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Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)

Abteilung Mikrobiologie
Technische Universität München
Weihenstephaner Berg 3
D-85350 Freising

Biodiversity of microbial populations in industrial habitats

Group leader: Dr. Mareike Wenning

 The focus of our research is the microbiota of different habitats like raw milk and products thereof, wine or the pharmaceutical environment. We are analysing the biodiversity as well as shifts and stabilities of microbial populations at both species and strain level. Of further interest are microorganisms harbouring a particular potential for food spoilage such as tolerance to refrigeration temperatures or production of enzymes.  

A second focus is the description of novel hitherto unknown species and genera, which are frequently found in biodiversity studies. The new isolates are characterised by molecular, biochemical and chemotaxonomic techniques and are integrated into bacterial systematics. In addition, we are using the Next Generation Sequencing technology for generating whole genomes of bacteria used for conducting phylogenetic analyses. 


Our Team

Dr. Mareike Wenning                                   Gruppenleitung
Dr. Genia Lücking                                         Projektleitung
Dr. Etienne Doll                                            wissenschaftliche Mitarbeiterin

M.Sc. Christopher Huptas                            Doktorand
M.Sc. Anna Dettling                                      Doktorandin
M.Sc. Christopher Maier                               Doktorand
M.Sc. Annemarie Siebert                              Doktorandin

Charon Fuhrmann                                         technische Angestellte
Inge Celler                                                     technische Angestellte
Angela Felsl                                                   technische Angestellte
Patrick Schiwek                                             technischer Angestellter

Current Research Projects

Regulation of peptidase production in Pseudomonas, AiF-FV 18326 N (Dr. Genia Lücking, M.Sc. Christopher Maier)

Thermophilic spore-formers in milk powder, AiF-FV 18356 N (M.Sc. Anna Dettling)

Description and definition of bacterial species on the basis of whole genome sequences (M.Sc. Christopher Huptas) 

Farm specific raw milk microbiota (M.Sc. Annemarie Siebert, Dr. Mareike Wenning) 

Finished Research Projects

2017  Thermophilic spore-formers in milk powder

2017  Psychrotolerant spore-formers in ESL milk

2014   Heat-stable microbial enzymes in raw materials of the dairy industry
            - quality control, development of a testing system and technological

Analysis of natural site-specific yeast populations in wine yards 
           and their importance for spontaneously fermented wine

2011   Microbial biodiversity in air and pharmaceutical products plants

2011    Identification of pathogenic yeasts from humans

2009    Microbiota of raw and processed milk
2009    Identification and differentiation of yeast occurring in the brewing 

2009    Differentiation of probiotic bacilli and lactic acid bacteria used as
            feed additives

2007    Differentiation of probiotic and ubiquitous yeast from animal feed

2007    Precise and simplified identification of microbial FTIR spectra for 
            quality assurance in food processing companies


Oguntoyinbo FA, Cnockaert M, Cho GS, Kabisch J, Neve H, Boeckelmann W, Wenning M, Franz CMAP, Vandamme P (2018) Halomonas nigrificans sp. nov., isolated from cheese. Int J Syst Evol Microbiol 68(1): 371-6

Wedel  C, Wunsch A, Wenning M, Dettling A, Kayser K-H, Lehner W-D, Hinrichs J (2018) Thermal treatment of skim milk concentrates in a novel shear-heating device: Reduction of thermophilic spores and physical properties. Food Res Int 107:19-26.

Reich C, Wenning M, Dettling A, Luma KE, Hinrichs J (2017) Thermal resistance of vegetative thermophilic spore forming bacilli in skim milk isolated from dairy environments. Food Control 82:114-120.

Koob J, Jacob F, Wenning M, Hutzler M (2017) Lactobacillus cerevisiae sp. nov., isolated from a spoiled brewery sample. Int. J Syst Evol Microbiol 67(9): 3452-3457.

Loscar ME, Schmid, Huptas C, Wenning M and Sieber V (2016) Draft genome sequence of Lysinibacillus xylanilyticus SR-86. Genome Announc 16:01317-16

Schmid J, Huptas C and Wenning M (2016) Draft genome of the xanthan Producer Xanthomonas campestris LMG 8031. Genome Announc 16:e01069-16

Stoeckel M, Lidolt M, Stressler T, Fischer L, Wenning M and Hinrichs J (2016). Heat stability of endogenous milk plasmin and peptidases from Pseudomonas: a challenge in the production of UHT milk products. Int Dairy 60:250-61.

Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F,
Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B and Clavel T (2016) The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 1(10):16131, doi:10.1038/nmicrobiol.2016.131.

Huptas C, Scherer S and Wenning M (2016)
Optimized Illumina PCR-free Library Preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly, BMC Research Notes 9:269. 

von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M, Stressler T, Fischer L, Hinrichs J, Scherer S and Wenning M (2016)
Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow’s milk. Int J Syst Evol Microbiol, 66:163–1173.

Stoeckel M, Friedl N, Achberger V, Lidolt M, Glück C, Krewinkel M, Stressler T, von Neubeck M, Wenning M, Scherer S, Fischer L and Hinrichs J
Growth of Pseudomonas weihenstephanensis, Pseudomonas proteolytica and Pseudomonas sp. in raw milk: Impact of residual heat-stable enzyme activity on stability of UHT milk during shelf-life. Int Dairy J 59:20-28.

Glück C,
Rentschler E, Krewinkel M, Merz M, von Neubeck M, Wenning M,  Scherer S, Stoeckel M, Hinrichs J,  Stressler T and Fischer L (2016) Thermostability of peptidases secreted by raw milk associated microorganisms. Int Dairy J 56:186-197.

Kabisch J, Erl-Höning C, Wenning M, Böhnlein C, Gareis M, Pichner R (2016)
Spoilage of vacuum-packed beef by the yeast Kazachstania psychrophila. Food Microbiol 53:15-23

von Neubeck M, Baur C, Krewinkel M, Stoeckel M, Kranz B, Stressler T, Fischer L, Hinrichs J, Scherer S and Wenning M (2015) Biodiversity of refrigerated raw mild microbiota and their enzymatic spoilage potential. Int. J Food Microbiol. 211:57-65

Krewinkel M, Baur C, Kranz B, von Neubeck M, Wenning M, Scherer S, Stoeckel M, Hinrichs J and Fischer L (2016) A sensitive and robust method for direct determination of lipolytic activity in natural milk environment. Food Anal Methods 9:646-655

Müller A, Huptas C, Wenning M, Schmidt H and Weiss A (2015)
Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, isolated from South Tyrolean Ham. Genome Announc 14:e00456-15

Baur C, Krewinkel M, Kutzli I, Kranz B, von Neubeck M, Huptas C, Wenning M, Scherer S, Stoeckel M, Hinrichs J, Stressler T and Fischer L (2015) Isolation and characterisation of a heat-restistant peptidas from Pseudomonas panacis withstanding General UHT processes. Int.Dairy J 49:46-55

Baur C, Krewinkel M, Kutzli I, Kranz B, von Neubeck M, Scherer S, Stoeckel M, Hinrichs J, Stressler T and Fischer L (2015) Quantification of the proteolytic and lipolytic activity of microorganisms isolated from raw milk. Int.Dairy J 49:23-29

Kläring K, Just S, Lagkouvardos I, Hanske L, Haller D, Blaut M, Wenning M and Clavel T (2015) Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the Family Lachnospiraceae isolated from the mouse gut. IJSEM 65:870-8

Schabauer L, Wenning M, Huber I and Ehrling-Schulz M (2014) Novel physico-chemical diagnostic tools for high throughput identification of bovine Mastitis associated gram-positive, catalase-negative cocci. BMC VetRes 10:156

Wenning M, Breitenwieser F, Konrad R, Huber I, Busch U and Scherer S (2014) Identification and differentiation of food-related bacteria: a comparison of FTIR spectroscopy and MALDI-TOF mass spectrometry. J Microbiol Methods 103:44-52

Daniel H, Moghaddas Gholami A, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P, Rothballer M, Walker A, Böhm C, Binder U, Wenning M, Skerra A, Wagner M, Blaut M, Schmitt-Kopplin P, Kuster B, Haller D and Clavel T:  (2014) High fat diets alters gut microbiota physiology in mice. ISME J 8:295-308

Kabisch J, Höning C, Böhnlein C, Pichner R, Gareis M, Wenning M (2013) Kazachstania psychrophila sp.nov., a novel psychrophilic yeast isolated from vacuum-packed beef. Antonie Van Leeuwenhoek 104:925-931

Seiler H and Wenning M  (2013) Virgibacillus halotolerans sp. nov., isolated from a dairy product. Int J Syst Evol Microbiol 63:3358-3363

