Table 2.

Taxa identified in differential abundance analysis (ALDEx2) as differing significantly with repeated courses (1-2 vs 3+ courses) of β-lactam, vancomycin or AAb.

taxa	wilcoxon p	wilcoxon pBH	effect of repeated courses	phylum
β-lactams
Eggerthella sp.	6.80E-06	0.0004	–	Actinobacteria
Bifidobacterium longum	0.0178	0.0936	–	Actinobacteria
Collinsella aerofaciens	0.0444	0.1416	–	Actinobacteria
Alistipes putredinis	0.0115	0.0580	–	Bacteroidetes
Clostridium symbiosum	0.0005	0.0084	–	Firmicutes
Faecalibacterium prausnitzii	0.0015	0.0195	–	Firmicutes
Oscillibacter sp.	0.0026	0.0252	–	Firmicutes
Ruminococcus obeum	0.0192	0.0748	–	Firmicutes
Clostridium bolteae	0.0254	0.1114	–	Firmicutes
Enterococcus faecalis	0.0003	0.0047	+	Firmicutes
Clostridioides difficile	0.0045	0.0313	+	Firmicutes
Streptococcus mitis oralis pneumoniae	0.0068	0.0467	+	Firmicutes
Streptococcus peroris	0.0148	0.0660	+	Firmicutes
Granulicatella adiacens	0.0174	0.0746	+	Firmicutes
Enterococcus faecium	0.0251	0.0921	+	Firmicutes
Granulicatella sp.	0.0240	0.0986	+	Firmicutes
Streptococcus parasanguinis	0.0453	0.1589	+	Firmicutes
Klebsiella pneumoniae	0.0008	0.0097	+	Proteobacteria
Alcaligenes sp.	0.0079	0.0430	+	Proteobacteria
Brevundimonas diminuta	0.0147	0.0605	+	Proteobacteria
Bordetella sp.	0.0141	0.0615	+	Proteobacteria
Escherichia coli	0.0169	0.0786	+	Proteobacteria
Agrobacterium tumefaciens	0.0222	0.0851	+	Proteobacteria
Agrobacterium sp.	0.0216	0.0871	+	Proteobacteria
Achromobacter piechaudii	0.0293	0.1084	+	Proteobacteria
vancomycin
Eggerthella sp.	0.0371	0.3778	–	Actinobacteria
Enterococcus faecalis	0.0185	0.3222	+	Firmicutes
Clostridioides difficile	0.0244	0.3612	+	Firmicutes
Streptococcus parasanguinis	0.0304	0.4243	+	Firmicutes
AAb
Eggerthella sp.	0.0004	0.0054	–	Actinobacteria
Collinsella aerofaciens	0.0097	0.0443	–	Actinobacteria
Bifidobacterium longum	0.0182	0.0771	–	Actinobacteria
Alistipes putredinis	0.0001	0.0021	–	Bacteroidetes
Bacteroides ovatus	0.0004	0.0055	–	Bacteroidetes
Bacteroides caccae	0.0229	0.0764	–	Bacteroidetes
Alistipes onderdonkii	0.0275	0.0832	–	Bacteroidetes
Parabacteroides merdae	0.0329	0.1028	–	Bacteroidetes
Faecalibacterium prausnitzii	0.0000	0.0008	–	Firmicutes
Oscillibacter sp.	0.0016	0.0139	–	Firmicutes
Clostridium symbiosum	0.0033	0.0222	–	Firmicutes
Ruminococcus obeum	0.0037	0.0226	–	Firmicutes
Clostridium bolteae	0.0391	0.1201	–	Firmicutes
Rothia mucilaginosa	0.0031	0.0213	+	Actinobacteria
Bifidobacterium animalis	0.0424	0.1034	+	Actinobacteria
Enterococcus faecalis	0.0008	0.0078	+	Firmicutes
Clostridioides difficile	0.0022	0.0150	+	Firmicutes
Granulicatella adiacens	0.0047	0.0224	+	Firmicutes
Granulicatella sp.	0.0118	0.0447	+	Firmicutes
Streptococcus peroris	0.0150	0.0524	+	Firmicutes
Streptococcus mitis oralis pneumoniae	0.0168	0.0659	+	Firmicutes
Enterococcus faecium	0.0246	0.0748	+	Firmicutes
Ruminococcus gnavus	0.0230	0.0850	+	Firmicutes
Blautia producta	0.0497	0.1177	+	Firmicutes
Klebsiella pneumoniae	0.0019	0.0125	+	Proteobacteria
Alcaligenes sp.	0.0075	0.0306	+	Proteobacteria
Brevundimonas diminuta	0.0070	0.0321	+	Proteobacteria
Agrobacterium tumefaciens	0.0117	0.0421	+	Proteobacteria
Agrobacterium sp.	0.0114	0.0451	+	Proteobacteria
Achromobacter piechaudii	0.0191	0.0608	+	Proteobacteria
Bordetella sp.	0.0274	0.0716	+	Proteobacteria
Escherichia coli	0.0243	0.0821	+	Proteobacteria

Bolded values indicate values <0.05.

Analyses were performed on the reduced patient dataset (see Supplemental Table S3 for breakdown of samples and patients).