Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions

Stolze Y, Zakrzewski M, Maus I, Eikmeyer FG, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A (2015)
Biotechnology for Biofuels 8(1): 14.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. Results High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2T revealed that dominant methanogens within the dry fermentation process were highly related to the reference. Conclusions Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2T dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
Biogas; Dry fermentation; Wet fermentation; Microbial communities; Methanogenesis; Metagenomics; 16S rRNA; Methanoculleus bourgensis; Fragment recruitment
Biotechnology for Biofuels
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
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Stolze Y, Zakrzewski M, Maus I, et al. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels. 2015;8(1): 14.
Stolze, Y., Zakrzewski, M., Maus, I., Eikmeyer, F. G., Jaenicke, S., Rottmann, N., Siebner, C., et al. (2015). Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels, 8(1), 14. doi:10.1186/s13068-014-0193-8
Stolze, Yvonne, Zakrzewski, Martha, Maus, Irena, Eikmeyer, Felix Gregor, Jaenicke, Sebastian, Rottmann, Nils, Siebner, Clemens, Pühler, Alfred, and Schlüter, Andreas. 2015. “Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions”. Biotechnology for Biofuels 8 (1): 14.
Stolze, Y., Zakrzewski, M., Maus, I., Eikmeyer, F. G., Jaenicke, S., Rottmann, N., Siebner, C., Pühler, A., and Schlüter, A. (2015). Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels 8:14.
Stolze, Y., et al., 2015. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels, 8(1): 14.
Y. Stolze, et al., “Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions”, Biotechnology for Biofuels, vol. 8, 2015, : 14.
Stolze, Y., Zakrzewski, M., Maus, I., Eikmeyer, F.G., Jaenicke, S., Rottmann, N., Siebner, C., Pühler, A., Schlüter, A.: Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels. 8, : 14 (2015).
Stolze, Yvonne, Zakrzewski, Martha, Maus, Irena, Eikmeyer, Felix Gregor, Jaenicke, Sebastian, Rottmann, Nils, Siebner, Clemens, Pühler, Alfred, and Schlüter, Andreas. “Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions”. Biotechnology for Biofuels 8.1 (2015): 14.
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Daten bereitgestellt von Europe PubMed Central.

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis.
Fischer MA, Güllert S, Refai S, Künzel S, Deppenmeier U, Streit WR, Schmitz RA., Microb Biotechnol 12(2), 2019
PMID: 30381904
Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis.
Xiao Z, Lin M, Fan J, Chen Y, Zhao C, Liu B., Appl Microbiol Biotechnol 102(1), 2018
PMID: 29079864
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.
Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A., Microb Biotechnol 11(4), 2018
PMID: 29205917
Methanogens: biochemical background and biotechnological applications.
Enzmann F, Mayer F, Rother M, Holtmann D., AMB Express 8(1), 2018
PMID: 29302756
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.
Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A., Appl Microbiol Biotechnol 102(12), 2018
PMID: 29713790
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics.
Treu L, Campanaro S, Kougias PG, Sartori C, Bassani I, Angelidaki I., Front Microbiol 9(), 2018
PMID: 29892275
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.
Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M., Biotechnol Biofuels 11(), 2018
PMID: 29951113
Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion.
Bonk F, Popp D, Weinrich S, Sträuber H, Kleinsteuber S, Harms H, Centler F., Biotechnol Biofuels 11(), 2018
PMID: 30323859
Metabolic Interactions of a Chain Elongation Microbiome.
Han W, He P, Shao L, Lü F., Appl Environ Microbiol 84(22), 2018
PMID: 30217839
Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production.
Pyzik A, Ciezkowska M, Krawczyk PS, Sobczak A, Drewniak L, Dziembowski A, Lipinski L., Microb Cell Fact 17(1), 2018
PMID: 30572955
The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor.
Tomazetto G, Hahnke S, Langer T, Wibberg D, Blom J, Maus I, Pühler A, Klocke M, Schlüter A., J Biotechnol 257(), 2017
PMID: 28595834
Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.
Ransom-Jones E, McCarthy AJ, Haldenby S, Doonan J, McDonald JE., mSphere 2(4), 2017
PMID: 28776044
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE., Genome Biol 18(1), 2017
PMID: 28934964
Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage.
