Table 1.
Summary of methodologies employed and results (reads and OTUs) of tephritid NGS microbiome studies
| Study | Fly Species | Wild (i.e. field) or Domesticated (i.e. laboratory) | Life Stage | Tissue | Sequencing Method | Primers | Pipeline | Number of Samples | Number of Reads after Quality Control | OTUs (97% similarity) |
|---|---|---|---|---|---|---|---|---|---|---|
| Morrow et al. [37] | B. tryoni | laboratory | adult | whole flies | 454 Pyrosequencing | 341f 806r | QIIME | 3 pools of 8 | 3019, 5994, 5991 | 10,7,14 |
| B. tryoni | field (citrus) | adult | whole flies | 1 pool of 8 | 6133 | 16 | ||||
| B. neohumeralis | laboratory | adult | whole flies | 3 pools of 8 | 4761, 6741, 6344 | 6, 18, 14 | ||||
| B. jarvisi | laboratory | adult | whole flies | 1 pool of 8 | 13,200 | 7 | ||||
| B. cacuminata | laboratory | adult | whole flies | 1 pool of 8 | 8202 | 4 | ||||
| B. cacuminata | field (wild tobacco) | adult | whole flies | 1 pool of 8 | 7357 | 8 | ||||
| C. capitata | laboratory | adult | whole flies | 1 pool of 8 | 7134 | 1 | ||||
| D. pornia | field (citrus) | adult | whole flies | 1 pool of 8 | 8022 | 17 | ||||
| Aharon et al. [22] | C. capitata | field (apricot) | adult | midgut | 454 Pyrosequencing | 926f 1392r | Mothur | 5 individual adults | 5000-12000 | 5-23 |
| field (apricot) | larval | midgut | 15 pooled as 3 samples | 1700-3200 | 7-13 | |||||
| Andongma et al. [38] | B. dorsalis | field (healthy fruit) | eggs | whole egg | 454 Pyrosequencing | 27f 533r | Mothur | approx. 50 insects pooled | Total reads 46332 (lowest number of reads per sample was 5967) | 76 |
| field (healthy fruit) | first instar | whole larva | as above | 77 | ||||||
| field (fallen fruit) | third instar | whole gut (proventriculus to rectum) | as above | 81 | ||||||
| field (3rd instar larvae collected from fallen fruit allowed to pupate in a laboratory) | pupae | whole pupa (without puparium) | as above | 60 | ||||||
| field (ME traps) a | adult (F) | whole gut (proventriculus to rectum) | as above | 59 | ||||||
| field (protein traps) | adult (M) | whole gut (proventriculus to rectum) | as above | 54 | ||||||
| Ben-Yosef et al. [19] | B. oleae | field (unripe and ripe 'Souri' olives) | third instar | gastric caeca at the proximal section of the midgut | Illumina MiSeq | 515f 806r | Mothur | 5 individuals per unripe and ripe olives | 73868 ± 8677 reads per sample | 5.4 ± 3.4c |
| field (ovipositing in unripe and ripe 'Souri' olives) | adult (F) | midgut and esophageal bulb |
4 individuals (ripe olives) 5 individuals (unripe olives) |
as aboveb | as aboveb | |||||
| mass-reared (ovipositing) | adult (F) | midgut and esophageal bulb | 6 individuals | as above | not reported | |||||
| Ben-Yosef et al. [20] | B. oleae | field (green “Manzanillo” olives) | third instar | gastric caeca at the anterior section of the midgut | 454 Pyrosequencing | 926f 1392r | Mothur | 5 individuals | 8351 - 15,098 sequences per sample | 1-2 per sample |
| field (soil under olive trees) | pupae | midgut and esophageal bulb | 5 individuals | 6596-18,335 sequences per sample | 1-3 per sample | |||||
| field collected pupae eclosed in cage | adult (F) | midgut and esophageal bulb | 5 individuals | 8344 - 12,599 sequences per sample | 1-2 per sample | |||||
| Wang et al. [39] | B. minax | field (citrus) | adult (F) | intestine | 454 Pyrosequencing | 343f 798r | DOTUR | 3 pools of 15 | 7857 | 319 |
| field (citrus) | adult (F) | ovaries | 3 pools of 15 | 8124 | 415 | |||||
| field (citrus) | adult (M) | intestine | 3 pools of 15 | 7353 | 322 | |||||
| field (citrus) | adult (M) | testes | 3 pools of 15 | 8957 | 389 | |||||
| Yong et al. [40] | B. carambolae | field (ME traps)a | adult (M) | whole fly | Illumina MiSeq | 341f | MEGAN5 | 4 individuals | 1,561,203 – 2,077,403 | 44-75 genera |
| B. dorsalis | field (ME traps)a | adult (M) | whole fly | 518r | 2 individuals | 1,584,084 – 1,607,064 | 55-75 genera | |||
| Ventura et al. [41] | A. ludens | field (bitter orange) | third instar | whole gut | 454 Pyrosequencing |
8f 556r |
QIIME | 30 insects pooled | 110,073 reads | 72 |
| field (CeraTrap®) | adult | whole gut | as above | 121 | ||||||
| A. obliqua | field (mango) | third instar | whole gut | as above | 38 | |||||
| field (CeraTrap®) | adult | whole gut | as above | 100 | ||||||
| A. serpentina | field (mamey sapote) | third instar | whole gut | as above | 82 | |||||
| field (CeraTrap®) | adult | whole gut | as above | 121 | ||||||
| A. striata | field (guava) | third instar | whole gut | as above | 75 | |||||
| field (CeraTrap®) | adult | whole gut | as above | 57 | ||||||
| Malacrinò et al. [42] | C. capitata | field (orange) | first instar | whole larvae | Illumina MiSeq |
515f 806r |
QIIME | 15 individuals | not specified | a total of 3,169 |
| field (orange) | third instar | whole larvae | as above | |||||||
| field larvae pupate in laboratory (orange) | pupae | whole pupae | as above | |||||||
| from field collected larvae (orange) | adults | whole flies | as above | |||||||
| field (fig) | third instar | whole larvae | as above | not specified | a total of 1,118 | |||||
| field (prickly pear) | third instar | whole larvae | as above | |||||||
| field (peach) | third instar | whole larvae | as above | |||||||
| field (cherimoya) | third instar | whole larvae | as above | |||||||
| field (orange fruits) | third instar | whole larvae | as above |
aME methyl eugenol
baverage calculated from all field samples, i.e. both larvae and adults
c>10 reads per OTU and OTU clustered at 98% similarity