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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)