Wojcieszak M, Pyzik A, Poszytek K, Krawczyk PS, Sobczak A, Lipinski L, Roubinek O, Palige J, Sklodowska A, Drewniak L., Front Microbiol 8(), 2017
PMID: 29033919
Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.
Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A., Biotechnol Biofuels 10(), 2017
PMID: 29158776
Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm.
Pampillón-González L, Ortiz-Cornejo NL, Luna-Guido M, Dendooven L, Navarro-Noya YE., J Mol Microbiol Biotechnol 27(5), 2017
PMID: 29186720
DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison.
Lebuhn M, Derenkó J, Rademacher A, Helbig S, Munk B, Pechtl A, Stolze Y, Prowe S, Schwarz WH, Schlüter A, Liebl W, Klocke M., Bioengineering (Basel) 3(1), 2016
PMID: 28952569
Enhancing metaproteomics--The value of models and defined environmental microbial systems.
Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH., Proteomics 16(5), 2016
PMID: 26621789
Assessment of hydrogen metabolism in commercial anaerobic digesters.
Kern T, Theiss J, Röske K, Rother M., Appl Microbiol Biotechnol 100(10), 2016
PMID: 26995607
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR., Biotechnol Biofuels 9(), 2016
PMID: 27279900
Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.
Maus I, Wibberg D, Winkler A, Pühler A, Schnürer A, Schlüter A., Genome Announc 4(3), 2016
PMID: 27340059
Efficiency and biotechnological aspects of biogas production from microalgal substrates.
Klassen V, Blifernez-Klassen O, Wobbe L, Schlüter A, Kruse O, Mussgnug JH., J Biotechnol 234(), 2016
PMID: 27449486
Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.
Koeck DE, Hahnke S, Zverlov VV, Zverlov VV., Int J Syst Evol Microbiol 66(10), 2016
PMID: 27453473
Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.
Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW., Environ Microbiol 18(9), 2016
PMID: 27317862
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type.
Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U., Biotechnol Biofuels 9(), 2016
PMID: 27462366
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A., Biotechnol Biofuels 9(), 2016
PMID: 27462367
Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.
Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M., Biotechnol Biofuels 9(), 2016
PMID: 27525040
Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities.
Dziewit L, Pyzik A, Romaniuk K, Sobczak A, Szczesny P, Lipinski L, Bartosik D, Drewniak L., Front Microbiol 6(), 2015
PMID: 26217325
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant.
Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A, Pühler A, Schlüter A, Sczyrba A., Gigascience 4(), 2015
PMID: 26229594

87 References

Daten bereitgestellt von Europe PubMed Central.

Biogas production: current state and perspectives.
Weiland P., Appl. Microbiol. Biotechnol. 85(4), 2009
PMID: 19777226
Enhancement of biogas production from solid substrates using different techniques--a review.
Yadvika , Santosh , Sreekrishnan TR, Kohli S, Rana V., Bioresour. Technol. 95(1), 2004
PMID: 15207286
Anaerobic bacterial degradation for the effective utilization of biomass
Ohmiya K, Sakka K, Kimura T., 2005
Biogas from Energy Crop Digestion
Braun R., 2009
Changes in the Archaea microbial community when the biogas fermenters are fed with protein-rich substrates.
Acs N, Kovacs E, Wirth R, Bagi Z, Strang O, Herbel Z, Rakhely G, Kovacs KL., Bioresour. Technol. 131(), 2012
PMID: 23340109
Unexpected stability of Bacteroidetes and Firmicutes communities in laboratory biogas reactors fed with different defined substrates.
Kampmann K, Ratering S, Kramer I, Schmidt M, Zerr W, Schnell S., Appl. Environ. Microbiol. 78(7), 2012
PMID: 22247168
Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity.
Wei H, Tucker MP, Baker JO, Harris M, Luo Y, Xu Q, Himmel ME, Ding SY., Biotechnol Biofuels 5(1), 2012
PMID: 22490508
Stability of a biogas-producing bacterial, archaeal and fungal community degrading food residues.
Bengelsdorf FR, Gerischer U, Langer S, Zak M, Kazda M., FEMS Microbiol. Ecol. 84(1), 2012
PMID: 23228065
Diversity of the resident microbiota in a thermophilic municipal biogas plant.
