What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review
Abstract
:1. Introduction
2. Methods
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Study, Year | Country | Study Population | Test Sample | Study Methods | Study Time points | Key Findings |
---|---|---|---|---|---|---|
Aerssens, 2008 [17] | United States | 36 IBS patients (21 IBS-D and 15 IBS-C) and 25 healthy controls; Rome II criteria for diagnosis | Colon biopsy samples | Histological assessment, microarray analysis and real-time quantitative PCR | Two time points, ~3 months interval |
|
Ankersen, 2021 [18] | Denmark | 34 IBS patients (either IBS-D or IBS-M) randomised to receive either web-based low FODMAP diet intervention or probiotic; Rome III criteria for diagnosis | Stool sample | CeGaT GmbH culture-independent, whole-genome, shotgun metagenomic, next-generation sequencing of genomic DNA | Four time points, during the course of 1 year |
|
Bonfrate, 2020 [19] | Italy | 25 IBS patients randomised to receive either probiotic or placebo; Rome IV criteria for diagnosis | Stool sample | Counts of viable bacteria and community level catabolic profiles; chromatogram peak identification for faecal metabolome | Four time points, 0, 30, 45 and 60 days |
|
Ek, 2015 [20] | Sweden | 534 IBS patients and 4932 healthy controls; adapted version of Rome II criteria | GWA genotyping data and rectal mucosal biopsies | Genotyping with Illumina OmniExpress arrays, SNP-expression quantitative trait loci interactions testing; real-time PCR for candidate gene expression | GWA study in a general population sample, followed by case-control cohorts to study suggestive association signals |
|
Kim, 2019 [21] | South Korea | 63 IBS-D patients randomised to receive either probiotics or placebo; Rome II criteria | Urine sample | Q-TOF-MS metabolomics | Two time points, baseline and after 8 weeks |
|
Kuo, 2015 [22] | United States | 19 IBS patients and 29 IBD patients enrolled in a 9-week relaxation response based mind-body group intervention; Rome III criteria | Whole blood sample | Total RNA isolated from whole blood samples, high-throughput Affymetrix GeneTitan system peripheral blood transcriptome | Two time points, at baseline and after 9 weeks |
|
Le Gall, 2011 [23] | United Kingdom | 10 IBS patients, 13 ulcerative colitis patients and 22 healthy controls; Rome III criteria | Stool sample | High resolution 1H NMR-based metabolomics | Four time points, over 2 years |
|
Mack, 2020 [24] | Germany | 22 IBS patients subjected to two weeks of sugar elimination diet and 7 IBS patients used as controls; Rome IV criteria | Stool sample | 16S rRNA amplicon and shotgun-metagenome sequencing | Three time points, at baseline, after 2-weeks sugar elimination diet and after 4-weeks tolerance phase |
|
Mars, 2020 [16] | United States | 29 IBS-D, 22 IBS-C and 24 healthy controls; Rome III criteria | Mucosal biopsy and stool samples | 16S rRNA sequencing and metagenome sequencing | >1 time point, baseline and then monthly for 6 months |
|
Moser, 2019 [25] | Austria | 10 IBS-D patients treated with an oral synbiotic for four weeks; S3 guidelines for diagnosis | Gastrointestinal mucosal and stool samples | Fluorescence activated cell sorting analysis and 16S rRNA gene analysis of gastrointestinal mucosal specimens; GC-MS analysis and 16S rRNA gene analysis of stool samples | Two time points, baseline and after 4 weeks |
|
Ng, 2013 [26] | Hong Kong | 10 IBS patients and 10 healthy controls treated with oral probiotic mix VSL#3 for four weeks; Rome III criteria | Rectal biopsy samples | 16S rRNA gene sequencing | Two time points, baseline and after 4 weeks |
|
Noorbakhsh, 2019 [27] | Iran | 8 IBS-D patients and 16 healthy controls given synbiotic yoghurt for four weeks; Rome III criteria | Urine and serum specimens | 1H NMR-based metabolomics | Two time points, baseline and after 4 weeks |
|
Nybacka, 2021 [28] | Sweden | 56 IBS patients randomised to low FODMAP or traditional diet interventions for four weeks; Rome III criteria | Urine and serum specimens | 1H NMR-based metabolomics | Two time points, baseline and after 4 weeks |
|
