Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann K-H, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, et al. (2011)
PLoS ONE 6(1): e14519.
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Autor*in
Jaenicke, SebastianUniBi;
Ander, ChristinaUniBi;
Bekel, ThomasUniBi;
Bisdorf, ReginaUniBi;
Dröge, Marcus;
Gartemann, Karl-HeinzUniBi ;
Jünemann, SebastianUniBi;
Kaiser, Olaf;
Krause, Lutz;
Tille, Felix;
Zakrzewski, MarthaUniBi;
Pühler, AlfredUniBi
Alle
Alle
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation.
Erscheinungsjahr
2011
Zeitschriftentitel
PLoS ONE
Band
6
Ausgabe
1
Art.-Nr.
e14519
ISSN
1932-6203
eISSN
1932-6203
Page URI
https://pub.uni-bielefeld.de/record/2003276
Zitieren
Jaenicke S, Ander C, Bekel T, et al. Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE. 2011;6(1): e14519.
Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K. - H., Jünemann, S., et al. (2011). Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE, 6(1), e14519. https://doi.org/10.1371/journal.pone.0014519
Jaenicke, Sebastian, Ander, Christina, Bekel, Thomas, Bisdorf, Regina, Dröge, Marcus, Gartemann, Karl-Heinz, Jünemann, Sebastian, et al. 2011. “Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing”. PLoS ONE 6 (1): e14519.
Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K. - H., Jünemann, S., Kaiser, O., Krause, L., Tille, F., et al. (2011). Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE 6:e14519.
Jaenicke, S., et al., 2011. Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE, 6(1): e14519.
S. Jaenicke, et al., “Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing”, PLoS ONE, vol. 6, 2011, : e14519.
Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K.-H., Jünemann, S., Kaiser, O., Krause, L., Tille, F., Zakrzewski, M., Pühler, A., Schlüter, A., Goesmann, A.: Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE. 6, : e14519 (2011).
Jaenicke, Sebastian, Ander, Christina, Bekel, Thomas, Bisdorf, Regina, Dröge, Marcus, Gartemann, Karl-Heinz, Jünemann, Sebastian, Kaiser, Olaf, Krause, Lutz, Tille, Felix, Zakrzewski, Martha, Pühler, Alfred, Schlüter, Andreas, and Goesmann, Alexander. “Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing”. PLoS ONE 6.1 (2011): e14519.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
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Bacosa HP, Liu Z, Erdner DL., Front Microbiol 6(), 2015
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Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads.
Nolla-Ardèvol V, Peces M, Strous M, Tegetmeyer HE., BMC Microbiol 15(), 2015
PMID: 26680455
Nolla-Ardèvol V, Peces M, Strous M, Tegetmeyer HE., BMC Microbiol 15(), 2015
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Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity.
Lü F, Bize A, Guillot A, Monnet V, Madigou C, Chapleur O, Mazéas L, He P, Bouchez T., ISME J 8(1), 2014
PMID: 23949661
Lü F, Bize A, Guillot A, Monnet V, Madigou C, Chapleur O, Mazéas L, He P, Bouchez T., ISME J 8(1), 2014
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Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters.
St-Pierre B, Wright AD., Appl Microbiol Biotechnol 98(6), 2014
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St-Pierre B, Wright AD., Appl Microbiol Biotechnol 98(6), 2014
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Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.
Stark L, Giersch T, Wünschiers R., Anaerobe 29(), 2014
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Alauzet C, Marchandin H, Courtin P, Mory F, Lemée L, Pons JL, Chapot-Chartier MP, Lozniewski A, Jumas-Bilak E., Syst Appl Microbiol 37(1), 2014
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Alauzet C, Marchandin H, Courtin P, Mory F, Lemée L, Pons JL, Chapot-Chartier MP, Lozniewski A, Jumas-Bilak E., Syst Appl Microbiol 37(1), 2014
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Methanogenic archaea diversity in Hanwoo (Bos taurus coreanae) rumen fluid, rectal dung, and barn floor manure using a culture-independent method based on mcrA gene sequences.
Daquiado AR, Cho KM, Kim TY, Kim SC, Chang HH, Lee YB., Anaerobe 27(), 2014
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Daquiado AR, Cho KM, Kim TY, Kim SC, Chang HH, Lee YB., Anaerobe 27(), 2014
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Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants.
Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T., Appl Microbiol Biotechnol 98(12), 2014
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Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T., Appl Microbiol Biotechnol 98(12), 2014
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Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure.
