Table 2.
Abundance of reads (TPM) and abundance of transcripts (Depth) per fungal species detected with metatranscriptomics. True members of the mock community – at species level – are shown in bold
| Speciesa | TPM (read-level) | Depth (transcript-level) | Relative abundance (transcript-level %) |
|---|---|---|---|
| Cryptococcus neoformans | 149,692.28 | 11,049.04 | 22.464 |
| Candida tropicalis | 142,496.47 | 9424.30 | 19.161 |
| Pichia kudriavzevii | 62,133.74 | 9234.05 | 18.774 |
| Clavispora lusitaniae | 57,317.81 | 7107.80 | 14.451 |
| Candida auris | 13,402.41 | 3354.39 | 6.820 |
| Candida dubliniensis | 52,027.94 | 1706.41 | 3.469 |
| Pichia membranifaciens | 10,860.75 | 1498.26 | 3.046 |
| Candida albicans | 42,948.69 | 1441.56 | 2.931 |
| Yarrowia lipolytica | 52,376.03 | 1384.29 | 2.814 |
| Candida orthopsilosis | 44,531.25 | 1308.09 | 2.660 |
| Candida glabrata | 50,404.11 | 992.55 | 2.018 |
| Cryptococcus gattii VGI | 9350.81 | 463.71 | 0.943 |
| Candida glycerinogenes | 2345.13 | 41.51 | 0.084 |
| Nakaseomyces delphensis | 12,821.76 | 35.45 | 0.072 |
| Candida parapsilosis | 15,989.78 | 31.11 | 0.063 |
| Candida nivariensis | 1411.36 | 12.72 | 0.026 |
| Kluyveromyces marxianus | 47.70 | 8.90 | 0.018 |
| Torulaspora delbrueckii | 15.01 | 6.00 | 0.012 |
| Kluyveromyces lactis | 9.24 | 3.93 | 0.008 |
| Saccharomyces cerevisiae | 22.84 | 3.77 | 0.008 |
| Eremothecium sinecaudum | 25.93 | 3.67 | 0.008 |
| Pichia cecembensis | 751.23 | 3.60 | 0.007 |
| Lodderomyces elongisporus | 34.30 | 3.59 | 0.007 |
| Uncultured Candida | 885.35 | 3.13 | 0.006 |
| Eremothecium gossypii | 10.13 | 3.04 | 0.006 |
| Naumovozyma dairenensis | 17.37 | 2.80 | 0.006 |
| Suhomyces tanzawaensis | 30.87 | 2.25 | 0.005 |
| Dipodascaceae sp. LM136 | 24,286.11 | 2.16 | 0.004 |
| Cyberlindnera jadinii | 12.32 | 2.04 | 0.004 |
| Metschnikowia bicuspidata | 16.02 | 1.29 | 0.003 |
| Brettanomyces naardenensis | 96.13 | 1.19 | 0.002 |
| Pichia norvegensis | 783.06 | 1.11 | 0.002 |
| Debaryomyces fabryi | 22.87 | 0.92 | 0.002 |
| Candida neerlandica | 487.65 | 0.69 | 0.001 |
| Melanotaenium endogenum | 262.12 | 0.59 | 0.001 |
| Pichia kluyveri | 51,814.00 | 0.55 | 0.001 |
| Candida pseudohaemulonis b | 560.14 | 0.49 | 0.001 |
| Candida sp. (in: Saccharomycetales) | 330.15 | 0.49 | 0.001 |
| Pichia sp. 2 TMS-2011 | 0.00 | 0.45 | 0.001 |
| Cryptococcus neoformans AD hybrid | 0.00 | 0.44 | 0.001 |
| Saccharomycetales sp. LM594 | 2.60 | 0.30 | 0.001 |
| Naumovozyma castellii | 4.56 | 0.29 | 0.001 |
| Saccharomyces pastorianus | 0.81 | 0.26 | 0.001 |
| Cryptococcus gattii VGIII | 0.48 | 0.21 | 0.000 |
| Other Eukaryotes | 936.75 | 18.83 | 0.038 |
| Bacteria | 423.36 | 15.79 | 0.032 |
| Unclassified | 198,000.57 | 8.00 | 0.016 |
| TOTAL | 1,000,000 | 49,186 | 100 |
a Species defined according to the NCBI taxonomy database. Strain numbers may indicate vouchers rather than genetically different lineages. bCandida pseudohaemulonis is also referred to as C. pseudohaemulonii