Marine Sponge Metagenomics References 471
Part C | 17
(Demospongiae, Dictyoceratida) and accompanying tissue changes, J. Invertebr. Pathol. 31, 246–254
(1978)
17.20 J.E. Lohr, F. Chen, R.T. Hill: Genomic analysis of
bacteriophage PhiJL001: Insights into its interaction
with a sponge-associated alpha proteobacterium,
Appl. Environ. Microbiol. 71, 1598–1609 (2005)
17.21 J.J. Banik, S.F. Brady: Recent application of
metagenomic approaches toward the discovery of antimicrobials and other bioactive small
molecules, Curr. Opin. Microbiol. 13, 603–609
(2010)
17.22 G. Wang: Diversity and biotechnological potential of the sponge-associated microbial consortia,
J. Ind. Microbiol. Biotechnol. 33, 545–551 (2006)
17.23 C.R. Woese: Bacterial evolution, Microbiol. Rev. 51,
221–271 (1987)
17.24 D.J. Lane, B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin,
N.R. Pace: Rapid determination of 16S ribosomal
RNA sequences for phylogenetic analyses, Proc.
Natl. Acad. Sci. USA 82, 6955–6959 (1985)
17.25 M. Ferrer, F. Martínez-Abarca, P.N. Golyshin: Mining
genomes and ‘metagenomes’ for novel catalysts,
Curr. Opin. Biotechnol. 16, 588–593 (2005)
17.26 J.C. Venter, K. Remingto, J.F. Heidelber,
A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu,
I. Paulsen, K.E. Nelson, W. Nelson, D.E. Fouts,
S. Levy, A.H. Knap, M.W. Lomas, K. Nealson,
O. White, J. Peterson, J. Hoffman, R. Parsons,
H. Baden-Tillson, C. Pfannkoch, Y.H. Rogers,
H.O. Smith: Environmental genome shotgun sequencing of the Sargasso Sea, Science 304, 66–74
(2004)
17.27 D.E. Gillespie, S.F. Brady, A.D. Bettermann,
N.P. Cianciotto, M.R. Liles, M.R. Rondon, J. Clardy,
R.M. Goodman, J. Handelsman: Isolation of
antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA, Appl. Environ.
Microbiol. 68, 4301–4306 (2002)
17.28 O. Yongchang, S. Dai, L. Xie, M.S. Ravi Kumar,
W. Sun, H. Sun, D. Tang, X. Li: Isolation of high
molecular weight DNA from marine sponge bacteria for BAC library construction, Mar. Biotechnol. 12,
318–325 (2010)
17.29 O. Beja: To BAC or not to BAC: Marine ecogenomics,
Curr. Opin. Biotechnol. 15, 187–190 (2004)
17.30 J.R. de la Torre, L.M. Christianson, O. Beja,
M.T. Suzuki, D.M. Karl, J. Heidelberg, E.F. DeLong:
Proteorhodopsin genes are distributed among divergent marine bacterial taxa, Proc. Natl. Acad. Sci.
USA. 100, 12830–12835 (2003)
17.31 P.D. Schloss, J. Handelsman: Biotechnological
prospects from metagenomics, Curr. Opin. Biotechnol. 14, 303–310 (2003)
17.32 J. Kennedy, J.R. Marchesi, A.D. Dobson: Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges, Appl. Microbiol. Biotechnol. 75, 11–20
(2007)
17.33 J. Staunton, K.J. Weissman: Polyketide biosynthesis: a millennium review, Nat. Prod. Rep. 18(4),
380–416 (2001)
17.34 M.L. Metzker: Sequencing technologies – The next
generation, Nat. Rev. Genet. 1, 31–46 (2010)
17.35 M. Ronaghi, S. Karamohamed, B. Pettersson,
M. Uhlen, P. Nyren: Real-time DNA sequencing
using detection of pyrophosphate release, Anal.
