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Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems.

Carabeo-Pérez A, Guerra-Rivera G, Ramos-Leal M, Klocke M, Jiménez-Hernández J.

Appl Microbiol Biotechnol. 2019 Aug 16. doi: 10.1007/s00253-019-10052-5. [Epub ahead of print] Review.


Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems.

Jeong D, Klocke M, Agarwal S, Kim J, Choi S, Franco E, Kim J.

Methods Protoc. 2019 May 14;2(2). pii: E39. doi: 10.3390/mps2020039. Review.


Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants.

Heyer R, Schallert K, Siewert C, Kohrs F, Greve J, Maus I, Klang J, Klocke M, Heiermann M, Hoffmann M, Püttker S, Calusinska M, Zoun R, Saake G, Benndorf D, Reichl U.

Microbiome. 2019 Apr 27;7(1):69. doi: 10.1186/s40168-019-0673-y.


Screening of microbial communities associated with endive lettuce during postharvest processing on industrial scale.

Fröhling A, Rademacher A, Rumpold B, Klocke M, Schlüter O.

Heliyon. 2018 Jul 11;4(7):e00671. doi: 10.1016/j.heliyon.2018.e00671. eCollection 2018 Jul.


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. 2018 Jun 19;11:167. doi: 10.1186/s13068-018-1162-4. eCollection 2018.


Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A.

Biotechnol Rep (Amst). 2018 Apr 30;18:e00254. doi: 10.1016/j.btre.2018.e00254. eCollection 2018 Jun.


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. 2018 Jun;102(12):5045-5063. doi: 10.1007/s00253-018-8976-7. Epub 2018 Apr 30. Review.


Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

Hahnke S, Abendroth C, Langer T, Codoñer FM, Ramm P, Porcar M, Luschnig O, Klocke M.

Genome Announc. 2018 Apr 5;6(14). pii: e00030-18. doi: 10.1128/genomeA.00030-18.


Proteiniborus indolifex sp. nov., isolated from a thermophilic industrial-scale biogas plant.

Hahnke S, Langer T, Klocke M.

Int J Syst Evol Microbiol. 2018 Jan 25. doi: 10.1099/ijsem.0.002591. [Epub ahead of print]


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. 2017 Nov 13;10:264. doi: 10.1186/s13068-017-0947-1. eCollection 2017.


Microbial communities involved in biogas production exhibit high resilience to heat shocks.

Abendroth C, Hahnke S, Simeonov C, Klocke M, Casani-Miravalls S, Ramm P, Bürger C, Luschnig O, Porcar M.

Bioresour Technol. 2018 Feb;249:1074-1079. doi: 10.1016/j.biortech.2017.10.093. Epub 2017 Oct 31.


Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.

Abendroth C, Hahnke S, Codoñer FM, Klocke M, Luschnig O, Porcar M.

Genome Announc. 2017 Oct 5;5(40). pii: e00686-17. doi: 10.1128/genomeA.00686-17.


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. 2017 Sep 10;257:178-186. doi: 10.1016/j.jbiotec.2017.05.027. Epub 2017 Jun 6.


Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals.

Jiménez J, Theuerl S, Bergmann I, Klocke M, Guerra G, Romero-Romero O.

Water Sci Technol. 2016;74(4):824-35. doi: 10.2166/wst.2016.170.


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, Liebl W, Pühler A, Schlüter A, Klocke M.

Biotechnol Biofuels. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3. eCollection 2016.


Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.

Klocke M, Wolf DE.

Beilstein J Nanotechnol. 2016 May 17;7:708-20. doi: 10.3762/bjnano.7.63. eCollection 2016.


Reorganisation of a mesophilic biogas microbiome as response to a stepwise increase of ammonium nitrogen induced by poultry manure supply.

Alsouleman K, Linke B, Klang J, Klocke M, Krakat N, Theuerl S.

Bioresour Technol. 2016 May;208:200-204. doi: 10.1016/j.biortech.2016.02.104. Epub 2016 Mar 7.


Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism.

Graf K, Ulrich A, Idler C, Klocke M.

