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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.