Biochem. 242, 84–89 (1996)
17.36 S. Marsh: Pyrosequencing applications, Methods
Mol. Biol. 373, 15–24 (2007)
17.37 J. Jonasson, M. Olofsson, H.J. Monstein: Classification, identification and subtyping of bacteria based
on pyrosequencing and signature matching of 16S
rDNA fragments, APMIS 110, 263–272 (2002)
17.38 T. Thomas, J. Gilbert, F. Meyer: Metagenomics – A
guide from sampling to data analysis, Microb. Inform. Exp. 2, 1–12 (2012)
17.39 R. He, T. Wakimoto, Y. Egami, H. Kenmoku, T. Ito,
Y. Asakawa, I. Abe: Heterologously expressed ˇhydroxyl fatty acids from a metagenomic library
of a marine sponge, Bioorg. Med. Chem. Lett. 22,
7322–7325 (2012)
17.40 Y.D. Nam, H.W. Lee, M. Lee, K.J. Yim, K.N. Kim,
S.W. Roh, D. Kim: Draft genome sequence of Gillisia
sp. strain CBA3202, a novel member of the genus
Gillisia, which belongs to the family Flavobacteriaceae, J. Bacteriol. 194(14), 3739 (2012)
17.41 S.M. Huse, J.A. Huber, H.G. Morrison, M.L. Sogin,
D.M. Welch: Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biol. 8, R143
(2007)
17.42 T.Z. DeSantis, I. Dubosarskiy, S.R. Murray, G.L. Andersen: Comprehensive aligned sequence construction for automated design of effective probes
(CASCADE-P) using 16S rDNA, Bioinformatics 19,
1461–1468 (2003)
17.43 R.C. Edgar: MUSCLE: a multiple sequence alignment
method with reduced time and space complexity,
BMC Bioinformatics 5, 113 (2004)
17.44 T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas,
E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu,
G.L. Andersen: Greengenes, a chimera checked 16S
rRNA gene database and workbench compatible
with ARB, Appl. Environ. Microbiol. 72, 5069–5072
(2006)
17.45 J.R. Cole, B. Chai, R.J. Farris, Q. Wang, A.S. KulamSyed-Mohideen, D.M. McGarrell, A.M. Bandela,
E. Cardenas, G.M. Garrity, J.M. Tiedje: The ribosomal database project (RDP-II): introducing myRDP
space and quality controlled public data, Nucleic
Acids Res. 35, 169–172 (2007)
17.46 T. Huber, G. Faulkner, P. Hugenholtz: Bellerophon:
a program to detect chimeric sequences in multiple
sequence alignments, Bioinformatics 20, 2317–2319
(2004)
17.47 K.E. Ashelford, N.A. Chuzhanova, J.C. Fry, A.J. Jones,
A.J. Weightman: At least 1 in 20 16S rRNA sequence
records currently held in public repositories is es-
Part C | 17
(Demospongiae, Dictyoceratida) and accompanying tissue changes, J. Invertebr. Pathol. 31, 246–254
(1978)
17.20 J.E. Lohr, F. Chen, R.T. Hill: Genomic analysis of
bacteriophage PhiJL001: Insights into its interaction
with a sponge-associated alpha proteobacterium,
Appl. Environ. Microbiol. 71, 1598–1609 (2005)
17.21 J.J. Banik, S.F. Brady: Recent application of
metagenomic approaches toward the discovery of antimicrobials and other bioactive small
molecules, Curr. Opin. Microbiol. 13, 603–609
(2010)
17.22 G. Wang: Diversity and biotechnological potential of the sponge-associated microbial consortia,
J. Ind. Microbiol. Biotechnol. 33, 545–551 (2006)
17.23 C.R. Woese: Bacterial evolution, Microbiol. Rev. 51,
221–271 (1987)
17.24 D.J. Lane, B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin,
N.R. Pace: Rapid determination of 16S ribosomal
RNA sequences for phylogenetic analyses, Proc.
Natl. Acad. Sci. USA 82, 6955–6959 (1985)
17.25 M. Ferrer, F. Martínez-Abarca, P.N. Golyshin: Mining
genomes and ‘metagenomes’ for novel catalysts,
Curr. Opin. Biotechnol. 16, 588–593 (2005)
17.26 J.C. Venter, K. Remingto, J.F. Heidelber,
A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu,
I. Paulsen, K.E. Nelson, W. Nelson, D.E. Fouts,
S. Levy, A.H. Knap, M.W. Lomas, K. Nealson,
O. White, J. Peterson, J. Hoffman, R. Parsons,
H. Baden-Tillson, C. Pfannkoch, Y.H. Rogers,
H.O. Smith: Environmental genome shotgun sequencing of the Sargasso Sea, Science 304, 66–74
(2004)
17.27 D.E. Gillespie, S.F. Brady, A.D. Bettermann,
N.P. Cianciotto, M.R. Liles, M.R. Rondon, J. Clardy,
R.M. Goodman, J. Handelsman: Isolation of
antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA, Appl. Environ.
