High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval

Figures & data

Figure 1. Rarefaction curves of observed species number clustered at 97% sequence identity across all samples. Sample named to refer to samples as described in Table 1.

Figure 2. Shared operational taxonomic unit (OTU) analysis of the different communities. Venn diagrams showing the unique and shared OTUs in the different communities, (A) for the AM1, AM2, BM1, and BM2 communities, (B) for the AM1, AM2, CM1, and CM2 communities, (C) for the AA1, AA2, BA1, and BA2 communities and (D) for the AA1, AA2, CA1, and CA2 communities. Sample names refer to samples as described in Table 1.

Table 1. Operational taxonomic unit (OTU)-based diversity index in New Zealand rabbit buccal cavity and rectum samples during decomposition.

Sample name	Sample group	Sample region	Sample time	Raw sequences	Clean sequences	OTUs	Chao 1	Observed species	Shannon index
AM1	Group A	Buccal cavity	Alive	45 348	42 485	238	359.33	238	1.87
AM2	Group A	Buccal cavity	0 h	47 843	42 986	581	705.32	581	2.23
AM3	Group A	Buccal cavity	2 h	48 713	43 012	911	946.25	911	4.58
AM4	Group A	Buccal cavity	6 h	45 512	42 229	772	801.38	772	4.20
AM5	Group A	Buccal cavity	12 h	45 878	42 114	732	758.00	732	4.57
AM6	Group A	Buccal cavity	1 d	47 970	42 852	853	890.68	853	4.21
AM7	Group A	Buccal cavity	3 d	46 569	42 943	460	526.41	460	1.71
AM8	Group A	Buccal cavity	5 d	43 887	42 161	37	56.50	37	1.13
AM9	Group A	Buccal cavity	10 d	44 334	42 127	56	73.50	56	1.72
AM10	Group A	Buccal cavity	20 d	45 575	42 512	60	79.43	60	1.39
AA1	Group a	Rectum	Alive	50 581	42 793	401	478.03	401	4.30
AA2	Group a	Rectum	0 h	49 489	42 829	721	900.15	721	4.93
AA3	Group a	Rectum	2 h	46 426	42 859	612	671.35	612	4.71
AA4	Group a	Rectum	6 h	47 917	43 259	476	542.07	476	4.44
AA5	Group a	Rectum	12 h	48 195	42 497	468	561.72	468	4.29
AA6	Group a	Rectum	1 d	48 865	43 086	816	1 034.48	816	4.76
AA7	Group a	Rectum	3 d	45 781	42 614	366	556.12	366	2.28
AA8	Group a	Rectum	5 d	44 537	42 221	102	154.56	102	2.04
AA9	Group a	Rectum	10 d	45 778	42 867	62	108.00	62	1.62
AA10	Group a	Rectum	20 d	47 138	42 792	65	98.00	65	2.18
BM1	Group B	Buccal cavity	Alive	44 923	41 923	350	521.27	350	2.37
BM2	Group B	Buccal cavity	0 h	42 889	41 643	371	496.26	371	2.85
BM3	Group B	Buccal cavity	2 h	43 256	41 950	343	460.16	343	2.34
BM4	Group B	Buccal cavity	6 h	45 642	42 150	483	534.00	483	4.25
BM5	Group B	Buccal cavity	12 h	46 444	42 228	968	1 007.51	968	4.66
BM6	Group B	Buccal cavity	1 d	49 463	43 118	626	665.07	626	3.66
BM7	Group B	Buccal cavity	3 d	47 913	43 042	667	685.42	667	4.15
BM8	Group B	Buccal cavity	5 d	44 666	42 697	73	125.93	73	0.69
BM9	Group B	Buccal cavity	10 d	45 979	42 684	51	70.43	51	1.49
BM10	Group B	Buccal cavity	20 d	46 415	42 636	57	74.14	57	1.80
BA1	Group b	Rectum	Alive	46 540	42 297	340	471.09	340	1.56
BA2	Group b	Rectum	0 h	50 243	43 295	545	686.57	545	4.79
BA3	Group b	Rectum	2 h	45 965	42 532	616	677.32	616	4.75
BA4	Group b	Rectum	6 h	47 512	43 027	601	659.45	601	4.84
BA5	Group b	Rectum	12 h	46 253	42 398	662	735.99	662	4.65
BA6	Group b	Rectum	1 d	47 091	42 471	664	784.38	664	4.68
BA7	Group b	Rectum	3 d	46 183	42 297	625	753.89	625	3.15
BA8	Group b	Rectum	5 d	44 888	42 711	275	476.92	275	1.36
BA9	Group b	Rectum	10 d	45 258	42 648	82	148.11	82	2.19
BA10	Group b	Rectum	20 d	45 882	42 344	58	64.88	58	1.75
CM1	Group C	Buccal cavity	Alive	45 712	42 580	472	539.05	472	2.56
CM2	Group C	Buccal cavity	0 h	47 423	42 469	662	729.16	662	4.53
CM3	Group C	Buccal cavity	2 h	45 988	42 303	572	631.21	572	3.66
CM4	Group C	Buccal cavity	6 h	46 393	42 785	564	694.28	564	2.80
CM5	Group C	Buccal cavity	12 h	47 108	43 055	690	755.25	690	3.81
CM6	Group C	Buccal cavity	1 d	47 373	42 798	657	733.42	657	3.46
CM7	Group C	Buccal cavity	3 d	45 692	42 224	528	624.23	528	2.22
CM8	Group C	Buccal cavity	5 d	44 076	42 228	47	75.88	47	0.51
CM9	Group C	Buccal cavity	10 d	44 998	42 362	53	76.1	53	0.38
CM10	Group C	Buccal cavity	20 d	44 576	42 121	61	124.33	61	0.98
CA1	Group c	Rectum	Alive	48 480	43 454	273	392.05	273	1.94
CA2	Group c	Rectum	0 h	48 281	42 932	178	318.58	178	1.69
CA3	Group c	Rectum	2 h	47 957	42 881	538	709.59	538	2.92
CA4	Group c	Rectum	6 h	47 662	43 016	575	596.00	575	4.37
CA5	Group c	Rectum	12 h	48 953	42 967	656	694.04	656	4.51
CA6	Group c	Rectum	1 d	47 750	42 977	639	764.56	639	3.25
CA7	Group c	Rectum	3 d	46 471	42 754	54	111.75	54	1.54
CA8	Group c	Rectum	5 d	44 987	42 846	49	73.00	49	1.60
CA9	Group c	Rectum	10 d	44 944	42 377	73	115.86	73	2.11
CA10	Group c	Rectum	20 d	45 718	42 777	68	83.11	68	2.15