J Appl Microbiol. 2016 Jun;120(6):1479-91. doi: 10.1111/jam.13114. Epub 2016 Apr 4.


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). 2016 Jan 13;3(1). pii: E7. doi: 10.3390/bioengineering3010007.


Impact of surface structure and feed gas composition on Bacillus subtilis endospore inactivation during direct plasma treatment.

Hertwig C, Steins V, Reineke K, Rademacher A, Klocke M, Rauh C, Schlüter O.

Front Microbiol. 2015 Aug 6;6:774. doi: 10.3389/fmicb.2015.00774. eCollection 2015.


Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery.

Goux X, Calusinska M, Lemaigre S, Marynowska M, Klocke M, Udelhoven T, Benizri E, Delfosse P.

Biotechnol Biofuels. 2015 Aug 19;8:122. doi: 10.1186/s13068-015-0309-9. eCollection 2015.


Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor.

Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Pühler A, Klocke M, Schlüter A.

J Biotechnol. 2016 Aug 20;232:38-49. doi: 10.1016/j.jbiotec.2015.08.001. Epub 2015 Aug 6.


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. 2015 Sep;99(18):7791-803. doi: 10.1007/s00253-015-6627-9. Epub 2015 May 22.


Determination of methanogenic pathways through carbon isotope (δ13C) analysis for the two-stage anaerobic digestion of high-solids substrates.

Gehring T, Klang J, Niedermayr A, Berzio S, Immenhauser A, Klocke M, Wichern M, Lübken M.

Environ Sci Technol. 2015 Apr 7;49(7):4705-14. doi: 10.1021/es505665z. Epub 2015 Mar 19.


Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage.

Klang J, Theuerl S, Szewzyk U, Huth M, Tölle R, Klocke M.

Microb Biotechnol. 2015 Sep;8(5):764-75. doi: 10.1111/1751-7915.12263. Epub 2015 Feb 25.


Dissipation signals due to lateral tip oscillations in FM-AFM.

Klocke M, Wolf DE.

Beilstein J Nanotechnol. 2014 Nov 10;5:2048-57. doi: 10.3762/bjnano.5.213. eCollection 2014.


Microbial communities involved in biogas production from wheat straw as the sole substrate within a two-phase solid-state anaerobic digestion.

Heeg K, Pohl M, Sontag M, Mumme J, Klocke M, Nettmann E.

Syst Appl Microbiol. 2014 Dec;37(8):590-600.


Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor.

Hahnke S, Maus I, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A.

J Biotechnol. 2015 Jan 10;193:34-6. doi: 10.1016/j.jbiotec.2014.11.010. Epub 2014 Nov 20.


Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation.

Tomazetto G, Hahnke S, Maus I, Wibberg D, Pühler A, Schlüter A, Klocke M.

J Biotechnol. 2014 Dec 20;192 Pt A:59-61. doi: 10.1016/j.jbiotec.2014.09.011. Epub 2014 Sep 19.


Assessment of mutagenic potential of pyrolysis biochars by Ames Salmonella/mammalian-microsomal mutagenicity test.

Anjum R, Krakat N, Toufiq Reza M, Klocke M.

Ecotoxicol Environ Saf. 2014 Sep;107:306-12. doi: 10.1016/j.ecoenv.2014.06.005. Epub 2014 Jul 20.


Whole genome sequence of Clostridium bornimense strain M2/40 isolated from a lab-scale mesophilic two-phase biogas reactor digesting maize silage and wheat straw.

Hahnke S, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A.

J Biotechnol. 2014 Aug 20;184:199-200. doi: 10.1016/j.jbiotec.2014.05.026. Epub 2014 Jun 4.


Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor.

Hahnke S, Striesow J, Elvert M, Mollar XP, Klocke M.

Int J Syst Evol Microbiol. 2014 Aug;64(Pt 8):2792-7. doi: 10.1099/ijs.0.059691-0. Epub 2014 May 23.


Towards molecular biomarkers for biogas production from lignocellulose-rich substrates.

Lebuhn M, Hanreich A, Klocke M, Schlüter A, Bauer C, Pérez CM.

