Table 1.
Summary of the methodological approaches used by studies that have compared infant microbiota profiles between cesarean section (CS) and vaginal deliveries.
| Study | N[cesarean section delivered (CSD)] | Bead beating step? | Gene target/s | Sequencing platform/bioinformatics pipeline | 16S rRNA gene region | Primer coverage (%)a | Major genera with poor coverage | Negative controls used? | Conclusion |
|---|---|---|---|---|---|---|---|---|---|
| Neonatal studies | |||||||||
| Ardissone et al. (38) | 52 (33) | Yes | 16S rRNA | Ion Torrent PGM/Bioinformatics performed manually | V4 | 86.3 | None | Yesf | Delivery mode has an effect on the gut microbiome of preterm neonates |
| Biasucci et al. (43) | 46 (23) | Not specified | Variousc | Targeted qualitative polymerase chain reaction (qPCR) | Various | N/A | N/A | No | Mode of delivery is associated with differences in the gut microbiota composition in neonates at day 3 of life |
| Chu et al. (37) | 157 (52) | Yes | 16S rRNA | 454/QIIME v1.9.0 | V5–V3 | 67.7 | Bifidobacterium: 0.6% Escherichia/Shigella: 0.8% Enterobacter: 0% | No | Minor differences in the microbial communities of CSD neonates in some body sites, but not in meconium |
| Dominguez-Bello et al. (44) | 10 (6) | Yes | 16 S rRNA | 454/Bioinformatics performed manually | V2 | 59.7 | Bifidobacterium: 15% Escherichia/Shigella: 23% Enterobacter: 21% | No | Mode of delivery is a strong determinant of the skin, oral, and gut microbiota composition in neonates |
| Dong et al. (34) | 2 (1) | No | 16S rRNA | Genome sequencer FLX/Mothur | V3–V5 | 83.1 | Bifidobacterium: 0.6% | No | Similar bacterial communities were found in the meconium of CSD and vaginally delivered (VD) neonates |
| Hu et al. (32) | 23 (10) | No | 16S rRNA | Pacbio RS/QIIME v1.5.0 | V3–V4 | 77.7 | None | No | Meconium microbiota is not affected by the mode of delivery |
| Mshvildadze et al. (33) | 23 (13) | No | 16S rRNA | 454/RDP pyrosequencing pipeline | V1–V2 | 59.7 | Bifidobacterium: 15% Escherichia/Shigella: 23% Enterobacter: 21% | No | Meconium microbiota is not affected by the mode of delivery |
| Sakwinska et al. (49) | 42 (8) | Not specified | 16S rRNA | 454/QIIME v1.8.0 | V4–V6 | Primers not specified | Primers not specified | No | Although the nasal and gut microbiomes of CSD and VD neonates vary, this is not due to transfer of maternal vaginal microbes |
| Shi et al. (42) | 18 (10) | No | 16S rRNA | Illumina Hiseq2500/Bioinformatics performed manually | Primers not specified | N/A | N/A | Yesf | Mode of delivery is associated with differences in the gut microbiota composition in neonates at day 1 of life |
| Wampach et al. (31) | 15 (7) | Yes | 16S rRNA, 18S rRNA | Illumina MiSeq/LotuS | V4 | 86.4 | None | Noe | CSD infants experienced a delay in microbial colonization and succession in the gut, which began after day 5 of life |
| Infant studies | |||||||||
| Azad et al. (50) | 24 (6) | Yes | 16S rRNA | Illumina SI-Seq/QIIME v1.6.0 | V5–V7 | 56.5b | Bifidobacterium: 36% Bacteroides: 32% | No | Mode of delivery is a strong determinant of the gut microbiota composition in infants |
| Bäckhed et al (51) | 98 (15) | Yes | 16S rRNA | Illumina Hiseq2000/Bioinformatics performed manually | Primers not specified | Primers not specified | Primers not specified | No | Mode of delivery is a strong determinant of the gut microbiota composition in infants |
| Chu et al. (37) | 60 (22) | Yes | 16S rRNA | 454/QIIME v1.9.0 | V5–V3 | 67.7 | Bifidobacterium: 0.6% Escherichia/Shigella: 0.8% Enterobacter: 0% | No | By 6 weeks of age no differences between the skin, oral, nares, or gut microbiota of CSD and VD infants |
| Penders et al. (52) | 1,032 (108) | Yes | Variousd | Targeted qPCR | Various | N/A | N/A | No | Mode of delivery is a strong determinant of the gut microbiota composition in infants |
| Sakwinska et al. (49) | 42 (8) | Not specified | 16 S rRNA | 454/QIIME v1.8.0 | V4–V6 | Primers not specified | Primers not specified | No | Although the nasal and gut microbiomes of CSD and VD infants vary, this is not due to transfer of maternal vaginal microbes |
aFor domain bacteria, identified using Silva TestPrime.
bPrimers contained too many ambiguities to be analyzed with Silva TestPrime. RDP probe match was used instead.
cTargeted to Bifidobacterium spp., Ruminococcus spp., and Bacteroides spp.
dTargeted to Bifidobacterium spp., E. coli, C. difficile, B. fragilis, and Lactobacillus spp.
eNo extraction controls used, but low yield and negative amplicon samples were discarded.
fNegative extraction controls used for amplification, but not for sequencing.