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Table 2 Comparison of phylotype coverage and diversity estimation of the 16S rRNA gene libraries at 97% similarity from the MiSeq analysis

From: Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets

Group No. of reads No. of OTUa Coverageb Richness estimator Diversity index
Ace(95% CI) Chao(95% CI) Shannon (95% CI) Simpson(95% CI)
Jejunum
 Control 22,244 148 99.85% 178 (162–210) 198 (168–271) 2.91 (2.89–2.93) 0.09 (0.095–0.099)
 Diarrhea 8672 121 99.51% 199 (171–242) 183 (149–258) 2.67(2.64–2.7) 0.10(0.10–0.11)
 Resistant 11,338 152 99.86% 161 (155–176) 161 (155–182) 3.35 (3.33–3.38) 0.069 (0.067–0.071)
 Transplanted-ND 20,681 113 99.83% 186 (158–231) 166 (135–236) 2.64 (2.63–2.66) 0.117(0.115–0.119)
 Transplanted-D 15,902 108 99.81% 137 (122–168) 130 (117–161) 2.21(2.18–2.23) 0.225 (0.219–0.231)
Feces
 Control 19,789 305 99.81% 326 (316–346) 326 (314–352) 3.85(3.83–3.88) 0.065 (0.063–0.067)
 Pre-diarrhea 11,543 277 99.61% 308 (294–332) 305 (290–336) 3.71 (3.67–3.74) 0.076 (0.073–0.079)
 Diarrhea 22,342 327 99.72% 372 (254–402) 392 (290–336) 2.94(2.91–2.97) 0.176 (0.172–0.18)
 Resistant 17,855 288 99.75% 314 (302–335) 322 (304–360) 3.49(3.46–3.52) 0.094 (0.091–0.097)
 Transplanted-ND 12,222 276 99.60% 309 (295–339) 325 (300–376) 3.9(3.87–3.93) 0.048(0.046–0.05)
 Transplanted-D 11,545 295 99.43% 347 (327–381) 360 (330–416) 3.66(3.63–3.7) 0.075(0.072–0.078)
  1. aThe operational taxonomic units (OTUs) were defined at the 97% similarity level (n = 4 before pooling)
  2. bThe coverage percentage, richness estimators (ACE and Chao) and diversity indices (Shannon and Simpson) were calculated using the mothur program
  3. Piglets after the development of watery diarrhea by transplantation were scarified and defined as transplanted diarrheal piglets (Transplanted-D). At day 6, piglets without diarrhea after transplantation were scarified and defined as transplanted non-diarrheal piglets (Transplanted-ND)