Li J, Rui J, Pei Z, Sun X, Zhang S, Yan Z, Wang Y, Liu X, Zheng T, Li X., Appl Microbiol Biotechnol 98(10), 2014
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Li J, Rui J, Pei Z, Sun X, Zhang S, Yan Z, Wang Y, Liu X, Zheng T, Li X., Appl Microbiol Biotechnol 98(10), 2014
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Two-stage biogas production by co-digesting molasses wastewater and sewage sludge.
Lee JY, Yun J, Kim TG, Wee D, Cho KS., Bioprocess Biosyst Eng 37(12), 2014
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Lee JY, Yun J, Kim TG, Wee D, Cho KS., Bioprocess Biosyst Eng 37(12), 2014
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Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate.
Röske I, Sabra W, Nacke H, Daniel R, Zeng AP, Antranikian G, Sahm K., Appl Microbiol Biotechnol 98(21), 2014
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Röske I, Sabra W, Nacke H, Daniel R, Zeng AP, Antranikian G, Sahm K., Appl Microbiol Biotechnol 98(21), 2014
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Biomethane production and dynamics of microflora in response to copper treatments during mesophilic anaerobic digestion.
Ke X, Wang C, Li R, Zhang Y, Zhang H, Gui S., Waste Manag Res 32(8), 2014
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Ke X, Wang C, Li R, Zhang Y, Zhang H, Gui S., Waste Manag Res 32(8), 2014
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A metagenomic study of the microbial communities in four parallel biogas reactors.
Solli L, Håvelsrud OE, Horn SJ, Rike AG., Biotechnol Biofuels 7(1), 2014
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Solli L, Håvelsrud OE, Horn SJ, Rike AG., Biotechnol Biofuels 7(1), 2014
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MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
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Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
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Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples.
Barret M, Gagnon N, Kalmokoff ML, Topp E, Verastegui Y, Brooks SP, Matias F, Neufeld JD, Talbot G., Appl Environ Microbiol 79(2), 2013
PMID: 23104405
Barret M, Gagnon N, Kalmokoff ML, Topp E, Verastegui Y, Brooks SP, Matias F, Neufeld JD, Talbot G., Appl Environ Microbiol 79(2), 2013
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Comparative study of changes in reaction profile and microbial community structure in two anaerobic repeated-batch reactors started up with different seed sludges.
Kim J, Lee S, Lee C., Bioresour Technol 129(), 2013
PMID: 23266851
Kim J, Lee S, Lee C., Bioresour Technol 129(), 2013
PMID: 23266851
Microbial diversity and dynamics during methane production from municipal solid waste.
Bareither CA, Wolfe GL, McMahon KD, Benson CH., Waste Manag 33(10), 2013
PMID: 23318155
Bareither CA, Wolfe GL, McMahon KD, Benson CH., Waste Manag 33(10), 2013
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A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor.
Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S., Biotechnol Biofuels 6(1), 2013
PMID: 23320936
Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S., Biotechnol Biofuels 6(1), 2013
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Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment.
Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park TJ, Chen Y, Leung FC., Biotechnol Biofuels 6(1), 2013
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Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park TJ, Chen Y, Leung FC., Biotechnol Biofuels 6(1), 2013
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Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation.
Wu YR, He J., Bioresour Technol 139(), 2013
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Wu YR, He J., Bioresour Technol 139(), 2013
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Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms.
Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke S, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M, Schlüter A., Biotechnol Biofuels 6(1), 2013
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Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke S, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M, Schlüter A., Biotechnol Biofuels 6(1), 2013
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Metagenomic analysis of methanogen populations in three full-scale mesophilic anaerobic manure digesters operated on dairy farms in Vermont, USA.
St-Pierre B, Wright AD., Bioresour Technol 138(), 2013
PMID: 23624045
St-Pierre B, Wright AD., Bioresour Technol 138(), 2013
PMID: 23624045
A preliminary metagenomic study of puer tea during pile fermentation.
Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
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Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
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Investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge.
Tomazetto G, Oliveira VM., World J Microbiol Biotechnol 29(11), 2013
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Tomazetto G, Oliveira VM., World J Microbiol Biotechnol 29(11), 2013
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A new framework to accurately quantify soil bacterial community diversity from DGGE.