Wenning M and Scherer S (2013) Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method. Appl Microbiol Biotechnol 97:7111-7120

Clavel T, Charrier C, Wenning M and Haller D (2013) Parvibacter ceacicola gen.nov., sp.nov., a bacterium of the family Coriobacteriaceae isolated from the caecum of a mouse. Int J Syst Evol Microbiol 63:2642-2648

Grunert T, Wenning M, Barbagelata MS, Fricker M, Sordelli DO, Buzzola F and Ehling-Schulz M (2013) Rapid and reliable identification of Staphylococcus aureus capsular serotypes by means of artificial neural network-assisted Fourier-Transform Infrared Spectroscopy. J Clin Microbiol 51:2261-2266

Seiler H, Wenning M and Scherer S (2013) Domibacillus robiginosus gen. nov., sp. nov. isolated from a pharmaceutical clean room. Int J Syst Evol Microbiol 63:2054-2061.

Seiler H, Scherer S and Wenning M (2013) Lysinibacillus meyeri sp. nov., isolated from a medical practice. Int J Syst Evol Microbiol 63:1512-18.

Seiler H, Wenning M, Schmidt V and Scherer S (2013) Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site. Int J Syst Evol Microbiol 63:867-72.

Rieser G, Scherer S, Wenning M (2013) Micrococcus cohnii sp. nov., isolated from air of a medical practice. Int.J Syst Evol Microbiol 63:80-85

Rieser G, Scherer S, Wenning M (2012) Naumannella halotolerans gen. nov., sp. nov., a new Gram-positive coccus of the family Propionibacteriaceae isolated from a pharmaceutical clean room and from food. Int J Syst Evol Microbiol 63:3042-48

Schmidt VSJ, Kaufmann V, Kulozik U, Scherer S, Wenning M Microbial biodiversity, quality and shelf life of microfiltered and pasteurized extended shelf life (ESL) milk form Germany, Austria and Switzerland. Int J Food Microbiol 154:1-9

Schmidt VSJ, Wenning M, Scherer S  Sphingobacterium lactis sp.nov. and Sphingobacterium alimentarium sp.nov., isolated from raw milk and the dairy environment. Int. J Syst Evol Micobiol 62:1506-1511

Seiler H, Schmidt V, Wenning M and Scherer S  Bacillus kochii sp.nov.; isolated from foods and a pharmaceutical manufacturing site. Int J Syst Evol Microbiol 62:1093-1098

Gulitz A, Stadie J, Wenning M, Ehrmann MA and Vogel R  (2011) The microbial diversity of water kefir. Int J Food Microbiol 151:284-288.

Büchl NR, Hutzler M, Mietke-Hofmann H, Wenning M and Scherer S (2010) Differentation of probiotic and environmental Saccharomyces cerevisiae strains in animal feed. J.Appl. Microbiol.109:783-791.

Clavel T, Duck W, Charrier C, Wenning M, Elson C and Haller D (2010) Enterorhabdus caecimuris sp.nov., a member of the family Coriobacteriaceae isolated from a mouse model of spontaneous colitis, and emended description of the genus Enterorhabdus Clavel et al. 2009. Int J Syst Evol Microbiol 60:1527-1531.

Wenning M, Büchl NR and Scherer S (2010) Species and strain identification of lactic acid bacteria using FTIR spectroscopy and artificial neural networks. J Biophoton 3:493-505.

Wenning M, Rieser G, Scherer S, von Brehmer S und Schuffenhauer G (2010) Rapid, simple and cost-efficient environmental monitoring of microorganisms by Fourier-transform infrared spectroscopy. In: Moldenhauer J (ed) Environmental Monitoring - A Comprehensive Handbook Vol.4 DHI Publishing LLC, River Grove, 203.221.

Clavel T, Charrier C, Braune A, Wenning M, Blaut M and Haller D (2009) Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov. Int J Syst Evol Microbiol 59:1805-12.

Schmidt VSJ, Mayr R, Wenning M, Glöckner J, Busse HJ Scherer S (2009) Bavariicoccus seileri gen. nov., sp. nov., isolated from surface and smear water of German red smear soft cheese. Int J Syst Evol Microbiol, 59:2437-2443.

Büchl NR, Wenning M, Seiler H, Mietke-Hofmann H, Scherer S (2008) Reliable identification of closely related Issatchenkia and Pichia species using artificial neural network analysis of Fourier-transform infrared spectra. Yeast 25:787-98.

