Table 1. The basic statistics of the microbiome of cockatiels: number of reads, OTUs and diversity indexes.
Diversity indexes were calculated with phyloseq (McMurdie & Holmes, 2013), Breakaway R package (Willis, Bunge & Whitman, 2015), and CatchAll (Bunge et al., 2012).
| Cockatiel 1 | Cockatiel 2 | Cockatiel 3 | Total | |
|---|---|---|---|---|
| OTUs total diversity | ||||
| Total sequences (raw paired-end) | 1,256,170 | 1,255,086 | 1,216,644 | 3,727,900 |
| Total sequences (merged, after QC) | 90,520 | 97,161 | 107,536 | 295,217 |
| Observed OTUs | 6,957 | 7,566 | 7,154 | 19,280 |
| Assigned phylotypes (Greengenes DB) | 6,932 | 7,537 | 7,129 | 19,206 |
| Assigned phylotypes (Closed OTUs DB) | 109 | 206 | 115 | 309 |
| Chao1 | 32,790 ± 1,260 | 36,659 ± 1,364 | 42,278 ± 1,822 | |
| Shannon | 3.2 | 3.47 | 3.27 | |
| Simpson | 0.779 | 0.841 | 0.845 | |
| Breakaway estimate diversity | 169,674 | 29,391 | 8,502 | |
| CatchAll | 152,809 | 101,814 | 160,648 | |
| CatchAll best parametric model | ThreeMixedExp | FourMixedExp | ThreeMixedExp | |
| OTUs diversity without singletons | ||||
| Observed OTUs | 879 | 1,000 | 991 | 2,870 |
| Chao1 | 976 ± 23.45 | 1119 ± 25.42 | 1138 ± 28.23 | |
| Shannon | 2.46 | 2.76 | 2.65 | |
| Simpson | 0.74 | 0.81 | 0.82 | |
| Breakaway estimate diversity | 933 | 1,068 | 1,088 | |
| CatchAll | 1,093 | 1,251 | 1,276 | |
| CatchAll best parametric model | ThreeMixedExp | ThreeMixedExp | TwoMixedExp |