Hi @Diptaraj
MetaPhlAn 3 does include (micro)eukaryotic species in the database. In particular you can check the list of species in the last database version here: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2
If you are really sure your samples should contain micro eukaryotic species, you could try to run MetaPhlAn changing the --stat_q parameter in order to be more sensitive. This parameter is used when MetaPhlAn calculates the robust average coverage of a species, and defines the trimming of the markers distribution at both ends (more details about this in the following paper: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife). Its default value is 0.2, meaning that you need at least 20% of the markers of a species have to be present in the reads for a species to be detected. Adding to your MetaPhlAn 3 execution the parameter --stat_q 0.1 (or lower) might help in your case.