Table 3.
Microbiome assessment and diversity.
| Study | Type of Samples | Method | Shannon Diversity Index MEAN ± SD |
Abundance | ||||
|---|---|---|---|---|---|---|---|---|
| before | after | control group | before | after | control group | |||
| Ashton et al. [4] | faecal samples | high-throughput 16S rRNA gene sequencing | 4.84 | 5.20 | 5.6 | 8780 (observed species) | 9599 (observed species) | 11 119 (observed species) (cohabiting sibling controls) |
| Schwerd et al. [15] | faecal samples | high-throughput 16S rRNA gene sequencing | 8–50 (range during treatment) | 8–15 | 271 OTUs |
no significant difference | N/A | |
| Kaakoush et al. [13] | faecal samples | high-throughput 16S rRNA gene sequencing | 2.25 ± 0.24 | N/A | 2.75 ± 0.14 | 121 ± 33 OTUs | N/A | 117 ± 12 OTUs |
| Lewis et al. [12] | faecal samples | sequenced using the Illumina HiSeq paired-end method |
N/A | N/A | N/A | 3.49 × 109 total reads | 3.47 × 109 total reads | N/A |
| Shiga et al. [10] | faecal samples | Terminal restriction fragment length polymorphism analysis of bacterial 16srDNA, Specific quantitative PCR |
N/A | N/A | N/A | 10.9 ± 0.6 (log10 cells per gram of faeces) | 10.8 ± 0.8 (log10 cells per gram of faeces) |
11.8 (log10 cells per gram of faeces) |
| Jia et al. [17] | faecal samples | PCR amplification, then intensity of the bands was measured and quantified by comparison with known amounts of a 1-kb ladder | N/A | N/A | N/A | Faecalibacterium prausnitzii A2-165 subgroup: 103 (average yield ng of PCR product generated) |
Faecalibacterium prausnitzii A2-165 subgroup: 44 (average yield ng of PCR product generated) |
170 (average yield ng of PCR product generated) |
| blood samples | N/A | N/A | N/A | Faecalibacterium prausnitzii M21/2 subgroup: 127 (average yield ng of PCR product generated) |
Faecalibacterium prausnitzii M21/2 subgroup: 113 (average yield ng of PCR product generated) |
248 (average yield ng of PCR product generated) |
||
| D’Argenio et al. [14] | ileum tissue sample | 16S rRNA next-generation sequencing strategy | 3.9 | 6.2 | 7.1 | 705 OTUs | 1328 OTUs | 2171 OTUs |
| Gerasimidis et al. [16] | faecal samples | Quantitative Real-Time PCR | N/A | N/A | N/A | N/A | 9 (median number of bands *) | 11 (median number of bands) |
| Quince et al. [8] | faecal samples | 16S rRNA gene sequencing and Shotgun metagenome sequencing | 18.49 | N/A | 14.30 | N/A | N/A | N/A |
* bacterial diversity richness.