Table 3.
Sample frequency and sequencing details.
| Author | Method of Analysis | Number of Samples per Participant | Sample Collection Timepoints (Weeks) | Dietary Control (for Study Period) | Dietary Assessment | Taxonomic Labelling Tool Used |
|---|---|---|---|---|---|---|
| Craven et al., 2021 [18] |
16S | 4 | 0 (×2), 6 (AFT), 7 (Taper) | No | 3-day diet diary at each testing point | NCBI database |
| Tabone et al., 2021 [19] |
16S | 2 | 0, <1 | No | FFQ and 3 × 24-h food diary recall | Silva reference database |
| Zeppa et al., 2021 [20] |
16S | 2 | 0, 9 | No | Daily diaries for duration of study (plus two weeks prior) | GreenGenes and UCLUST |
| Karl et al., 2017 [21] |
16S | 2 | 0, <1 | Yes | No | RDP classifier |
| Zhao et al., 2018 [22] | 16S | 2 | 0, <1 | Yes (type of food) | Questionnaire | Not Reported |
| Grosicki et al., 2019 [23] |
16S | 4 | 1, 19, 21 (after competition), 23 | No | No | PAST: Paleontological Statistics Software |
| Keohane et al., 2019 [24] |
metagenomic | 4 | 0 (BEF), ~2, <5 (AFT), +3 months | No | FFQ (baseline), daily diet diary | MetaPhlAn2.0 |
| Barton et al., 2020 [25] |
metagenomic | 14 | Fortnightly (0–26) | No | daily diary—My Fitness Pal App | MetaPhlAn2 database |
| Oliveira et al., 2022 [26] |
16S | 2 | 0, <1 | 24-h food records | Kraken taxonomy + Bracken custom data base (GutHealth_DB) |
|
| Bycura et al., 2021 [27] |
16S | 28 | −3, 0 (BEF), 8 (AFT), 11 (two samples per week) | No | No | Bayes classifier in q2-feature Classifier Genome Taxonomy Database |
| Erlandson et al., 2021 [28] | 16S | 2 | 0, 24 | No | 3-day diet diary | SINA |
| Resende et al., 2021 [29] |
16S | 2 | 0, 10 | No | 48 h food record, FFQ and 3-day food diary | Greengenes |
| Huber et al., 2019 [30] |
NR | 2 (n = 9) | 0, 8 | No | No | NR |
| Verheggen et al., 2021 [31] | 16S | 2 | 0, 8 | No (recommended to not change dietary pattern) | 24-h diary prior to sample, FFQ | NG-Tax |
| Cronin et al., 2018 [32] |
metagenomic | 2 | 0, 8 | No | FFQ | Kraken taxonomy |
| Shukla et al., 2015 [33] |
16S | 3 | 0 (BEF), 48 h (AFT), 72 h | No | RDP classifier | |
| Allen et al., 2018 [34] | 16S | 3 | 0 (BEF), 6 (AFT), 12 weeks | 3-days prior to sample collection | 3-day food menu was followed prior to each faecal collection. Menu organised from 7-day diet diary |
RDP classifier |
| Morita et al., 2019 [35] |
16S | 2 | 0, 12 | No | FFQ | Human Faecal Microbiota T RFLP profiling (10 groups) |
| Rettedal et al., 2020 [36] |
16S | 4 | 0 (x 2), 3 | Recommended to not change dietary pattern | FFQ | SILVA database v.132 |
| Taniguchi et al., 2018 [37] |
16S | 3 | 0, 5 (AFT), 10 | No | Yes (Diet history questionnaire) | UCLUST |
| Munukka et al., 2018 [38] |
Metagenomic and 16S | 3 | 0, 6 (BEF), 12 (AFT) | No | 3-day food diary | Silva 123.4 database |
| Cronin et al., 2019 [39] |
Metagenomic | 3 | 0, 8 (AFT), 16 | No | No | Kaiju taxonomic assignment |
| Kern et al., 2020 [40] |
16S | 3 | 0 (BEF), 12, 24 (AFT) | No | 3-day food diary | RDP classifier |
| Motiani et al., 2020 [41] |
16S | 2 | 0, 2 | No | No | Greengenes GG 13.8 Database |
| Warbeck et al., 2020 [42] |
16S | 3 | 0, 12 (AFT, BEF for WLC), 24 (Follow up, AFT for WLC) |
No | 3-day diet diary | Silva 136 database |
| Dupuit et al., 2021 [43] |
16S | 2 | 0, 12 | Recommended to not change dietary pattern | 5-day food intake diary | Greengenes GG 13.8 Database |
| Mahdieh et al., 2021 [44] |
16S | 2 | 0, 10 | No | 72 h recall | Other: Targeted analysis of Lactobacillus and Bifidobacterium |
| Mokhtarzade et al., 2021 [45] | QPCR | 2 | 0, 26 | No | 72 h recall | Other: Targeted analysis of Prevotella, Akkermansia mucinophila, Faecalibacterium prausnitzii and Bacteroides |
NR = Not reported, BEF = Before intervention, AFT = After intervention, 16S = 16S mRNA (or DNA) sequencing, FFQ = Food frequency questionnaire, ME = Myalgic encephalomyelitis, Ex = Exercise, AT = Aerobic training.