Table 6.
Taxa identified by 4 or more different methods as being differentially abundant based on antifungal use in the 15 days before sampling identified in 16S rDNA and shotgun metagenome sequence data.
| Phylum | Class | Family | Species | W | Ad | Ai | L | Md | Mc | data |
|---|---|---|---|---|---|---|---|---|---|---|
| decreased | ||||||||||
| Actinobacteria | Actinobacteria | Bifidobacteriaceae | Bifidobacterium longum | X | X | X | X | X | X | MGS |
| Actinobacteria | Coriobacteriia | Coriobacteriaceae | Collinsella aerofaciens | X | X | X | X | X | X | MGS |
| Bacteroidetes | Bacteroidia | Bacteroidaceae | Bacteroides sp. | X | X | X | X | X | X | 16S |
| Bacteroidetes | Bacteroidia | Rikenellaceae | Alistipes finegoldii | X | X | X | X | X | X | MGS |
| Bacteroidetes | Bacteroidia | Rikenellaceae | Alistipes putredinis | X | X | X | X | X | X | MGS |
| Bacteroidetes | Bacteroidia | Rikenellaceae | Alistipes sp. | X | X | X | X | X | X | 16S |
| Bacteroidetes | Bacteroidia | Tannerellaceae | Parabacteroides merdae | X | X | X | X | X | X | 16S |
| Bacteroidetes | Bacteroidia | Tannerellaceae | Parabacteroides merdae | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Lachnospiraceae | Anaerostipes hadrus | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Lachnospiraceae | Anaerostipes sp. | X | X | X | X | X | X | 16S |
| Firmicutes | Clostridia | Lachnospiraceae | Blautia faecis | X | X | X | X | 16S | ||
| Firmicutes | Clostridia | Lachnospiraceae | Blautia obeum | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Lachnospiraceae | Fusicatenibacter saccharivorans | X | X | X | X | MGS | ||
| Firmicutes | Clostridia | Ruminococcaceae | Faecalibacterium prausnitzii | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Ruminococcaceae | Faecalibacterium sp. | X | X | X | X | X | X | 16S |
| Firmicutes | Clostridia | Ruminococcaceae | Ruminococcus sp. | X | X | X | X | X | X | 16S |
| Firmicutes | Clostridia | Ruminococcaceae | Subdoligranulum sp. | X | X | X | X | X | 16S | |
| Firmicutes | Clostridia | Oscillospiraceae | UCG-002 sp. | X | X | X | X | 16S | ||
| Firmicutes | Clostridia | Oscillospiraceae | Oscillospiraceae sp. | X | X | X | X | X | 16S | |
| increased | ||||||||||
| Actinobacteria | Actinobacteria | Actinomycetaceae | Actinomyces sp oral taxon 181 | X | X | X | X | MGS | ||
| Actinobacteria | Actinobacteria | Micrococcaceae | Rothia mucilaginosa | X | X | X | X | X | X | MGS |
| Actinobacteria | Actinobacteria | Micrococcaceae | Rothia sp | X | X | X | X | 16S | ||
| Firmicutes | Bacilli | Aerococcaceae | Abiotrophia sp HMSC24B09 | X | X | X | X | X | MGS | |
| Firmicutes | Bacilli | Enterococcaceae | Enterococcus faecalis | X | X | X | X | X | X | MGS |
| Firmicutes | Bacilli | Enterococcaceae | Enterococcus faecium | X | X | X | X | X | X | MGS |
| Firmicutes | Bacilli | Enterococcaceae | Enterococcus sp. | X | X | X | X | X | X | 16S |
| Firmicutes | Bacilli | Streptococcaceae | Streptococcus infantis | X | X | X | X | X | MGS | |
| Firmicutes | Bacilli | Streptococcaceae | Streptococcus peroris | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Clostridiaceae | Clostridium paraputrificum | X | X | X | X | X | X | MGS |
| Firmicutes | Clostridia | Clostridiaceae | Clostridium paraputrificum | X | X | X | X | X | X | 16S |
| Firmicutes | Clostridia | Peptostreptococcaceae | Clostridioides difficile | X | X | X | X | MGS | ||
| Firmicutes | Clostridia | Peptostreptococcaceae | Clostridioides sp. | X | X | X | X | X | 16S | |
| Firmicutes | Erysipelotrichia | Erysipelotrichaceae | Erysipelatoclostridium ramosum | X | X | X | X | MGS | ||
| Firmicutes | Negativicutes | Veillonellaceae | Veillonella dispar | X | X | X | X | MGS | ||
| Firmicutes | Negativicutes | Veillonellaceae | Veillonella parvula | X | X | X | X | MGS | ||
| Proteobacteria | Gammaproteobacteria | Enterobacteriaceae | Enterobacter cloacae complex | X | X | X | X | MGS | ||
| Proteobacteria | Gammaproteobacteria | Enterobacteriaceae | Escherichia coli | X | X | X | X | X | MGS | |
| Proteobacteria | Gammaproteobacteria | Enterobacteriaceae | Klebsiella variicola | X | X | X | X | MGS | ||
| Proteobacteria | Gammaproteobacteria | Enterobacteriaceae | Enterobacteriaceae sp. | X | X | X | X | X | 16S | |
| Proteobacteria | Gammaproteobacteria | Pasteurellaceae | Haemophilus parainfluenzae | X | X | X | X | X | MGS | |
W, Wilcoxon test on CLR transformed data corrected for multiple tests using BH. Ad, ALDEx2 using CLR transformed data with all features used as the denominator for the geometric mean calculations. Ai, ALDEx2 using CLR transformed data using the “iqlr” (features with variance between lower and upper quartile variance) set of features as the denominator for the geometric mean calculation. L, LEfSe analysis using the p value (p<0.015 16S; p<0.005 MGS) that controls the FDR and an LDA >2, this analysis included all taxonomic levels but only Species level results are shown. Md, MaasLin2 with default parameters TSS normalization and LOG transformation. Mc, MaasLin2 analysis on CLR transformed data.