Table 1.
Case–control studies investigating differences in gut microbiome diversity and composition between healthy children and children with acute lymphoblastic leukaemia at the time of diagnosis
| Study | Country | Age of casesa | Cases (N) | Ab (time)b % of n | Type of control | Age of controla | Control (N) | Ab (time)b % of n | Seq | HVR | Reported levels of taxonomy | Method of analysis of relative abundance | Reporting threshold for relative abundance | FDR |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| De Pietri et al., 2020 (ref. 71) | USA | 3.7 | 51 | NR | HS | 6.8 | 18 | No (30 days) | 16s rRNA | V3–V4 | NR | NR | NR | NR |
| Gao et al., 2020 (ref. 72) | China | 6.3 | 18 | No (14 days) | UHC | 5.9 | 18 | No (14 days) | 16s rRNA | V3–V4 | Genus | WMW | FC > 1.5 | <0.05 |
| Chua et al., 2020 (ref. 75) | Malaysia | 2–6 | 7 | Yes (30 days), 100% | UHC | 2–6 | 7 | No (30 days) | 16s rRNA | V4 | Phylum, Genus | DESeq2 | FC > 4 | <0.1 BHP |
| Rajagopala et al., 2020 (ref. 73) | USA | 5.0 | 29 | Yes (60 days), 61% | HS | 6.0 | 23 | No (60 days) | 16s rRNA | V4 | Phylum, Genus | DESeq2 | FC > 1.5 | <0.05 BHP |
| Bai et al., 2017c (ref. 74) | China | 5.5 | 20 | Yes (30 days), 100% | UHC | 4.3 | 16 | Yes (30 days), 100% | 16s rRNA | V3–V4 | Phylum, Class, Order, Family, Genus | LEfSE | LDA > 2 | <0.05 |
| 5.6 | 10 | No (90 days) | UHC | 4.5 | 17 | No (90 days) | ||||||||
| Liu et al., 2020 (ref. 70) | China | 7.2 | 58 | No (90 days) | UHC | 7.6 | 23 | No (90 days) | 16s rDNA micro -array | V1–V9 | Phylumd, Classd, Orderd, Familyd, Genusd, Species | LEfSE | LDA > 2 | <0.05 |
Ab, antibiotics; BHP, Benjamini–Hochberg procedure; DESeq2, differential gene expression analysis based on the negative binomial distribution; FC, fold change; FDR, false discovery rate; HS, healthy sibling; HVR, hypervariable region (the region of the 16s rRNA gene targeted for sequencing); LDA, linear discriminant analysis score; LEfSE, linear discriminant analysis (LDA) of effect size; N, sample number; NR, not reported; Seq, sequencing platform; UHC, unrelated healthy child; WMW, Wilcoxon–Mann–Whitney test. aAge reported as arithmetic mean or range (in years). bTime interval within which patients were exposed to antibiotics before sample collection or antibiotic-free time interval before sample collection. cThe study included two independent cohorts of antibiotic-exposed and antibiotic-unexposed participants. dFor this taxonomic level, we used participant-level data provided by the study to determine, through linear discriminant analysis of effect size, differences in relative abundances between study groups.