The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing

Table 1 Summary of 16S rRNA gene sequencing analyses comparing paired swabs and tissue biopsies from 20 diabetic foot ulcerss

Parameter	Swabs Means (±s.d.)	Tissue Means (±s.d.)	w/t value¹	p value
No. of reads ^a	32,014(±16,068)	15,256(±16,699)	− 162	0.001*
^dAbundance ^b	564.7(±566.9)	266.5(±535.5)	− 108	0.03*
16S/18S ratio	0.201(±0.35)	1.06(±1.08)	150	0.004*
Bacterial richness^c	25.1 (±8.2)	38(±11.7)	4.423	0.0003*
Shannon’s diversity	1.8(±0.58)	2.4(±0.78)	2.921	0.009*
^dStaphylococcus spp.	49.3(±58.2)	14.4(±19.3)	− 158	< 0.001*
^dStreptococcus spp.	32.6(±39.3)	12.9(±37.9)	− 131	0.003*
^dEnterococcus spp.	7.3 (±8.0)	9.2(±22.4)	− 57	0.224
^dCorynebacterium spp.	42.9(±35.8)	18.3 (±20.0)	− 128	0.015*
^dEnterobacteriaceae	49.3 (±49.1)	24.7(±35.5)	− 120	0.024*
^dPseudomonas spp.	11.8(±26.9)	16.6(±38.5)	8	0.776
^dAnaerococcus spp.	39.1(±35.9)	17(±26.1)	− 132	0.012*
^dFinegoldia spp.	20.8(±15.6)	17.8(±22.4)	−32	0.535

¹ As most of the data analysed was nonparametric, Wilcoxin signed rank tests were used except for bacterial richness and Shannon’s diversity data which were subject to paired t-test analyses
^a reads in filtered OTU table (> 0.05%)
^b no. of copies of 16S rRNA gene/μl
^c Bacterial richness rarefied to 1500 reads
^d square root transformed data
* Significant results (p < 0.05)

ISSN: 1471-2180