Fig. 4

Phylogenetic tree of MAGs obtained by per-sample assembly and binning of metagenomic reads. A Phylogenetic tree constructed with the ANI distance matrix generated by using the dRep software. Concentric circles indicate, from inside to outside, the quality of MAGs; producer, cave, and surface origin of the sample; genus and species classification of the MAGs; and importance of the MAGs. Only the 24 most abundant taxa at genus level (or above) are indicated, while the rest are grouped in “Other.” Some taxa are classified in higher taxonomic levels (phylum, family, or order) according to the deep level of taxonomic assignment obtained by using the CAT/BAT software. Indicated species were taxonomically reassigned by building additional phylogenetic trees employing reference genomes (RefSeq database) or other representative genomes from the NCBI. The last circle indicates clusters of interest for cave and producer effects on the microbiome. Only new species within the genera of interest (Brevibacterium, Corynebacterium, Lactobacillus, Tetragenococcus, and Yaniella) were marked with red color on the “species” circle. B Principal coordinate analysis of the MAGs functional composition by level 3 of KEGG Orthology classification. Only functional groups belonging to 09100 Metabolism were employed. Only MAGs of interest due to their importance related to the producer and/or cave influence were employed. Lactobacillus includes all the newly established genera that formerly belonged to the genus Lactobacillus (e.g., Lacticaseibacillus, Lactiplantibacillus)