Successful research with a PhD on bioaerosols

Symposia on this topic held across Germany filled seminar rooms. During those years, the main focus – alongside the detection and defence against airborne biological weapons – was, above all, on investigating the contamination levels in exhaust air. For example, the question arose as to whether exhaust air from poultry farms posed a health risk in addition to causing odour nuisance – a particularly relevant question in Saxony, given its tradition of poultry farming. Investigating this is one of the tasks of the State Operating Company for the Environment and Agriculture (BfUL) in Nossen and the Federal Institute for Occupational Safety and Health (BAUA) in Berlin. To determine the microbiological load, the exhaust air is filtered and the filters are then distributed across various selective culture media in the laboratory. Bacteria that grow must have been present as pathogens in the exhaust air. Quantification is virtually impossible, and anything that does not grow under laboratory conditions cannot be detected.

As Robert Leidenfrost had established modern DNA sequencing using nanopores in Professor Wünschiers’ laboratory whilst working on his Master’s thesis, it seemed obvious to put forward the following bold hypothesis: If the DNA of the germs contained in the exhaust air could be sequenced (i.e. read), these microorganisms could be identified. Wow. When we proposed this to the BfUL and the BAUA, we were met with scepticism: Is the DNA sufficient? Is nanopore sequencing good enough? Is searching genetic databases for DNA sequences similar to the DNA from the filters quick enough? To make matters worse, we did not want to limit ourselves to small genetic markers, but rather analyse – and quantify – the entire DNA. But PD Dr Jäckel and Dr Pöther from the BAUA and Dr Mietke from the BfUL became curious, and we planned a feasibility study – Robert Leidenfrost’s PhD project. Fortunately, we were able to find a partner in the Sächsische Aufbaubank, which awarded Robert a doctoral scholarship. Professor Göttfert from TU Dresden supervised the doctoral programme, as Mittweida University of Applied Sciences does not have its own right to award doctorates.

In January 2018, Robert received four samples from BAUA containing DNA from twelve bacteria unknown to us, each with a different mix. Now things were getting serious: would Robert’s DNA sequencing pipeline, followed by identification and quantification, work? In August 2018, we presented our results at the BAUA in Berlin – and they were quite astonished: one hundred per cent correct. This was promising and paved the way for the key scientific publication based on Robert’s work [1]. We had thus successfully countered the scepticism: yes, the DNA is sufficient; the quality of the sequences is sufficient; the search can be optimised; and the DNA composition is quantifiable. And, unlike the microbiological approach, unidentifiable DNA is at least recorded. Furthermore, our method can also detect viruses in bioaerosols.

[1] Leidenfrost, R. M., Pöther, D.-C., Jäckel, U., & Wünschiers, R. (2020). Benchmarking the MinION: Evaluating long reads for microbial profiling. Sci. Rep., 10(1), 1–10. https://doi.org/10.1038/s41598-020-61989-x

[2] Neubert, K., Zuchantke, E., Leidenfrost, R. M., Wuenschiers, R., Grützke, J., Malorny, B., Brendebach, H., Al Dahouk, S., Homeier, T., Hotzel, H., Reinert, K., Tomaso, H., & Busch, A. (2021). Testing assembly strategies for Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics, 22(1). https://doi.org/10.1186/s12864-021-08115-x

[3] Leidenfrost, R. M., Wappler, N., & Wünschiers, R. (2020). Draft Genome Assembly of Rhodobacter sphaeroides 2.4.1 Substrain H2 from Nanopore Data. Microbiol Resour Announc, 9(29), 1. https://doi.org/10.1128/MRA.00414-20

[4] Leidenfrost, R. M., Bänsch, S., Prudnikow, L., Brenig, B., Westphal, C., & Wünschiers, R. (2020). Analysing the Dietary Diary of a Bumblebee. Front. Plant Sci., 11, 1572. doi.org/10.3389/fpls.2020.00287