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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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.
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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. doi:10.1371/journal.pone.0014519
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), p 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, pp. 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.

91 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater.
Han G, Shin SG, Cho K, Lee J, Kim W, Hwang S., Environ Sci Pollut Res Int (), 2018
PMID: 29327188
Proteiniborus indolifex sp. nov., isolated from a thermophilic industrial-scale biogas plant.
Hahnke S, Langer T, Klocke M., Int J Syst Evol Microbiol (), 2018
PMID: 29458500
Redundancy of anaerobic digestion microbiomes during disturbances by the antibiotic monensin.
Spirito CM, Daly SE, Werner JJ, Angenent LT., Appl Environ Microbiol (), 2018
PMID: 29500266
Flexible metagenome analysis using the MGX framework.
Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A., Microbiome 6(1), 2018
PMID: 29690922
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
The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels.
Ayginin AA, Pimkina EV, Matsvay AD, Speranskaya AS, Safonova MV, Blinova EA, Artyushin IV, Dedkov VG, Shipulin GA, Khafizov K., Adv Virol 2018(), 2018
PMID: 30158979
Genetic repertoires of anaerobic microbiomes driving generation of biogas.
Grohmann A, Vainshtein Y, Euchner E, Grumaz C, Bryniok D, Rabus R, Sohn K., Biotechnol Biofuels 11(), 2018
PMID: 30250507
Effects of Copper Oxide Nanoparticles on Paddy Soil Properties and Components.
Shi J, Ye J, Fang H, Zhang S, Xu C., Nanomaterials (Basel) 8(10), 2018
PMID: 30332772
Dynamics of microbial community during ensiling direct-cut alfalfa with and without LAB inoculant and sugar.
Zheng ML, Niu DZ, Jiang D, Zuo SS, Xu CC., J Appl Microbiol 122(6), 2017
PMID: 28370869
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
The effect of Mg2+ on digestion performance and microbial community structures in sludge digestion systems.
Liu C, Huang C, Sun X, Li R, Li J, Shen J, Han W, Wang L., Environ Sci Pollut Res Int 24(21), 2017
PMID: 28593543
Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge.
Wilkens C, Busk PK, Pilgaard B, Zhang WJ, Nielsen KL, Nielsen PH, Lange L., Biotechnol Biofuels 10(), 2017
PMID: 28649277
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
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction.
Laehnemann D, Borkhardt A, McHardy AC., Brief Bioinform 17(1), 2016
PMID: 26026159
Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.
Resende JA, Godon JJ, Bonnafous A, Arcuri PB, Silva VL, Otenio MH, Diniz CG., Microb Ecol 71(3), 2016
PMID: 26219266
Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor.
Ma J, Wang Z, Li H, Park HD, Wu Z., Appl Microbiol Biotechnol 100(11), 2016
PMID: 26816093
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
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
Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample.
Stöveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer FG, Pühler A, Schlüter A, Moerschbacher BM., J Biotechnol 201(), 2015
PMID: 25240439
Augmented biogas production from protein-rich substrates and associated metagenomic changes.
Kovács E, Wirth R, Maróti G, Bagi Z, Nagy K, Minárovits J, Rákhely G, Kovács KL., Bioresour Technol 178(), 2015
PMID: 25316194
Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition.
De Francisci D, Kougias PG, Treu L, Campanaro S, Angelidaki I., Bioresour Technol 176(), 2015
PMID: 25460984
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants.
Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A., J Biotechnol 201(), 2015
PMID: 25455016
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 F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A., Biotechnol Biofuels 8(), 2015
PMID: 25688290
Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation.
Chojnacka A, Szczęsny P, Błaszczyk MK, Zielenkiewicz U, Detman A, Salamon A, Sikora A., PLoS One 10(5), 2015
PMID: 26000448
Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.
Theuerl S, Kohrs F, Benndorf D, Maus I, Wibberg D, Schlüter A, Kausmann R, Heiermann M, Rapp E, Reichl U, Pühler A, Klocke M., Appl Microbiol Biotechnol 99(18), 2015
PMID: 25998656
Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany.
Abendroth C, Vilanova C, Günther T, Luschnig O, Porcar M., Biotechnol Biofuels 8(), 2015
PMID: 26097504
Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure.
Sun L, Pope PB, Eijsink VG, Schnürer A., Microb Biotechnol 8(5), 2015
PMID: 26152665
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
Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing.
Wang H, He Q, Chen D, Wei L, Zou Z, Zhou J, Yang K, Zhang H., Appl Microbiol Biotechnol 99(24), 2015
PMID: 26286515
Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation.
Wang Y, Xia Y, Ju F, Zhang T., Appl Microbiol Biotechnol 99(24), 2015
PMID: 26359182
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
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
Multilocus analysis reveals diversity in the genus Tissierella: description of Tissierella carlieri sp. nov. in the new class Tissierellia classis nov.
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
PMID: 24268443
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
PMID: 24633414
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
PMID: 24633443
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
PMID: 24871275
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
PMID: 25012784
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
PMID: 25328537
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
PMID: 23026555
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
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
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
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
PMID: 23506434
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
PMID: 23557021
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
PMID: 23553377
A new framework to accurately quantify soil bacterial community diversity from DGGE.
Lalande J, Villemur R, Deschênes L., Microb Ecol 66(3), 2013
PMID: 23640274
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
PMID: 23728808
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
PMID: 23880441
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
PMID: 24048207
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
PMID: IND500690354
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
PMID: 24184088
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
PMID: 22102576
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
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
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
PMID: 22268671
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
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
Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P., BMC Bioinformatics 13 Suppl 19(), 2012
PMID: 23282463
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
PMID: 21908188
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
PMID: 22022440