Weiss A, Jerome V, Freitag R, Mayer HK., Appl. Microbiol. Biotechnol. 81(1), 2008
PMID: 18820906
Investigation of factors influencing biogas production in a large-scale thermophilic municipal biogas plant.
Weiss A, Jerome V, Burghardt D, Likke L, Peiffer S, Hofstetter EM, Gabler R, Freitag R., Appl. Microbiol. Biotechnol. 84(5), 2009
PMID: 19618178
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann KH, Junemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Puhler A, Schluter A, Goesmann A., PLoS ONE 6(1), 2011
PMID: 21297863
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
Krause L, Diaz NN, Edwards RA, Gartemann KH, Kromeke H, Neuweger H, Puhler A, Runte KJ, Schluter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18611419
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
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovacs E, Maroti G, Bagi Z, Rakhely G, Kovacs KL., Biotechnol Biofuels 5(), 2012
PMID: 22673110
Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.
Rademacher A, Zakrzewski M, Schluter A, Schonberg M, Szczepanowski R, Goesmann A, Puhler A, Klocke M., FEMS Microbiol. Ecol. 79(3), 2011
PMID: 22126587
Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling.
Eikmeyer FG, Kofinger P, Poschenel A, Junemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Puhler A, Schwab H, Schluter A., J. Biotechnol. 167(3), 2013
PMID: 23880441
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC., PLoS Biol. 5(3), 2007
PMID: 17355176
Biomass digestion in agriculture: a successful pathway for the energy production and waste treatment in Germany
Weiland P., 2006
Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus
Jans C, Gerber A, Bugnard J, Njage PMK, Lacroix C, Meile L., Food Microbiol. 31(1), 2012
PMID: IND44689904
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J., Nucleic Acids Res. 39(14), 2011
PMID: 21586583
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Puhler A, Rupp O, Stoye J, Schluter A, Goesmann A., J. Biotechnol. 167(2), 2012
PMID: 23026555
Absence of intestinal microbiota does not protect mice from diet-induced obesity.
Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, Blaut M., Br. J. Nutr. 104(6), 2010
PMID: 20441670
Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2.
Brown SD, Lamed R, Morag E, Borovok I, Shoham Y, Klingeman DM, Johnson CM, Yang Z, Land ML, Utturkar SM, Keller M, Bayer EA., J. Bacteriol. 194(12), 2012
PMID: 22628515
Complete Genome Sequence of Clostridium clariflavum DSM 19732.
Izquierdo JA, Goodwin L, Davenport KW, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land M, Hauser L, Jeffries CD, Han J, Pitluck S, Nolan M, Chen A, Huntemann M, Mavromatis K, Mikhailova N, Liolios K, Woyke T, Lynd LR., Stand Genomic Sci 6(1), 2012
PMID: 22675603
[New alkaliphilic peptide fermenting and Fe(III) regenerating bacteria Alkaliphilus peptidofermentans sp.nov. from soda lake]
Zhilina TN, Zavarzina DG, Kolganova TV, Lysenko AM, Turova TP., Mikrobiologiia 78(4), 2009
PMID: 19827715
Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.
Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA., PLoS ONE 4(8), 2009
PMID: 19680555
Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system.
Dassa B, Borovok I, Lamed R, Henrissat B, Coutinho P, Hemme CL, Huang Y, Zhou J, Bayer EA., BMC Genomics 13(), 2012
PMID: 22646801
Complete genome sequence of Streptococcus suis serotype 14 strain JS14.
Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Xiao J, Jin M., J. Bacteriol. 193(9), 2011
PMID: 21398551
Fructanolytic and saccharolytic enzymes of the rumen bacterium Pseudobutyrivibrio ruminis strain 3--preliminary study.
Kasperowicz A, Stan-Glasek K, Guczynska W, Piknova M, Pristas P, Nigutova K, Javorsky P, Michalowski T., Folia Microbiol. (Praha) 55(4), 2010
PMID: 20680564
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.
Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ., PLoS ONE 6(4), 2011
PMID: 21526192

Deublein D, Steinhauser A., 2010
Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche.
