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FTIR spectroscopy
Microbial strain collection








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

Contact: PD Dr. Mareike Wenning
<mareike.wenning@lgl.bayern.de>

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:

·        
Yeasts
·        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.





News

Paper
High Counts of thermophilic spore Formers in dairy powders originate from persisting strains in processing lines (2020)

Paper
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic (Okt. 2020)

Paper
Are antisense proteins in prokaryotes functional (2020)

Paper
Complementary use of cultivation and high-throughput amplicon sequencing reveals high biodiversity within raw milk microbiota (2020)

Paper
Recommendations for bacterial ribosome profiling experiments based on bioinformatics evaluation of published data (2020)

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OLGenie: Estimating natural selection to predict functional overlapping genes (2020)

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Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk (2020)

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Brevilactibacter flavus gen.nov., sp. nov., a novel bacterium of the family Propionibactericeae isolated form raw milk and dairy products and reclassification of Probioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov. (2020)

Paper
A novel pH-regulated, unusual 603 bp overlapping protein coding gene pop is encoded antisense to ompA in Escherichia coli O157:H7 (EHEC). (2020)

Paper
Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate (2020)

Paper
Pseudomonas saxonica sp.nov. isolated from raw milk and skimmed milk concentrate. (2020)