Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast

BMC Microbiology

Table 4 Mean relative abundances of 16S rRNA rRNA samples for each DNA extraction method and enrichment time

Genus	PowerFood			PowerSoil			Hybrid
Genus	0 h	6 h	18 h	0 h	6 h	18 h	0 h	6 h	18 h
Gram-positive
Brochothrix	0.71	0.32^b	0.46	0.65	0.11	0.14	0.72	0.06	0.38
Carnobacterium	3.46	23.43	15.38^ab	2.95	18.82	2.93	3.20	22.88	3.36
Clostridium sensu stricto 7	-	-	0.02	-	-	0.06	-	-	0.01
Clostridium sensu stricto 18	-	-	-	-	-	-	-	-	0.03
Enterococcus	-	-	0.61	-	-	0.52	-	-	1.18
Gallicola	-	-	0.07	-	-	-	-	-	0.01
Hathewaya	-	-	0.35	-	-	0.77	-	-	0.73
Lactobacillus	0.26^a	0.30	1.10^ab	0.08^b	0.19	0.18	0.26	0.28	0.23
Lactococcus	30.99	1.25^ab	0.78	21.96	0.52	0.20	19.14	0.73	0.26
Leuconostoc	4.00^a	1.51^a	1.60^a	2.38	0.30	0.32	3.68	0.84	0.49
Peptoniphilus	-	-	1.57	-	-	0.30	-	-	0.75
Vagococcus	0.58	0.61^b	0.50	0.64	1.02^b	0.07	1.20	6.13	0.13
Gram-negative
Acinetobacter	-	0.01	0.01	0.01	0.01	-	0.01	-	0.02
Aeromonas	2.67	0.32	0.21	0.60	0.33	0.45	-	0.29	0.72
Comamonas	-	-	0.01	-	-	0.06	-	-	0.01
Escherichia-Shigella	-	-	0.21	-	-	0.21	-	-	0.40
Hafnia	1.19	1.48	15.26^a	0.24	1.67	18.20	0.01	1.36	16.76
Janthinobacterium	0.02	0.02	0.01	0.01	-	-	0.01	-	0.01
Morganella	0.02	0.01	-	0.02	0.01	0.01	0.03	0.01	0.02
Myroides	-	-	-	-	-	-	0.01	-	-
Proteus	0.01	-	0.09	0.02	-	0.06	-	-	0.23
Providencia	0.01	0.01	-	0.05	0.02	-	0.02	0.01	-
Pseudomonas	35.59	51.84	11.35	51.39	50.06	13.16	51.40	41.48	17.61
Serratia	6.29	2.30^ab	2.78^ab	8.10	5.41	4.83	8.63	4.69	4.23
Yersinia	0.26	0.21	0.09	0.12	0.44	0.03	0.11	0.31	0.13

^asignificantly different to PowerSoil at this timepoint, P < 0.05; Significant differences were determined using DESeq2 with fold changes > 1.5 and false discovery rate adjusted P values
^bsignificantly different to the hybrid method at this timepoint, P < 0.05;
-not detected in the rarefied count table. Significant differences were determined using DESeq2 with fold changes > 1.5 and false discovery rate adjusted P values < 0.05 considered significant, n = 4

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