Purushe J, Fouts DE, Morrison M, White BA, Mackie RI; North American Consortium for Rumen Bacteria, Coutinho PM, Henrissat B, Nelson KE, Cann IK, Mackie RI, White BA, Forsberg CW, Mongodin E, Daugherty S, Russell JB, Wilson DB, Nelson WC, Nelson KE, Morrison M., Microb. Ecol. 60(4), 2010
PMID: 20585943
Anaerobic digestion of slaughterhouse waste: main process limitations and microbial community interactions.
Palatsi J, Vinas M, Guivernau M, Fernandez B, Flotats X., Bioresour. Technol. 102(3), 2010
PMID: 21030248
Aminobacterium colombiensegen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge.
Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P, Garcia JL, Patel BK., Anaerobe 4(5), 1998
PMID: 16887649
Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).
Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP., Stand Genomic Sci 2(3), 2010
PMID: 21304712
"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.
Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, Riviere D, Ganesan A, Daegelen P, Sghir A, Cohen GN, Medigue C, Weissenbach J, Le Paslier D., J. Bacteriol. 190(7), 2008
PMID: 18245282
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
Krober M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Puhler A, Schluter A., J. Biotechnol. 142(1), 2009
PMID: 19480946
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, Konig H, Puhler A, Schluter A., J. Bacteriol. 194(19), 2012
PMID: 22965103
Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants.
Walter A, Knapp BA, Farbmacher T, Ebner C, Insam H, Franke-Whittle IH., Microb Biotechnol 5(6), 2012
PMID: 22950603
Methanosaeta, the forgotten methanogen?
Smith KS, Ingram-Smith C., Trends Microbiol. 15(4), 2007
PMID: 17320399
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, Junemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sorensen S, Puhler A, Schluter A., J. Biotechnol. 158(4), 2012
PMID: 22342600
Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces.
Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M., Int. J. Syst. Evol. Microbiol. 62(Pt 8), 2012
PMID: 22859731
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants.
Nettmann E, Bergmann I, Pramschufer S, Mundt K, Plogsties V, Herrmann C, Klocke M., Appl. Environ. Microbiol. 76(8), 2010
PMID: 20154117
Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil.
Kitamura K, Fujita T, Akada S, Tonouchi A., Int. J. Syst. Evol. Microbiol. 61(Pt 6), 2010
PMID: 20639228
Complete genome sequence of Streptococcus suis serotype 3 strain ST3.
Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J, Jin M., J. Bacteriol. 193(13), 2011
PMID: 21572001
Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313.
Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, Cheng JF, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N., J. Bacteriol. 193(11), 2011
PMID: 21460082
Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis.
Rusniok C, Couve E, Da Cunha V, El Gana R, Zidane N, Bouchier C, Poyart C, Leclercq R, Trieu-Cuot P, Glaser P., J. Bacteriol. 192(8), 2010
PMID: 20139183
Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.
Heinl S, Wibberg D, Eikmeyer F, Szczepanowski R, Blom J, Linke B, Goesmann A, Grabherr R, Schwab H, Puhler A, Schluter A., J. Biotechnol. 161(2), 2012
PMID: 22465289
Complete genome and proteome of Acholeplasma laidlawii.
Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, Kostrjukova ES, Kovaleva GY, Kazanov MD, Malko DB, Vitreschak AG, Sernova NV, Gelfand MS, Demina IA, Serebryakova MV, Galyamina MA, Vtyurin NN, Rogov SI, Alexeev DG, Ladygina VG, Govorun VM., J. Bacteriol. 193(18), 2011
PMID: 21784942
Complete genome sequence of Mahella australiensis type strain (50-1 BON).
Sikorski J, Teshima H, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Ngatchou-Djao OD, Rohde M, Pukall R, Spring S, Abt B, Goker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP, Lapidus A., Stand Genomic Sci 4(3), 2011
PMID: 21886860
Genomic characterization of methanomicrobiales reveals three classes of methanogens.
Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N., PLoS ONE 4(6), 2009
PMID: 19495416
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1.
Anderson IJ, Sieprawska-Lupa M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Barry K, Saunders E, Han C, Brettin T, Detter JC, Bruce D, Mikhailova N, Pitluck S, Hauser L, Land M, Lucas S, Richardson P, Whitman WB, Kyrpides NC., Stand Genomic Sci 1(2), 2009
PMID: 21304656
Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO.