Anaerobe. 2014 Oct;29:10-21. doi: 10.1016/j.anaerobe.2014.04.006. Epub 2014 Apr 28.


H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments.

Janda JO, Popal A, Bauer J, Busch M, Klocke M, Spitzer W, Keller J, Merkl R.

BMC Bioinformatics. 2014 Apr 27;15:118. doi: 10.1186/1471-2105-15-118.


Impact of abrupt temperature increase on the performance of an anaerobic hybrid bioreactor and its intrinsic microbial community.

Kundu K, Bergmann I, Klocke M, Sharma S, Sreekrishnan TR.

Bioresour Technol. 2014 Sep;168:72-9. doi: 10.1016/j.biortech.2014.01.093. Epub 2014 Jan 30.


Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants.

Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U.

Anaerobe. 2014 Oct;29:59-67. doi: 10.1016/j.anaerobe.2013.11.009. Epub 2013 Dec 3.


Development of a flow-fluorescence in situ hybridization protocol for the analysis of microbial communities in anaerobic fermentation liquor.

Nettmann E, Fröhling A, Heeg K, Klocke M, Schlüter O, Mumme J.

BMC Microbiol. 2013 Dec 4;13:278. doi: 10.1186/1471-2180-13-278.


Carbon source--a strong determinant of microbial community structure and performance of an anaerobic reactor.

Kundu K, Bergmann I, Hahnke S, Klocke M, Sharma S, Sreekrishnan TR.

J Biotechnol. 2013 Dec;168(4):616-24. doi: 10.1016/j.jbiotec.2013.08.023. Epub 2013 Aug 27.


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, Schlüter A, Benndorf D, Heyer R, Rapp E, Pühler A, Reichl U, Klocke M.

Syst Appl Microbiol. 2013 Jul;36(5):330-8. doi: 10.1016/j.syapm.2013.03.006. Epub 2013 May 19.


Occurrence and genetic diversity of Arcobacter spp. in a spinach-processing plant and evaluation of two Arcobacter-specific quantitative PCR assays.

Hausdorf L, Neumann M, Bergmann I, Sobiella K, Mundt K, Fröhling A, Schlüter O, Klocke M.

Syst Appl Microbiol. 2013 Jun;36(4):235-43. doi: 10.1016/j.syapm.2013.02.003. Epub 2013 Apr 3.


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. 2013 Apr 4;6(1):49. doi: 10.1186/1754-6834-6-49.


Characterization of the cultivable microbial community in a spinach-processing plant using MALDI-TOF MS.

Hausdorf L, Mundt K, Winzer M, Cordes C, Fröhling A, Schlüter O, Klocke M.

Food Microbiol. 2013 Jun;34(2):406-11. doi: 10.1016/ Epub 2012 Nov 7.


Thalassic biogas production from sea wrack biomass using different microbial seeds: cow manure, marine sediment and sea wrack-associated microflora.

Marquez GP, Reichardt WT, Azanza RV, Klocke M, Montaño MN.

Bioresour Technol. 2013 Apr;133:612-7. doi: 10.1016/j.biortech.2013.01.082. Epub 2013 Feb 6.


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. 2013 Sep 25;30(6):614-22. doi: 10.1016/j.nbt.2013.01.002. Epub 2013 Jan 29.


Temperature increases from 55 to 75 °C in a two-phase biogas reactor result in fundamental alterations within the bacterial and archaeal community structure.

Rademacher A, Nolte C, Schönberg M, Klocke M.

Appl Microbiol Biotechnol. 2012 Oct;96(2):565-76. doi: 10.1007/s00253-012-4348-x. Epub 2012 Aug 17.


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. 2012 Jul;58(7):917-22. doi: 10.1139/w2012-058. Epub 2012 Jun 12.


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. 2012 Mar;79(3):785-99. doi: 10.1111/j.1574-6941.2011.01265.x. Epub 2011 Dec 20.


Analysis of the bacterial community within carrot wash water.

Hausdorf L, Fröhling A, Schlüter O, Klocke M.

Can J Microbiol. 2011 May;57(5):447-52. doi: 10.1139/W11-013. Epub 2011 May 5.


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