Table 1

The relative representation of individual phyla (in% of total microbiota) prior to, during and after the antibiotic therapy
Experiment 1 Experiment 2
Day 0 0 2 2 0 2 2 14 14 16 16
phyllum Str Tet Str Tet Str/Tet Str Tet Str Tet Str Tet
Bacteria. other 0.02 0.02 0.02 0.02 0.02 0.01 ND 0.09 0.46 ND ND
Actinobacteria 7.21 4.09 0.38 0.09 1.67 8.7 0.01 0.35 1.76 0.24 0.11
Bacteroidetes 13.04 3.56 0.07 0.02 6.61 0.57 ND 2.48 11.3 0.04 ND
Cyanobacteria 0.01 ND 0.02 0.01 ND ND ND ND ND ND ND
Deferribacteres ND ND ND ND 0.02 ND ND ND 0.23 ND ND
Firmicutes 61.83 86.60 45.07 27.81 89.88 90.3 99.88 89.84 82.94 99.22 99.8
Fusobacteria ND ND ND ND 0.77 0.12 ND 6.81 0.24 0.4 ND
Chloroflexi ND ND 0.003 ND ND ND ND ND ND ND ND
Lentisphaerae ND ND ND ND 0.003 ND ND ND ND ND ND
Proteobacteria 17.80 5.33 54.41 72.04 0.9 0.16 0.08 0.28 2.2 0.03 0.04
Spirochaetes ND ND ND ND 0.001 ND ND ND ND ND ND
Synergistetes ND ND ND ND 0.1 0.07 ND 0.11 0.82 ND ND
Tenericutes ND ND ND ND 0.001 ND ND ND ND ND ND
TM7 0.09 0.39 0.01 ND 0.01 0.02 ND 0.01 ND 0.01 ND
OTU* 590 709 172 273 2222 433 182 896 1028 236 228
Chao1 1106 932 488 263 4592 709 263 1675 1860 490 364
OTU 14,446 478 528 131 182 869 433 164 541 799 211 165
Chao1 14,446 769 887 209 240 1791 709 290 1043 1510 422 357
Evenness 0.615 0.57 0.3 0.24 0.37 0.47 0.2 0.39 0.45 0.22 0.28
Shannon index 4.03 3.68 1.71 1.26 2.87 2.85 1.03 2.65 3.12 1.25 1.53
Total n. of reads 22,885 29,269 32,010 25,031 76,785 14,446 19,834 37,707 22,615 17,808 27,703

ND – not detected.

* OTU – number of OTUs using all reads available for each sample, Chao1 index estimates OTUs richness; OTU 14,446 and Chao1 14,446 - as above but normalised to randomly selected 14,446 reads for each sample, i.e. to the number of reads available for the sample with the lowest coverage; “Evenness” characterises how close in numbers each OTUs were present in each microbial population; Shannon index combines both species richness and evenness of their distribution within given microbial population.

Videnska et al.

Videnska et al. BMC Veterinary Research 2013 9:30   doi:10.1186/1746-6148-9-30

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