Wenning M, Scherer S, Naumann D (2008) Infrared spectroscopy in the identification of micro-organisms. In: Diem M, Griffith PR, Chalmers JM (eds) Vibrational spectroscopy for medical diagnosis. John Wiley & Sons, Ltd., Chichester, 71-96.

Rebuffo-Scheer CA, Dietrich J, Wenning M, Scherer S (2008) Identification of five Listeria species based on infrared spectra (FTIR) using macrosamples is superior to a microsample approach. Anal Bioanal Chem, 390:1629-35.

Wenning M, Seiler H, Scherer S (2007) Auch Bakterien haben Fingerabdrücke: Identifizierung von Mikroorganismen in der Lebensmittelindustrie mittels FTIR-Spektroskopie. dmz 12:24-27.

Santivarangkna C, Wenning M, Foerst P, Kulozik U (2007) Damage of cell envelope of Lactobacillus helveticus during vacuum drying. J. Appl. Microbiol. 102:748-756.

Rebuffo CA, Schmitt J, Wenning M, von Stetten F, Scherer S (2006) Reliable and rapid identification of Listeria monocytogenes and Listeria Species by artificial neural network-based Fourier transform infrared spectroscopy. Appl. Environ. Microbiol. 72:994-1000.

Wenning M, Theilmann V, Scherer S. (2006) Rapid analysis of two food-borne microbial communities at the species level by Fourier-transform infrared microspectroscopy. Environ. Microbiol. 8:848-857. 

Wenning M, Seiler H, Scherer S (2002) Fourier-Transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Appl. Environ. Microbiol. 68:4717-4721. 


, AiF-FV 15047 N: „Prozessoptimierung zur Herstellung von länger haltbarer Frischmilch (ESL) unter Verwendung von thermischen und Membranverfahren.

2007, AiF-FV 14126 N: Präzise und vereinfachte Identifizierung von mikrobiellen FTIR-Spektren zur Qualitätssicherung in Lebensmittel verarbeitenden Betrieben.

2003, AiF-FV 12634 N: Diagnostik von Mikroorganismen durch mikroskopunterstützte FTIR-Spektroskopie: Schnelle mikrobielle Populationsanalysen bei Lebensmitteln.

2000, AiF-FV 11627 N: Schnellnachweis von technologisch wichtigen Bakterien durch FTIR-Spektroskopie zur Qualitätssicherung in milchverarbeitenden Betrieben.


Innovationspreis für Siegfried Scherer

Otto-von-Guericke Forschungspreis für Siegfried Scherer

A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting (2018)


Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection (2017)


Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq-ryhB encodes the regulatory RNA RyhB and a Peptide, RyhP. (2017)

Complete circular genome sequence and temperature independent adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698 (2017)

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai Genome (2017)

High binding affinity of repressor IolR avoids costs of untimely induction of myo-inositol utilization by Salmonella Typhimurium (2017)

Genetic characterization of the Galactitol utilization pathway of Salmonella enterica serovar Typhimurium. (2017)

Heat stability of indigenous milk plasmin and peptidases from Pseudomonas: a challenge in the production of ultra-high temperature milk products (2016)

Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination (2017)

Bakterieller Stoffwechsel als Pathogenitätsfaktor (2016)

Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation. (2016)

Hysteresis in myo-inositol utilization by Salmonella Typhimurium (2016)

Probiotic Enterococcus faecalis Symbioflor® down regulates virulence genes of EHEC in vitro and decrease pathogenicity in a Caenorhabditis elegans model (2017)

Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86 (Nov. 2016)

Permanent colonization of creek sediments, creek water and limnic water plants by four Listeria species in low population densities (November 2016)

Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031 (Oktober 2016)

Comparative Bioinformatics and Experimental Analysis of the Intergenic Regulatory Regions of Bacillus cereus hbl and nhe Enterotoxin Operons and the Impact of CodY on Virulence Heterogeneity (Mai 2016)

Regulation of fucose and 1,2-propanediol utilization by Salmonella enterica serovar Typhimurium (März 2016)

Acidified nitrite inhibits proliferation of Listeria monocytogenes - Transcriptional analysis of a preservation method (März 2016)

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

A sensitive and robust method for direct determination of lipolytic activity in natural milk environment (März 2016, online first)

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting (Dez. 2015)

Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe (Nov. 2015)

Chemodiversity of cereulide, the emetic Toxin of Bacillus cereus (2015)