Table 6.
Overview of the included animal-based studies that investigated the microbiome and asthma.
| Citation and Title of the Article | Country | Sample Size | Age | Type of Sample Collected | Time of Sample Collection | Microbiome Detection Method | Genomic DNA Extraction Kit | Sequencing Platform | Microbiome Diversity Assessment | Bioinformatics Pipeline Used | Study Findings |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Upper and lower airway microbiome | |||||||||||
| [47] ‘Respiratory Microbiota Profiles Associated with the Progression from Airway Inflammation to Remodelling in Mice With OVA-Induced Asthma’. |
China | Female BALB/c mice: n = 30 Control group: n = 6 Ovalbumin group: n = 24 |
4–6 weeks | Nasal lavage fluid and BAL |
Control group was sacrificed at the end of the experiment: n = 6 mice Experimental groups were sacrificed at different time points for sample collection as follows: 1 week: n = 6 mice 2 weeks: n = 6 mice 4 weeks: n = 6 mice 6 weeks: n = 6 mice |
16S rRNA gene sequencing (V3-V4 region) |
OMEGA soil DNA extraction kit | Illumina MiSeq | α-diversity: Shannon index and β-diversity: Weighted UniFrac distance |
QIIME 2 | Upper airway microbiome of the OVA induced mice had significantly higher α-diversity than control mice. Insignificant α-diversity difference in the lower airway microbiome of the OVA induced mice and control mice. Significant difference detected in β-diversity between the OVA-induced mice and control mice. The dominant respiratory microbiome in the acute inflammatory and airway remodelling stages were different. Acute inflammatory stage: ↑ Relative abundance of Pseudomonas spp. Airway remodelling stage: ↑ Relative abundance of Staphylococcus spp. and Cupriavidus spp. |
| Lower airway microbiome | |||||||||||
| [48] ‘High-throughput 16S rDNA sequencing of the pulmonary microbiome of rats with allergic asthma’ |
China | Normal control group: n = 4 Saline control group: n = 4 Allergic asthma group: n = 4 |
4–6 weeks | Lung tissues | 1 time point Normal control group: lung tissues on day 0 Saline control and allergic asthma groups: lung tissues on day 29 |
16S rRNA gene sequencing (V4−V5 region) |
No mention | Illumina high-throughput technology (Illumina PE250) | α-diversity: Chao index, coverage index, Shannon index, and Simpson index and β-diversity: Bray–Curtis |
Mothur | The α-diversity of the lower airway microbiome in the allergic asthma group increased. Significant difference between normal control group and allergic asthma group was detected. Normal control group: ↑ Proteobacteria. Allergic asthma group: ↑ Firmicutes. |
| Lower airway and gut microbiome | |||||||||||
| [49] ‘Alteration of Lung and Gut Microbiota in IL-13-Transgenic Mice Simulating Chronic Asthma’. |
Korea | IL-13 overexpressing transgenic (TG) mice: n = 30 C57BL/6 wild-type (WT) mice: n = 30 |
10-week-old mice for both groups | BAL, lung tissue and faecal | 1 time point | 16S rRNA gene sequencing (no mention of region) | FastDNA SPIN Kit | Illumina MiSeq | α-diversity: Shannon index, Chao1 index, and the Inverse Simpson’s diversity index and β-diversity: Weighted UniFrac distances |
QIIME | No significant difference in α-diversity was observed. Altered β-diversity in lung and gut microbiota in the IL-13 TG mice compared to the WT mice. IL-13 TG mice (lungs): ↑ Proportion of Proteobacteria and Cyanobacteria. ↓ Amount of Bacteroidetes IL-13 TG mice (gut): ↓ Firmicutes and Proteobacteria. |