Table 1 Summary of methodologies employed and results (reads and OTUs) of tephritid NGS microbiome studies

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 (3^rd 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 ± 3.4^c

field (ovipositing in unripe and ripe 'Souri' olives)

adult (F)

midgut and esophageal bulb

4 individuals (ripe olives)

5 individuals (unripe olives)

as above^b

as above^b

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