Lalande J, Villemur R, Deschênes L., Microb Ecol 66(3), 2013
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Lalande J, Villemur R, Deschênes L., Microb Ecol 66(3), 2013
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Biodegradation of endocrine disruptors in solid-liquid two-phase partitioning systems by enrichment cultures.
Villemur R, Dos Santos SC, Ouellette J, Juteau P, Lépine F, Déziel E., Appl Environ Microbiol 79(15), 2013
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Villemur R, Dos Santos SC, Ouellette J, Juteau P, Lépine F, Déziel E., Appl Environ Microbiol 79(15), 2013
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Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling.
Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A., J Biotechnol 167(3), 2013
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Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A., J Biotechnol 167(3), 2013
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Microbial anaerobic digestion (bio-digesters) as an approach to the decontamination of animal wastes in pollution control and the generation of renewable energy.
Manyi-Loh CE, Mamphweli SN, Meyer EL, Okoh AI, Makaka G, Simon M., Int J Environ Res Public Health 10(9), 2013
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Manyi-Loh CE, Mamphweli SN, Meyer EL, Okoh AI, Makaka G, Simon M., Int J Environ Res Public Health 10(9), 2013
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A preliminary metagenomic study of puer tea during pile fermentation
Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
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Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
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Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant.
Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A., J Biotechnol 168(4), 2013
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Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A., J Biotechnol 168(4), 2013
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Investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge
Tomazetto G, Oliveira VM., World J Microbiol Biotechnol 29(11), 2013
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Tomazetto G, Oliveira VM., World J Microbiol Biotechnol 29(11), 2013
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD., Nucleic Acids Res 40(database issue), 2012
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Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD., Nucleic Acids Res 40(database issue), 2012
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Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
Scholz MB, Lo CC, Chain PS., Curr Opin Biotechnol 23(1), 2012
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Scholz MB, Lo CC, Chain PS., Curr Opin Biotechnol 23(1), 2012
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Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.
Rademacher A, Zakrzewski M, Schlüter A, Schönberg M, Szczepanowski R, Goesmann A, Pühler A, Klocke M., FEMS Microbiol Ecol 79(3), 2012
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Rademacher A, Zakrzewski M, Schlüter A, Schönberg M, Szczepanowski R, Goesmann A, Pühler A, Klocke M., FEMS Microbiol Ecol 79(3), 2012
PMID: 22126587
Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing.
Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A., J Biotechnol 158(4), 2012
PMID: 22342600
Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A., J Biotechnol 158(4), 2012
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Methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks.
Barret M, Gagnon N, Morissette B, Topp E, Kalmokoff M, Brooks SP, Matias F, Massé DI, Masse L, Talbot G., FEMS Microbiol Ecol 80(2), 2012
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Barret M, Gagnon N, Morissette B, Topp E, Kalmokoff M, Brooks SP, Matias F, Massé DI, Masse L, Talbot G., FEMS Microbiol Ecol 80(2), 2012
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Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.
Illeghems K, De Vuyst L, Papalexandratou Z, Weckx S., PLoS One 7(5), 2012
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Illeghems K, De Vuyst L, Papalexandratou Z, Weckx S., PLoS One 7(5), 2012
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Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL., Biotechnol Biofuels 5(), 2012
PMID: 22673110
Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL., Biotechnol Biofuels 5(), 2012
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PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets.
Pinto AJ, Raskin L., PLoS One 7(8), 2012
PMID: 22905208
Pinto AJ, Raskin L., PLoS One 7(8), 2012
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Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2(T), Isolated from a sewage sludge digester.
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A., J Bacteriol 194(19), 2012
PMID: 22965103
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A., J Bacteriol 194(19), 2012
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Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P., BMC Bioinformatics 13 Suppl 19(), 2012
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Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P., BMC Bioinformatics 13 Suppl 19(), 2012
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Comparative analysis of hydrogen-producing bacterial biofilms and granular sludge formed in continuous cultures of fermentative bacteria.
Chojnacka A, Błaszczyk MK, Szczęsny P, Nowak K, Sumińska M, Tomczyk-Żak K, Zielenkiewicz U, Sikora A., Bioresour Technol 102(21), 2011
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Chojnacka A, Błaszczyk MK, Szczęsny P, Nowak K, Sumińska M, Tomczyk-Żak K, Zielenkiewicz U, Sikora A., Bioresour Technol 102(21), 2011
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Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.
Ausec L, Zakrzewski M, Goesmann A, Schlüter A, Mandic-Mulec I., PLoS One 6(10), 2011
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