74 References

Daten bereitgestellt von Europe PubMed Central.

Production and energetic use of biogas from energy crops and wastes in Germany.
Weiland P., Appl. Biochem. Biotechnol. 109(1-3), 2003
PMID: 12794299
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
The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides.
Bayer EA, Belaich JP, Shoham Y, Lamed R., Annu. Rev. Microbiol. 58(), 2004
PMID: 15487947
Hydrolysis and microbial community analyses in two-stage anaerobic digestion of energy crops.
Cirne DG, Lehtomaki A, Bjornsson L, Blackall LL., J. Appl. Microbiol. 103(3), 2007
PMID: 17714384
Microbial cellulose utilization: fundamentals and biotechnology.
Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS., Microbiol. Mol. Biol. Rev. 66(3), 2002
PMID: 12209002
Ecological consequences of the phylogenetic and physiological diversities of acetogens.
Drake HL, Kusel K, Matthies C., Antonie Van Leeuwenhoek 81(1-4), 2002
PMID: 12448719
Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?
Drake HL, Daniel SL, Kusel K, Matthies C, Kuhner C, Braus-Stromeyer S., Biofactors 6(1), 1997
PMID: 9233536
Anaerobic fermentation of cattle manure: modeling of hydrolysis and acidogenesis.
Myint M, Nirmalakhandan N, Speece RE., Water Res. 41(2), 2006
PMID: 17141822
Energetics of syntrophic cooperation in methanogenic degradation.
Schink B., Microbiol. Mol. Biol. Rev. 61(2), 1997
PMID: 9184013
Conversion of food waste into hydrogen by thermophilic acidogenesis.
Shin HS, Youn JH., Biodegradation 16(1), 2005
PMID: 15727153
Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids.
Sousa DZ, Smidt H, Alves MM, Stams AJ., FEMS Microbiol. Ecol. 68(3), 2009
PMID: 19490126
Life close to the thermodynamic limit: how methanogenic archaea conserve energy.
Deppenmeier U, Muller V., Results Probl Cell Differ 45(), 2008
PMID: 17713742
Methanogenic archaea: ecologically relevant differences in energy conservation.
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R., Nat. Rev. Microbiol. 6(8), 2008
PMID: 18587410
Metabolism of methanogens.
Blaut M., Antonie Van Leeuwenhoek 66(1-3), 1994
PMID: 7747931
The unique biochemistry of methanogenesis.
Deppenmeier U., Prog. Nucleic Acid Res. Mol. Biol. 71(), 2002
PMID: 12102556
Enzymology of one-carbon metabolism in methanogenic pathways.
Ferry JG., FEMS Microbiol. Rev. 23(1), 1999
PMID: 10077852
Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea.
Liu Y, Whitman WB., Ann. N. Y. Acad. Sci. 1125(), 2008
PMID: 18378594
Methanogenesis: genes, genomes, and who's on first?
Reeve JN, Nolling J, Morgan RM, Smith DR., J. Bacteriol. 179(19), 1997
PMID: 9324240
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
Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass.
Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B., Syst. Appl. Microbiol. 31(3), 2008
PMID: 18501543
Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester.
Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A., Environ. Microbiol. 7(8), 2005
PMID: 16011748
Microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16S rRNA and acetate kinase genes.
Shigematsu T, Era S, Mizuno Y, Ninomiya K, Kamegawa Y, Morimura S, Kida K., Appl. Microbiol. Biotechnol. 72(2), 2006
PMID: 16496142
Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste.
Sasaki K, Haruta S, Ueno Y, Ishii M, Igarashi Y., Appl. Microbiol. Biotechnol. 75(4), 2007
PMID: 17334757
Detection of methanogenic Archaea in peat: comparison of PCR primers targeting the mcrA gene.
Juottonen H, Galand PE, Yrjala K., Res. Microbiol. 157(10), 2006
PMID: 17070673
The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill.
Luton PE, Wayne JM, Sharp RJ, Riley PW., Microbiology (Reading, Engl.) 148(Pt 11), 2002
PMID: 12427943
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
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
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
DNA recovery from soils of diverse composition.
Zhou J, Bruns MA, Tiedje JM., Appl. Environ. Microbiol. 62(2), 1996
PMID: 8593035
R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
AUTHOR UNKNOWN, 2008
Applied linear statistical models.
Kutner M, Nachtsheim C, Neter J, Li W., 2005
Systematic artifacts in metagenomes from complex microbial communities.
Gomez-Alvarez V, Teal TK, Schmidt TM., ISME J 3(11), 2009
PMID: 19587772
Artificial and natural duplicates in pyrosequencing reads of metagenomic data.
