An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum S, Jaenicke S, Fracowiak J, Pühler A, Schlüter A (2016)
Journal of Biotechnology 231: 268-279.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Abstract / Bemerkung
To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins. Copyright 2016 Elsevier B.V. All rights reserved.
Biogas microbial community; Contig context information; Database impact on protein identification; Integrated metagenome/-proteome study; Taxonomic profile
Journal of Biotechnology
Page URI


Ortseifen V, Stolze Y, Maus I, et al. An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology. 2016;231:268-279.
Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., et al. (2016). An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology, 231, 268-279. doi:10.1016/j.jbiotec.2016.06.014
Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., Fracowiak, J., Pühler, A., and Schlüter, A. (2016). An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology 231, 268-279.
Ortseifen, V., et al., 2016. An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology, 231, p 268-279.
V. Ortseifen, et al., “An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant”, Journal of Biotechnology, vol. 231, 2016, pp. 268-279.
Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., Fracowiak, J., Pühler, A., Schlüter, A.: An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology. 231, 268-279 (2016).
Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan, Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, and Schlüter, Andreas. “An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant”. Journal of Biotechnology 231 (2016): 268-279.

3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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
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
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

58 References

Daten bereitgestellt von Europe PubMed Central.

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data
Alberti, BMC Genomics 15(1), 2014
Microbial ecology of anaerobic digesters: the key players of anaerobiosis
Ali, Sci. World J. (), 2014
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
HTSeq--a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W., Bioinformatics 31(2), 2014
PMID: 25260700
The roles of CRISPR-Cas systems in adaptive immunity and beyond
Barrangou, Curr. Opin. Immunol. 32C(January), 2015
Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J., Genome Biol. 13(12), 2012
PMID: 23259615
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, Puhler A, Schluter A, Sczyrba A., Gigascience 4(), 2015
PMID: 26229594
Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH., Nat. Methods 12(1), 2014
PMID: 25402007
Pullulan degrading enzymes of bacterial origin.
Doman-Pytka M, Bardowski J., Crit. Rev. Microbiol. 30(2), 2004
PMID: 15239382
Purification and properties of D-glycerate 3-kinase from Escherichia coli.
Doughty CC, Hayashi JA, Guenther HL., J. Biol. Chem. 241(3), 1966
PMID: 5325263
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease
Erickson, PLoS One 7(), 2012
Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea.
Garcia JL, Patel BK, Ollivier B., Anaerobe 6(4), 2000
PMID: 16887666
Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass.
Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M., Can. J. Microbiol. 58(7), 2012
PMID: 22690648
Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation.
Hanreich A, Schimpf U, Zakrzewski M, Schluter A, Benndorf D, Heyer R, Rapp E, Puhler A, Reichl U, Klocke M., Syst. Appl. Microbiol. 36(5), 2013
PMID: 23694815
Metaproteome analysis of the microbial communities in agricultural biogas plants.
Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U., N Biotechnol 30(6), 2013
PMID: 23369865
Metaproteomics of complex microbial communities in biogas plants.
Heyer R, Kohrs F, Reichl U, Benndorf D., Microb Biotechnol 8(5), 2015
PMID: 25874383
Integrative analysis of environmental sequences using MEGAN4.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC., Genome Res. 21(9), 2011
PMID: 21690186
Gene and translation initiation site prediction in metagenomic sequences.
Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC., Bioinformatics 28(17), 2012
PMID: 22796954
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing
Jaenicke, PLoS One 6(), 2011
Analysis of the metagenome from a biogas-producing microbial community by means of bioinformatics methods
Jaenicke, 2011
KEGG as a reference resource for gene and protein annotation
Kanehisa, Nucleic Acids Res. 4(44(D1)), 2016
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
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
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
An integrative study of a meromictic lake ecosystem in Antarctica.
Lauro FM, DeMaere MZ, Yau S, Brown MV, Ng C, Wilkins D, Raftery MJ, Gibson JA, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Thomas T, Cavicchioli R., ISME J 5(5), 2010
PMID: 21124488
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943
Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea.
Liu Y, Whitman WB., Ann. N. Y. Acad. Sci. 1125(), 2008
PMID: 18378594
Stimulus perception in bacterial signal-transducing histidine kinases.
Mascher T, Helmann JD, Unden G., Microbiol. Mol. Biol. Rev. 70(4), 2006
PMID: 17158704
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2T, related to dominant methanogens in biogas-producing plants
Maus, J. Biotechnol. 201(), 2014
Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment
Maus, J. Biotechnol. (), 2016
Methanogenic population structure in a variety of anaerobic bioreactors.
McHugh S, Carton M, Mahony T, O'Flaherty V., FEMS Microbiol. Lett. 219(2), 2003
PMID: 12620635
Recombinant bacterial amylopullulanases: developments and perspectives.
Nisha M, Satyanarayana T., Bioengineered 4(6), 2013
PMID: 23645215
Interactive metagenomic visualization in a Web browser
Ondov, BMC Bioinf. 12(1), 2011
Crystal structure of an efficacious gonococcal adherence inhibitor: an enolase from Lactobacillus gasseri.
Raghunathan K, Harris PT, Spurbeck RR, Arvidson CG, Arvidson DN., FEBS Lett. 588(14), 2014
PMID: 24859038
An iterative workflow for mining the human intestinal metaproteome.
Rooijers K, Kolmeder C, Juste C, Dore J, de Been M, Boeren S, Galan P, Beauvallet C, de Vos WM, Schaap PJ., BMC Genomics 12(), 2011
PMID: 21208423
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
A proteomic fingerprint of dissolved organic carbon and of soil particles.
Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED., Oecologia 142(3), 2004
PMID: 15449171
Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions
Stolze, Biotechnol. Biofuels 8(14), 2015
Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture
Tanca, PLoS One 8(), 2013
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
Recent advances in the formation of the bacterial peptidoglycan monomer unit
van, Nat. Prod. Rep. 18(), 2001
Marine metaproteomics: current status and future directions.
Wang DZ, Xie ZX, Zhang SF., J Proteomics 97(), 2013
PMID: 24041543
The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism.
Wendler S, Hurtgen D, Kalinowski J, Klein A, Niehaus K, Schulte F, Schwientek P, Wehlmann H, Wehmeier UF, Puhler A., J. Biotechnol. 167(2), 2012
PMID: 22944206
Metaproteomics provides functional insight into activated sludge wastewater treatment
Wilmes, PLoS One 3(), 2008
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
Methanogenic Community Dynamics during Anaerobic Utilization of Agricultural Wastes.
Ziganshin AM, Ziganshina EE, Kleinsteuber S, Proter J, Ilinskaya ON., Acta Naturae 4(4), 2012
PMID: 23346384


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 27312700
PubMed | Europe PMC

Suchen in

Google Scholar