S VIDAL¹, V PERRETEN¹, S RODRIGUEZ CAMPOS<sup>1

1</sup>Institute of Veterinary Bacteriology - Länggass-Str. 122 3001 Bern

Mycotic abortion is a sporadic reproductive problem of dairy cattle all over the world. It can be caused by different fungi, which are also present in the environment. However, the transmission and epidemiology of abortion-associated fungi has not yet been widely studied. In Switzerland, only few infectious agents are examined in routine abortion diagnosis due to the high costs associated with extended spectrum analysis. In order to get new insight into agents causing abortion in cattle, we used next generation sequencing (NGS) to study the population of fungi associated with abortion. Fungal microbiota of 95 samples of abortion material from cattle [placenta (n=73); abomasum (n=22)] has been disclosed using Illumina MiSeq sequencing technology. DNA was extracted with the QIAamp Mini Kit (Qiagen), and amplicon sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region was carried out. Data analysis was performed using the software Qiime, in combination with the reference database UNITE, to define operational taxonomic units (OTUs) and to assign each OTU the taxonomic identity at different taxonomic levels. An average of 34 (SD = 7.5) representative OTUs in placenta samples (55.55% Ascomycota, 8.38% Basidiomycota, 6.28% Neocallimastigomycota, 4.10% Zygomycota and 25.69% other - unidentified - unassigned) and an average of 31 (SD = 5.66) representative OTUs in abomasum samples (57.99% Ascomycota, 15.06% Basidiomycota, 0.29% Neocallimastigomycota, 1.83% Zygomycota and 24.82% other - unidentified - unassigned) were found. In both organs the most representative families were Saccharomycetaceae (19.39% in placenta and 12.28% in abomasum) and Mycosphaerellaceae (12.36% in placenta and 24.02% in abomasum). The results revealed some genera which may play a role in abortion including Aspergillus, Fusarium, Penicillium, Mucor, Candida, Cryptococcus and Mortierella. Moreover, Rhodotorula, Scedosporium and Alternaria, three genera that can cause opportunistic infections in animals and humans were found. Comparison of associated mycobiota with indicative histopathological findings is now necessary to determine which fungi families are involved in abortion.