Felix Gregor Eikmeyer


Metagenome and metatranscriptome analyses of microbial communities involved in fermentation of primary agricultural products.


Area: polyomics
Project Start: 1.06.2010
Supervisor(s): Dr. Andreas Schlüter, Prof. Dr. Alfred Pühler, Prof. Dr. Volker Wendisch
University: Bielefeld


Felix defended his thesis in February 2016 and is an alumnus of the CLIB-GC.

Project overview

Silaging is a method for conservation of green fodder. Anaerobic conditions and the formation of lactic and other organic acids by epiphytic lactic acid bacteria prevent growth of contaminating microorganisms. Metagenome and metatranscriptome analyses of microbial silaging communities originating from untreated and inoculated silage will be performed to better understand the processes underlying silage formation by identification of key transcripts and organisms and by tracking bacteria used for inoculation.

Metagenome and metatranscriptome analyses of microbial communities involved in fermentation of primary agricultural products.

Publication list

IncH-type plasmid harboring the blaCTX-M-15, blaDHA-1, and qnrB4 genes recovered from animal isolates. Schlüter A, Nordmann P, Bonnin RA, Millemann Y, Eikmeyer FG, Wibberg D, Pühler A, Poirel L (2014) Antimicrobial Agents and Chemotherapy 58(7): 3768–3773.

Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing. Kröber M, Wibberg D, Grosch R, Eikmeyer FG, Verwaaijen B, Chowdhury SP, Hartmann A, Pühler A, Schlüter A (2014) Frontiers in Microbiology 5.

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Wibberg D, Jelonek L, Rupp O, Kröber M, Eikmeyer FG, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A (2013) Journal of Biotechnology 167(2): 142–155.

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, Koenig H, Pühler A, Schlüter A (2013) Journal of Biotechnology 168(4): 734–736.

Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass silaging. Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A (2013) Journal of Biotechnology 167(3): 334–343.

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 (2013) Biotechnology for Biofuels 6(1): 49.

Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges. Shah V, Zakrzewski M, Wibberg D, Eikmeyer FG, Schlüter A, Madamwar D (2013) Microbial Ecology 66(3): 533–550.

The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant’s on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates. Wibberg D, Szczepanowski R, Eikmeyer FG, Pühler A, Schlüter A (2013) Plasmid 69(2): 127–137.

Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-beta-lactamase gene blaVIM-2 from Pseudomonas aeruginosa. Bonnin RA, Poirel L, Nordmann P, Eikmeyer FG, Wibberg D, Pühler A, Schlüter A (2013) Journal of Antimicrobial Chemotherapy 68(5): 1060–1065.

IncP-1 beta plasmids of Comamonas sp and Delftia sp strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet. Stolze Y, Eikmeyer FG, Wibberg D, Brandis G, Karsten C, Krahn I, Schneiker-Bekel S, Viehöver P, Barsch A, Keck M, Top EM, et al. (2012) Microbiology 158(Pt_8): 2060–2072.

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 FG, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A (2012) Journal of Biotechnology 158(4): 248–258.

Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids. Parreira VR, Costa M, Eikmeyer FG, Blom J, Prescott JF (2012) PLoS ONE 7(11): e49753.

Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, 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, Pühler A, et al. (2012) Journal of Bacteriology 194(19): 5487–5488.

Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. Heinl S, Wibberg D, Eikmeyer FG, Szczepanowski R, Blom J, Linke B, Goesmann A, Grabherr R, Schwab H, Pühler A, Schlüter A (2012) Journal of Biotechnology 161(2): 153–166.

The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Eikmeyer FG, Hadiati A, Szczepanowski R, Wibberg D, Schneiker-Bekel S, Rogers LM, Brown CB, Top EM, Pühler A, Schlüter A (In Press) Plasmid 68(1): 13–24.

Sequencing and comparative analysis of IncP-1 alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Szczepanowski R, Eikmeyer FG, Harfmann J, Blom J, Rogers LM, Top EM, Schlüter A (2011) Journal of Biotechnology 155(1): 95–103.


Felix´s project
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