D’Souza M et al (1999) The use of gene clusters to infer functional
coupling. Proc Natl Acad Sci U S A 96:2896–2901