Niu B, Fu L, Sun S, Li W., BMC Bioinformatics 11(), 2010
PMID: 20388221
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
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
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18039703
Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19900971
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17965431
Database resources of the National Center for Biotechnology Information.
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18940862
Flexible sequence similarity searching with the FASTA3 program package.
Pearson WR., Methods Mol. Biol. 132(), 2000
PMID: 10547837
PHYLIP - Phylogeny Inference Package (Version 3.2).
Felsenstein J., 1989
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
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.
Garcia-Vallve S, Guzman E, Montero MA, Romeu A., Nucleic Acids Res. 31(1), 2003
PMID: 12519978
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H., Nucleic Acids Res. 36(16), 2008
PMID: 18660515
ARB: a software environment for sequence data.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH., Nucleic Acids Res. 32(4), 2004
PMID: 14985472
The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions.
Dollhopf SL, Hashsham SA, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM., Appl. Microbiol. Biotechnol. 56(3-4), 2001
PMID: 11549033
Microbial diversity of a mesophilic hydrogen-producing sludge.
Fang HH, Zhang T, Liu H., Appl. Microbiol. Biotechnol. 58(1), 2002
PMID: 11833529
Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose.
Fernandez AS, Hashsham SA, Dollhopf SL, Raskin L, Glagoleva O, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM., Appl. Environ. Microbiol. 66(9), 2000
PMID: 10966429
Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions.
Li T, Mazeas L, Sghir A, Leblon G, Bouchez T., Environ. Microbiol. 11(4), 2008
PMID: 19128320
Modular arrangement of a cellulosomal scaffoldin subunit revealed from the crystal structure of a cohesin dyad.
Noach I, Levy-Assaraf M, Lamed R, Shimon L, Frolow F., 2010
Clostridium hastiforme is a later synonym of Tissierella praeacuta.
Bae JW, Park JR, Chang YH, Rhee SK, Kim BC, Park YH., Int. J. Syst. Evol. Microbiol. 54(Pt 3), 2004
PMID: 15143047
Effect of nitrite on a thermophilic, methanogenic consortium from an oil storage tank.
Kaster KM, Voordouw G., Appl. Microbiol. Biotechnol. 72(6), 2006
PMID: 16568311
Effect of high temperature on bacterial community dynamics in anaerobic acidogenesis using mesophilic sludge inoculum.
Kim W, Hwang K, Shin SG, Lee S, Hwang S., Bioresour. Technol. 101 Suppl 1(), 2009
PMID: 19362824
Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water.
Lee YJ, Romanek CS, Mills GL, Davis RC, Whitman WB, Wiegel J., Int. J. Syst. Evol. Microbiol. 56(Pt 9), 2006
PMID: 16957104
Garciella nitratireducens gen. nov., sp. nov., an anaerobic, thermophilic, nitrate- and thiosulfate-reducing bacterium isolated from an oilfield separator in the Gulf of Mexico.
Miranda-Tello E, Fardeau ML, Sepulveda J, Fernandez L, Cayol JL, Thomas P, Ollivier B., Int. J. Syst. Evol. Microbiol. 53(Pt 5), 2003
PMID: 13130040
Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe.
Plugge CM, Balk M, Zoetendal EG, Stams AJ., Int. J. Syst. Evol. Microbiol. 52(Pt 2), 2002
PMID: 11931148
Approaches to the study of the systematics of anaerobic, gram-negative, non-sporeforming rods: current status and perspectives.
Shah HN, Olsen I, Bernard K, Finegold SM, Gharbia S, Gupta RS., Anaerobe 15(5), 2009
PMID: 19695337
Alkaliflexus imshenetskii gen. nov. sp. nov., a new alkaliphilic gliding carbohydrate-fermenting bacterium with propionate formation from a soda lake.
Zhilina TN, Appel R, Probian C, Brossa EL, Harder J, Widdel F, Zavarzin GA., Arch. Microbiol. 182(2-3), 2004
PMID: 15340778
Characterization of an anaerobic population digesting a model substrate for maize in the presence of trace metals.
Pobeheim H, Munk B, Müller H, Berg G, Guebitz G., 2010
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum).
Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG, Ragsdale SW., Environ. Microbiol. 10(10), 2008
PMID: 18631365
Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors.
Schnürer A, Zellner G, Svensson B., 1999
A mathematical theory of communication.
Shannon CE., 1948

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