Fig 1.
Taxonomic profile of Eukaryote genera identified by MEGAN metagenome analyzer across coffee fermentation samples.
The bar plot in the x-axis shows the relative abundance (log₂-transformed) of each genus detected in metagenomic datasets, based on MEGAN metagenome analyzer taxonomic assignments. Each facet represents a different genus (Taxon), with bar heights corresponding to the abundance (number of scaffolds per taxa) per sample. Colors correspond to individual fermentation samples (y-axis).
Fig 2.
Maximum-likelihood phylogenomic tree of Saccharomycotina constructed from 832 conserved single-copy orthologous proteins across representative genomes.
Protein loci were selected based on their presence in at least 50% of the analyzed taxa, and paralogs were excluded to ensure accurate gene representation. The tree recapitulates the latest class-level taxonomy within Saccharomycotina, including nine major classes such as Lipomycetales, Trigonopsidales, and Saccharomycetales. Ultrafast bootstrap (UFB) support values are shown in respective branches, with most class and family clades receiving full support (UFB support = 100). Notable exceptions include the Saccharomycetes clade (UFB support = 97), a split within Debaryomycetaceae (internal node UFB support = 61). Vertical bars indicate the taxonomic boundaries of families.
Fig 3.
Species-level phylogenomic placement of yeast MAGs within the family Pichiaceae.
The tree was inferred from a concatenated alignment of 832 conserved single-copy orthologs and includes reference genomes alongside yeast MAGs recovered from coffee fermentation metagenomes. All nodes relevant to species-level resolution are supported by ultrafast bootstrap (UFB) values of 100. Nine MAGs clustered tightly with the Pichia kluyveri reference genome (GCA_030062975), forming a monophyletic clade with very short intra-clade branch lengths (0.0008–0.0098) and a small genetic distance to the reference (0.0070), supporting their conspecific identity. The boundaries of the Pichia genus are highlighted in red, and MAG labels are shown in blue.
Fig 4.
Phylogenomic placement of yeast MAGs within the class Saccharomycetes, focusing on the families Saccharomycodaceae and Saccharomycetaceae.
The tree was constructed from a concatenated alignment of 832 conserved single-copy orthologs, including yeast MAGs recovered from coffee fermentation metagenomes and publicly available reference genomes. Six MAGs clustered within the genus Hanseniaspora (Saccharomycodaceae) in two well-supported clades (UFB support = 100). One clade grouped with H. opuntiae, with short branch lengths. The second clade, sister to H. meyeri, H. clermontiae, H. nectarophila, and H. uvarum, showed intra-clade distances of 0.0044–0.0234 and inter-clade distances of 0.032–0.077, suggesting the presence of a potentially novel species. Two additional MAGs clustered with Torulaspora delbrueckii (Saccharomycetaceae), forming a distinct, well-supported clade. MAGs are labeled in blue; genus boundaries are highlighted with colored lines.
Fig 5.
Phylogenomic placement of yeast MAGs within the order Serinales, focusing on the family Debaryomycetaceae and the genus Kurtzmaniella.
The tree was inferred from a concatenated alignment of 832 conserved single-copy orthologs, including MAGs recovered from coffee fermentation metagenomes and relevant reference genomes. Three MAGs clustered within the genus Kurtzmaniella, forming a strongly supported monophyletic clade (UFB support = 100). This clade was most closely related to the Kurtzmaniella quercitrusa reference genome (GCA_030570095). Two additional MAGs, CF02scaffolds_bin_4 and CF14scaffolds_bin_31, also fell within Debaryomycetaceae but did not group within well characterized genera. CF02scaffolds_bin_4 clustered with Candida oleophila (UFB support = 100) but was separated by a relatively long branch (0.1082), while CF14scaffolds_bin_31 clustered with Candida corydali (UFB support = 100) with a branch length of 0.0386, forming a broader clade with Candida sojae. Due to their genetic distance and unresolved placement, both were conservatively labeled as Debaryomycetaceae sp. MAGs are shown in blue; genus boundaries are marked with colored lines.
Fig 6.
Visualization of scaffold coverage and length to estimate the relative abundance of yeast MAGs across coffee fermentation samples.
Each point represents a contig and is color-coded according to its species-level taxonomic assignment based on phylogenomic analysis. Contigs not assigned to yeast MAGs are shown in gray. Pichia kluyveri MAGs are highlighted in red, Hanseniaspora opuntiae in dark green, other Hanseniaspora sp. in green, Torulaspora delbrueckii in orange, Kurtzmaniella in blue, Debaryomycetaceae sp. near Candida corydali in cyan, and Debaryomycetaceae sp. near Candida oleophila in purple. Only contigs ≥4 kb are displayed to reduce noise from short sequences. Each panel (facet) represents a different sample, enabling visual comparison of yeast MAG abundance within the broader metagenomic context.