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Table 1 Basic characteristics of chicken cecal microbiota samples for individual time points shown as average ± SD out of 3 independent chickens

From: Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota

Experiment 1

NI4*

NI7

NI10

NI13

NI16

NI19

No. reads

2409±265

4198±1570

3314±1097

7577±455

14994±2354

9586±2045

Observed species

54±6

107±18

94±19

153±33

307±42

233±28

Chao1 estimate

69±8

199±81

146±40

276±88

605±103

418±79

Shannon index

3.15±0.33

4.33±0.20

4.54±0.02

4.78±0.26

5.39±0.22

5.42±0.11

Simpson index

0.82±0.04

0.91±0.01

0.94±0.00

0.93±0.02

0.96±0.00

0.96±0.00

Experiment 1

 

S7

S10

S13

S16

S19

No. reads

 

9940±3942

16514±2740

12725±3783

5840±921

17992±3235

Observed species

 

155±81

187±8

196±47

149±5

479±11

Chao1 estimate

 

277±98

298±66

289±76

265±36

846±80

Shannon index

 

4.15±0.36

4.61±0.18

4.53±0.39

5.05±0.37

5.55±0.14

Simpson index

 

0.89±0.02

0.92±0.02

0.92±0.03

0.94±0.02

0.96±0.00

Experiment 2

Lumen N7

Lumen N10

Lumen S10

Mucus NI7

Mucus NI10

Mucus S10

No. reads

3302±391

6958±4142

4107±3942

1307±161

4278±79

1826±404

Observed species

184±33

221±24

196±81

95±5

132±15

87±10

Chao1 estimate

283±76

319±42

298±98

150±21

204±26

110±2

Shannon index

5.24±0.31

4.98±0.43

5.00±0.36

4.82±0.07

4.64±0.08

4.63±0.26

Simpson index

0.95±0.01

0.93±0.03

0.93±0.02

0.93±0.01

0.93±0.00

0.92±0.02

  1. * NI - non-infected chicken followed by age of chickens in days; S - Salmonella Enteritidis infected chickens followed by age of chickens in days, Lumen and Mucus - luminal and mucus associated microbiota characterized separately in experiment 2.