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Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)

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

FTIR-reference-databases for the identification 
of bacteria and yeasts

Contact: Dr. Etienne Doll

In industrial settings, such as food and pharmaceutical processing lines, the identification of microorganisms is an omnipresent subject. Microbial analyses are crucial for control and assurance of product quality. They aim to determine the microbial status of products or the production environment, enable the risk assessment in case of product damages and reveal potential routes of contamination. Various methods are employed for this purpose. They include classical, phenotypic methods like profiling of sugar utilization and enzymatic activity, or molecular approaches. Easy and affordable techniques are often inaccurate and error-prone, and higher expenses usually accompany precision. Therefore, the demand for an approach that enables reliable results by requiring low expanses is growing.

Fourier-transform Infrared (FTIR) spectroscopy is a simple and affordable method for identification of microorganisms. It is universally applicable and additionally the high degree of automation allows for a high throughput of samples. FTIR-spectroscopy uses the ability of molecules to absorb infrared light in a very specific manner and thereby integrates all information of the complete, biochemical composition of the microbial cell in one spectrum. Infrared spectra of organisms are highly specific and the spectroscopy is therefore often referred to as ‘fingerprinting technique’.

Our group has been pursuing the construction of reference databases for more than 15 years and now provides extensive databases for most microbial groups. The databases contain a wide array of strains from official strain collections, food, and food processing environment, drinks, and the pharmaceutical production environment. The following microbial groups are standardly identified by FTIR-spectroscopy in our group:

·        Gram-positive non-sporeforming bacteria
·         Spore-forming bacteria (mesophilic, thermophilic)
·         Lactic acid bacteria
·         Pseudomonads
·         Acetic acid bacteria
·         Bifidobacteria
·         Clostridia

Additionally, a number of databases were optimized for specific fields of application:

·     Yeasts, beer production (Saccharomyces sensu stricto / sensu lato)
·         Yeasts of clinical relevance
·         Probiotic Saccharomyces cerevisiae, feed production
·         Probiotic lactic acid bacteria, feed production
·         Probiotic Bacillus licheniformis and Bacillus subtilis, feed production

For the development of reference-databases, we apply a large number of methods, covering classical microscopy, biochemical characterizations, specific PCRs, DNA restriction assays and DNA sequencing. Depending on the type of organism and the size of used databases, an interpretation of FTIR-spectra and the identification at species level can be challenging. In those cases artificial neuronal networks that originate from artificial intelligence offer additional support for enhanced data processing.

Using the spectrometers of the company Bruker Optics, the databases can be applied for external analyses. Moreover, the databases are the foundation for microbial identifications in our diagnostic service.


The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth Phase (Dec 2018)

The small RNA RssR regulates myo-inositol degradation by Salmonella enterica (Dec.2018)

Activity of a Holin-Endolysin System in the Insecticidal Pathogenicity Island of Yersinia enterocolitica (2018)

Reprogramming Human Siderocalin to Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus (2018)

Insecticidal Toxicity of Yersinia frederiksenii Involves the Novel Enterotoxin YacT (2018)

Dysfunction, Disease, and the Limits of Selection (2018)

Dynamic Proteome Alteration and Functional Modulation of Human Saliva Induced by Dietary Chemosensory Stimuli (2018)

Genome sequence of the novel virulent bacteriophage PMBT14 with lytic avtivity against Pseudomonas fluorescens DSM 50090 (2018)

The Novel Anaerobiosis-Responsive Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai (Mai 2018)

Thermal treatment of skim milk concentrates in a novel shear-heating device: Reduction of thermophilic spores and physical properties (Febr. 2018)

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)

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

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)

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)

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)

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)