Fig. 4

Heat tree and coverage diagrams produced by Wochenende/Haybaler for urgent clinical metagenome diagnostics. Microbial metagenome of respiratory secretions taken from an individual with inherited immune deficiency who during neutrophil depletion because of bone marrow cell transplantation developed within days a severe pneumonia that was refractory to standard therapeutic measures at the stem cell intensive care unit. Analysis of sequence data sets by the Wochenende pipeline revealed commensals of the oral microbiome as the major members of the microbial communities in the patient’s lungs. These include Lautropia mirabilis as the most dominant bacterium, a species that is known to preferentially replicate in immune deficient individuals [43]. Mycoplasma orale is also considered to be a normal inhabitant of the oral cavity [44]. However, there are cases reported where M. orale causes infections in immunocompromised individuals [45]. Turn-around time from bedside sampling to wet lab processing, sequencing on the Illumina NextSeq platform, data processing by Wochenende and delivery of the report to the clinician was 26 h