Parshina SN, Sipma J, Nakashimada Y, Henstra AM, Smidt H, Lysenko AM, Lens PN, Lettinga G, Stams AJ., Int. J. Syst. Evol. Microbiol. 55(Pt 5), 2005
PMID: 16166725
Evolutionary dynamics of Clostridium difficile over short and long time scales.
He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G, Parkhill J., Proc. Natl. Acad. Sci. U.S.A. 107(16), 2010
PMID: 20368420
Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).
Chovatia M, Sikorski J, Schroder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Goker M, Spring S, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA., Stand Genomic Sci 1(3), 2009
PMID: 21304665
The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production.
Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ., Environ. Microbiol. 12(8), 2010
PMID: 21966920
The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.
Seedorf H, Fricke WF, Veith B, Bruggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, Hagemeier C, Thauer RK, Gottschalk G., Proc. Natl. Acad. Sci. U.S.A. 105(6), 2008
PMID: 18218779
Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.
Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Kyrpides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Xing D, Ren N, Wang A, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J., J. Bacteriol. 192(24), 2010
PMID: 20889752
Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis.
Hinse D, Vollmer T, Ruckert C, Blom J, Kalinowski J, Knabbe C, Dreier J., BMC Genomics 12(), 2011
PMID: 21824414
Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198.
Papadimitriou K, Ferreira S, Papandreou NC, Mavrogonatou E, Supply P, Pot B, Tsakalidou E., J. Bacteriol. 194(7), 2012
PMID: 22408241
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.
Feng X, Xu Y, Chen Y, Tang YJ., BMC Syst Biol 6(), 2012
PMID: 22857267
Taxonomic distinction of saccharolytic thermophilic anaerobes: description of Thermoanaerobacterium xylanolyticum gen. nov., sp. nov., and Thermoanaerobacterium saccharolyticum gen. nov., sp. nov.; reclassification of Thermoanaerobium brockii, Clostridium thermosulfurogenes, and Clostridium thermohydrosulfuricum E100-69 as Thermoanaerobacter brockii comb. nov., Thermoanaerobacterium thermosulfurigenes comb. nov., and Thermoanaerobacter thermohydrosulfuricus comb. nov., respectively; and transfer of Clostridium thermohydrosulfuricum 39E to Thermoanaerobacter ethanolicus
Lee YE, Jain MK, Lee C, Zeikus JG., 1993
Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum.
Kosaka T, Uchiyama T, Ishii S, Enoki M, Imachi H, Kamagata Y, Ohashi A, Harada H, Ikenaga H, Watanabe K., J. Bacteriol. 188(1), 2006
PMID: 16352836
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota.
Kosaka T, Kato S, Shimoyama T, Ishii S, Abe T, Watanabe K., Genome Res. 18(3), 2008
PMID: 18218977
Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes.
Tamaru Y, Miyake H, Kuroda K, Nakanishi A, Matsushima C, Doi RH, Ueda M., Microb Biotechnol 4(1), 2011
PMID: 21255373
Petrotoga mobilis sp. nov., from a North Sea oil-production well.
Lien T, Madsen M, Rainey FA, Birkeland NK., Int. J. Syst. Bacteriol. 48 Pt 3(), 1998
PMID: 9734057
Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).
Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP., Stand Genomic Sci 3(3), 2010
PMID: 21304731
Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor.
Goberna M, Insam H, Franke-Whittle IH., Appl. Environ. Microbiol. 75(8), 2009
PMID: 19218417
Fungal volatiles as indicators of food and feeds spoilage.
Schnurer J, Olsson J, Borjesson T., Fungal Genet. Biol. 27(2-3), 1999
PMID: 10441446
Identification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays.
Zheng X, Zheng H, Lan R, Ye C, Wang Y, Zhang J, Jing H, Chen C, Segura M, Gottschalk M, Xu J., PLoS ONE 6(3), 2011
PMID: 21479213
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.
Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Puhler A, Schluter A., J. Biotechnol. 155(1), 2011
PMID: 21329740
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691
UCHIME improves sensitivity and speed of chimera detection.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R., Bioinformatics 27(16), 2011
PMID: 21700674
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
PMID: 19307242
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Price MN, Dehal PS, Arkin AP., Mol. Biol. Evol. 26(7), 2009
PMID: 19377059

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