95
Saxena A, Raghuwanshi R, Singh HB (2015) Trichoderma species mediated differential tolerance
against biotic stress of phytopathogens in Cicer arietinum L. J Basic Microbiol 55:195–206
Schadt CW, Zhou J (2005) Advances in microarrays for soil microbial community analyses. In:
Nannipieri P, Smalla K (eds) Soil biology: nucleic acids and proteins in soil. Springer-Verlag,
New York
Scheinert P, Kruse R, Ullmann U, Söller R, Krupp G (1996) Molecular differentiation of bacteria
by PCR amplification of the 16S-23S rRNA spacer. J Microbiol Methods 26:103–117
Schimak MP, Kleiner M, Wetzel S, Liebeke M, Dubilier N, Fuchsa BM (2016) MiL-FISH: multilabeled oligonucleotides for fluorescence in situ hybridisation improve visualisation of bacterial
cells. Appl Environ Microbiol 82:62–70
Schneider T, Keiblinger KM, Schmid E, Sterflinger-Gleixner K, Ellersdorfer G, Roschitzki B,
Richter A, Eberl L, Zechmeister-Boltenstern S, Riedel K (2012) Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions.
ISME J 6:1749–1762
Schreiber F, Gumrich P, Daniel R, Meinicke P (2010) Treephyler: fast taxonomic profiling of
metagenomes. Bioinformatics 26:960–961
Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2004) A proteomic
fingerprint of dissolved organic carbon and of soil particles. Oecologia 142:335–343
Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol
64:4870–4876
Sebastian R, Kim JY, Kim TH, Lee KT (2013) Metagenomics: a promising approach to assess
enzymes biocatalyst for biofuel production. Asian J Biotechnol 5:33–50
Sedlar K, Kupkova K, Provaznik I (2017) Bioinformatics strategies for taxonomy independent
binning and visualization of sequences in shotgun metagenomics. Comput Struct Biotechnol
J 15:48–55
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011)
Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012) Metagenomic
microbial community profiling using unique clade-specific marker genes. Nat Methods
9:811–814
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (2013) Computational
meta’omics for microbial community studies. Mol Syst Biol 9:666. https://doi.org/10.1038/
msb.2013.22
Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R (2003) An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization.
Appl Environ Microbiol 69:2928–2935
Selvakumar N, Ding BC, Wilson SM (1997) Separation of DNA strands facilitates detection of
point mutations by PCR-SSCP. BioTechniques 22:604–606
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for
metagenomics. PLoS Biol 5:e75
Shah N, Tang H, Doak TG, Ye Y (2011) Comparing bacterial communities inferred from 16S
rRNA gene sequencing and shotgun metagenomics. Symp Biocomput Pac:165–176. https://
doi.org/10.1142/97898143350580018
Shapiro BJ (2017) The population genetics of pangenomes. Nat Microbiol 2(12):1574–1574.
https://doi.org/10.1038/s41564-017-0066-6
Sharkey FH, Banat IM, Marchant R (2004) Detection and quantification of gene expression in
environmental bacteriology. Appl Environ Microbiol 70:3795–3806
Sharma, CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Stadler PF (2010) The
primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255.
https://doi.org/10.1038/nature08756.
Sharon I (2010) Computational methods for metagenomic analysis. Ph.D Thesis, The Technion –
Israel Institute of Technology
References
Saxena A, Raghuwanshi R, Singh HB (2015) Trichoderma species mediated differential tolerance
against biotic stress of phytopathogens in Cicer arietinum L. J Basic Microbiol 55:195–206
Schadt CW, Zhou J (2005) Advances in microarrays for soil microbial community analyses. In:
Nannipieri P, Smalla K (eds) Soil biology: nucleic acids and proteins in soil. Springer-Verlag,
New York
Scheinert P, Kruse R, Ullmann U, Söller R, Krupp G (1996) Molecular differentiation of bacteria
by PCR amplification of the 16S-23S rRNA spacer. J Microbiol Methods 26:103–117
Schimak MP, Kleiner M, Wetzel S, Liebeke M, Dubilier N, Fuchsa BM (2016) MiL-FISH: multilabeled oligonucleotides for fluorescence in situ hybridisation improve visualisation of bacterial
cells. Appl Environ Microbiol 82:62–70
Schneider T, Keiblinger KM, Schmid E, Sterflinger-Gleixner K, Ellersdorfer G, Roschitzki B,
Richter A, Eberl L, Zechmeister-Boltenstern S, Riedel K (2012) Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions.
ISME J 6:1749–1762
Schreiber F, Gumrich P, Daniel R, Meinicke P (2010) Treephyler: fast taxonomic profiling of
metagenomes. Bioinformatics 26:960–961
Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2004) A proteomic
fingerprint of dissolved organic carbon and of soil particles. Oecologia 142:335–343
Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol
64:4870–4876
Sebastian R, Kim JY, Kim TH, Lee KT (2013) Metagenomics: a promising approach to assess
enzymes biocatalyst for biofuel production. Asian J Biotechnol 5:33–50
Sedlar K, Kupkova K, Provaznik I (2017) Bioinformatics strategies for taxonomy independent
binning and visualization of sequences in shotgun metagenomics. Comput Struct Biotechnol
J 15:48–55
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011)
Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012) Metagenomic
microbial community profiling using unique clade-specific marker genes. Nat Methods
9:811–814
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (2013) Computational
meta’omics for microbial community studies. Mol Syst Biol 9:666. https://doi.org/10.1038/
msb.2013.22
Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R (2003) An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization.
Appl Environ Microbiol 69:2928–2935
Selvakumar N, Ding BC, Wilson SM (1997) Separation of DNA strands facilitates detection of
point mutations by PCR-SSCP. BioTechniques 22:604–606
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for
metagenomics. PLoS Biol 5:e75
Shah N, Tang H, Doak TG, Ye Y (2011) Comparing bacterial communities inferred from 16S
rRNA gene sequencing and shotgun metagenomics. Symp Biocomput Pac:165–176. https://
doi.org/10.1142/97898143350580018
Shapiro BJ (2017) The population genetics of pangenomes. Nat Microbiol 2(12):1574–1574.
https://doi.org/10.1038/s41564-017-0066-6
Sharkey FH, Banat IM, Marchant R (2004) Detection and quantification of gene expression in
environmental bacteriology. Appl Environ Microbiol 70:3795–3806
Sharma, CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Stadler PF (2010) The
primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255.
https://doi.org/10.1038/nature08756.
Sharon I (2010) Computational methods for metagenomic analysis. Ph.D Thesis, The Technion –
Israel Institute of Technology
References