Stenlund, 2021 [29] | Sweden | 91 IBS patients randomised to starch and sucrose restricted diet or control for four weeks; Rome IV criteria | Blood plasma specimen | GC-MS and LC-MS based metabolomics | Two time points, baseline and after 4 weeks |
|
Wang, 2022 [30] | United States | 188 IBS patients randomised to placebo treatment for six weeks | Blood sample | Genotyping with Illumina (Infinium Global Screening Array v2.0) and RNA sequencing | Two time points, baseline and after 6 weeks |
|
Yamamoto, 2019 [31] | Canada | 42 IBS patients and 20 healthy controls; Rome III criteria | Urine specimen | Q-TOF-MS based nontargeted metabolomics | Two time points, 6 weeks apart |
|
Study, Year | Taxonomy of Microbiota | Significant Alterations | |
---|---|---|---|
Ankersen, 2021 [18] | Low FODMAP diet group Streptococcacae (family), Streptococcus sp001556435 (species); Ruminococcaceae (family), MGYG-HGUT-03337 (species); Ruminococcaceae (family), MGYG-HGUT-02040 (species); Ruminococcaeceae (family), Faecalibacterium prausnitzii_H (species); Peptostreptococcaceae (family), Romboutsia timonensis (species; Peptococcaceae (family), MGYG-HGUT-04093 (species); Oscillospiraceae (family), MGYG-HGUT-02704 (species); Oscillospiraceae (family), MGYG-HGUT-02673 (species); Oscillospiraceae (family), MGYG-HGUT-02143 (species); Oscillospiraceae (family), MGYG-HGUT-00703 (species); Oscillospiraceae (family), Flavonifractor plautii (species); Oscillospiraceae (family), ER4 sp003522105 (species); Lachnospiraeceae (family), TF01-11 sp000436755 (species); Lachnospiraeceae (family), MGYG-HGUT-01758 (species); Lachnospiraeceae (family), MGYG-HGUT-01052 (species); Lachnospiraeceae (family), Lachnospira eligens_B (species); Lachnospiraeceae (family), CAG-95 sp900066375 (species); Butyricicoccaceae (family), MGYG-HGUT-01115 (species); Bacteroidaceae (family), Bacteroides caccae (species) | Probiotic group Streptococcaeceae (family), Streptococcus thermophilus (species); Ruminococcaeceae (family), Faecalibacterium prausnitzii_H (species); Lactobacillaceae (family), Lactobacillus_F plantarum (species); Lactobacillaceae (family), Lactobacillus_C paracasei (species); Lactobacillaceae (family), Lactobacillus adiophilus (species); Lachnospiraceae (family), MGYG-HGUT-04609 (species); Lachnospiraceae (family), Acetatifactor sp900066365 (species); Bifidobacteriaceae (family), Bifidobacterium animalis (species); Bacteriodaceae (family), Bacteroides eggerthii (species); Acutalibacteraceae (family), Clostridium_A leptum (species) |
|
Mack, 2020 [24] | Adlercreutzia (genera); Ruminococcus (genera); Coriobacteriaceae (family); Christensenellaceae (family); Ruminococcaceae (family) |
| |
Mars, 2020 [16] | Clostridium innocuum (species); Trueperella pyogenes (species); Citrobacter freundii (species); Ruminococcus sp. AT 10 (species); Granulicatella elegans (species); Streptococcus caballi (species); Streptococcus intermedius (species); Ruminococcus torques (species); Enterobacter lignolyticus (species); Streptococcus oralis (species); Streptococcus gordonii (species); Streptococcus mutans (species); Streptococcus pneumoniae (species); Streptococcus parasanguinis (species); Eubacterium brachy (species); Prevotella baroniae (species); Gardnerella vaginalis (species) |
|
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Ng, Q.X.; Yau, C.E.; Yaow, C.Y.L.; Chong, R.I.H.; Chong, N.Z.-Y.; Teoh, S.E.; Lim, Y.L.; Soh, A.Y.S.; Ng, W.K.; Thumboo, J. What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review. Metabolites 2023, 13, 484. https://doi.org/10.3390/metabo13040484
Ng QX, Yau CE, Yaow CYL, Chong RIH, Chong NZ-Y, Teoh SE, Lim YL, Soh AYS, Ng WK, Thumboo J. What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review. Metabolites. 2023; 13(4):484. https://doi.org/10.3390/metabo13040484
Chicago/Turabian StyleNg, Qin Xiang, Chun En Yau, Clyve Yu Leon Yaow, Ryan Ian Houe Chong, Nicolette Zy-Yin Chong, Seth En Teoh, Yu Liang Lim, Alex Yu Sen Soh, Wee Khoon Ng, and Julian Thumboo. 2023. "What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review" Metabolites 13, no. 4: 484. https://doi.org/10.3390/metabo13040484