Microbiol. 68, 4301–4306 (2002)
17.28 O. Yongchang, S. Dai, L. Xie, M.S. Ravi Kumar,
W. Sun, H. Sun, D. Tang, X. Li: Isolation of high
molecular weight DNA from marine sponge bacteria for BAC library construction, Mar. Biotechnol. 12,
318–325 (2010)
17.29 O. Beja: To BAC or not to BAC: Marine ecogenomics,
Curr. Opin. Biotechnol. 15, 187–190 (2004)
17.30 J.R. de la Torre, L.M. Christianson, O. Beja,
M.T. Suzuki, D.M. Karl, J. Heidelberg, E.F. DeLong:
Proteorhodopsin genes are distributed among divergent marine bacterial taxa, Proc. Natl. Acad. Sci.
USA. 100, 12830–12835 (2003)
17.31 P.D. Schloss, J. Handelsman: Biotechnological
prospects from metagenomics, Curr. Opin. Biotechnol. 14, 303–310 (2003)
17.32 J. Kennedy, J.R. Marchesi, A.D. Dobson: Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges, Appl. Microbiol. Biotechnol. 75, 11–20
(2007)
17.33 J. Staunton, K.J. Weissman: Polyketide biosynthesis: a millennium review, Nat. Prod. Rep. 18(4),
380–416 (2001)
17.34 M.L. Metzker: Sequencing technologies – The next
generation, Nat. Rev. Genet. 1, 31–46 (2010)
17.35 M. Ronaghi, S. Karamohamed, B. Pettersson,
M. Uhlen, P. Nyren: Real-time DNA sequencing
using detection of pyrophosphate release, Anal.
Biochem. 242, 84–89 (1996)
17.36 S. Marsh: Pyrosequencing applications, Methods
Mol. Biol. 373, 15–24 (2007)
17.37 J. Jonasson, M. Olofsson, H.J. Monstein: Classification, identification and subtyping of bacteria based
on pyrosequencing and signature matching of 16S
rDNA fragments, APMIS 110, 263–272 (2002)
17.38 T. Thomas, J. Gilbert, F. Meyer: Metagenomics – A
guide from sampling to data analysis, Microb. Inform. Exp. 2, 1–12 (2012)
17.39 R. He, T. Wakimoto, Y. Egami, H. Kenmoku, T. Ito,
Y. Asakawa, I. Abe: Heterologously expressed ˇhydroxyl fatty acids from a metagenomic library
of a marine sponge, Bioorg. Med. Chem. Lett. 22,
7322–7325 (2012)
17.40 Y.D. Nam, H.W. Lee, M. Lee, K.J. Yim, K.N. Kim,
S.W. Roh, D. Kim: Draft genome sequence of Gillisia
sp. strain CBA3202, a novel member of the genus
Gillisia, which belongs to the family Flavobacteriaceae, J. Bacteriol. 194(14), 3739 (2012)
17.41 S.M. Huse, J.A. Huber, H.G. Morrison, M.L. Sogin,
D.M. Welch: Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biol. 8, R143
(2007)
17.42 T.Z. DeSantis, I. Dubosarskiy, S.R. Murray, G.L. Andersen: Comprehensive aligned sequence construction for automated design of effective probes
(CASCADE-P) using 16S rDNA, Bioinformatics 19,
1461–1468 (2003)
17.43 R.C. Edgar: MUSCLE: a multiple sequence alignment
method with reduced time and space complexity,
BMC Bioinformatics 5, 113 (2004)
17.44 T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas,
E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu,
G.L. Andersen: Greengenes, a chimera checked 16S
rRNA gene database and workbench compatible
with ARB, Appl. Environ. Microbiol. 72, 5069–5072
(2006)
17.45 J.R. Cole, B. Chai, R.J. Farris, Q. Wang, A.S. KulamSyed-Mohideen, D.M. McGarrell, A.M. Bandela,
E. Cardenas, G.M. Garrity, J.M. Tiedje: The ribosomal database project (RDP-II): introducing myRDP
space and quality controlled public data, Nucleic
Acids Res. 35, 169–172 (2007)
17.46 T. Huber, G. Faulkner, P. Hugenholtz: Bellerophon:
a program to detect chimeric sequences in multiple
sequence alignments, Bioinformatics 20, 2317–2319
(2004)
17.47 K.E. Ashelford, N.A. Chuzhanova, J.C. Fry, A.J. Jones,
A.J. Weightman: At least 1 in 20 16S rRNA sequence
records currently held in public repositories is es-