Figure 3. Two-dimensional principal coordinates analysis (PCoA) plot of unweighted UniFrac distance matrices for buccal cavity and rectum samples during decomposition. The bacterial community of the buccal cavity from New Zealand rabbit carcasses in Group A (blue dot), in Group B (purple dot) and Group C (yellow dot), and the bacterial community of the rectum from New Zealand rabbit carcasses in the Group a (red dot), in Group b (green dot) and Group c (orange dot) were represented. Sample names refer to samples as described in Table 1.

Figure 4. Hierarchical clustering of buccal cavity and rectum samples by unweighted pair group method with arithmetic mean (UPGMA) according to their weighted UniFrac matrix. Sample names refer to samples as described in Table 1.

Figure 5. Bacterial community structure variation during decomposition in the buccal cavity at the phylum level and the family level. Relative abundance of bacterial phyla during decomposition in the buccal cavity in Group A (A), the buccal cavity in Group B (B), and buccal cavity in Group C (C). Relative abundance of bacterial families during decomposition in the buccal cavity in Group A (D), the buccal cavity in Group B (E) and buccal cavity in Group C (F). Sample names refer to samples as described in Table 1.

Figure 6. Bacterial community structure variation during decomposition in the rectum at the phylum level and the family level. Relative abundance of bacterial phyla during decomposition in the rectum in Group a (A), rectum in Group b (B), and rectum in Group c (C). Relative abundance of bacterial families during decomposition in the rectum in the Group a (D), the buccal cavity in Group b (E), and the buccal cavity in Group c (F). Sample names refer to samples as described in Table 1.