The Intestinal Microbiome in Children with Inflammatory Bowel Disease and Lactose Malabsorption

Dataset overview

Participants 185

Samples 459

Reuse readiness 7.7/10 evidence-backed score

The intestinal microbiome, but not clinical aspects of inflammatory bowel disease, is impacted by lactose malabsorption compared to lactose digestion in children.

Cohen A, Li J, Butcher J, Singleton R, Barbeau P, Stintzi A, Mack DR. · The American journal of clinical nutrition · 2024

Abstract

<h4>Background</h4>Dietary exclusion of lactose from patients with inflammatory bowel disease (IBD) persists with speculation that deleterious effects are mediated through intestinal microbes.<h4>Objectives</h4>To compare IBD characteristics and changes in the intestinal microbiome (IM) at diagnosis in children with and without lactose malabsorption (LM).<h4>Methods</h4>A cross-sectional cohort of children (8-17 y of age) diagnosed with Crohn's disease [n = 149 (63%)] or ulcerative colitis (n = 86) that had undergone lactose breath hydrogen testing was evaluated. The IM of mucosal luminal aspirates was profiled at the time of diagnosis using 16S ribosomal ribonucleic acid gene amplicon sequencing of the V6 hypervariable region.<h4>Results</h4>Of the 235 children, 61 (26%) had LM. Microbial characterization yielded differences in bacterial differential abundance between children who could and could not absorb lactose, which varied by intestinal site and between subtypes of IBD. There were no differences in the ages [13.2 ± 3.0 y (mean ± standard deviation) compared with 12.7 ± 3.4 y; P = 0.25], sex (P = 0.88), extent of disease involvement or severity of disease at presentation (P = 0.74) when comparing those that could or could not absorb lactose nor was there a difference in the need for initiation of biological agents (P = 0.43) during 2 y of follow-up.<h4>Conclusions</h4>LM does not affect the clinical presentation or outcomes of children with IBD. However, this study establishes that a single nonabsorbed fermentable food product can alter the IM in both a regional and disease-specific manner. As we continue to learn more about the pathophysiology of IBD and the role of the IM in disease onset and progression, it would be of benefit to examine the impact of other potential fermentable nutrients and their products on IBD outcomes.

doi:10.1016/j.ajcnut.2024.09.031 ↗ PMID 39374806 ↗ PMC11619786 ↗

Study facts

Organism: human gut metagenome
Platform: Illumina HiSeq 2500
Age group: paediatric
Disease groups: Crohn's disease, Ulcerative colitis
Anatomical sites: —

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Feature/OTU tables are advertised
Taxonomic tables are advertised
Participant counts are documented
Sample counts are documented

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.paired_end`	True	sequenced on an Illumina HiSeq to generate 100 bp paired-end reads Section `Methods — Amplicon sequencing of the 16S rRNA hypervariable region 6`, offset 9000
`assay.platform`	Illumina HiSeq 2500 from source	ENA instrument_model=Illumina HiSeq 2500 Section `ENA study report`, offset —
`assay.primers_reported`	True	The PCRs consisted of 50 ng of metagenomic DNA, 0.5 μmol of each primer Section `Methods — Amplicon sequencing of the 16S rRNA hypervariable region 6`, offset 8050
`assay.read_depth_reported`	150000	Samples with <150,000 reads were discarded from the analysis, and all samples were rarefied to 150,000 Section `Bioinformatic and statistical analyses — IM`, offset 10800
`assay.read_length`	100	generate 100 bp paired-end reads Section `Methods — Amplicon sequencing of the 16S rRNA hypervariable region 6`, offset 9000
`assay.sequencing_type`	amplicon_16s	using 16S rRNA amplicon sequencing of the V6 hypervariable region Section `study.description`, offset —
`assay.target_region`	V6 hypervariable region	The 16S rRNA hypervariable region 6 (V6-16S) gene amplicon libraries were constructed and sequenced Section `Methods — Amplicon sequencing of the 16S rRNA hypervariable region 6`, offset 7600

Cohort

Field	Value	Evidence
`cohort.age_group`	paediatric	evaluated children with Crohn's disease and Ulcerative Colitis Section `study.description`, offset —
`cohort.crohns_disease_participants`	118	a total of 185 participants (CD = 118; UC = 67) underwent MLI sampling Section `Results — Mucosal luminal aspirate IM characterization`, offset 12300
`cohort.disease_activity_metadata_available`	True	For CD, the clinical severity was reported using the Pediatric CD activity index, and for UC, the Pediatric UC activity index was used. Section `Methods — Participants`, offset 4100
`cohort.study_design`	cross_sectional	A cross-sectional cohort of 235 children diagnosed with IBD Section `Methods — Participants`, offset 3200
`cohort.total_participants`	185	a total of 185 participants (CD = 118; UC = 67) underwent MLI sampling Section `Results — Mucosal luminal aspirate IM characterization`, offset 12300
`cohort.treatment_exposure_documented`	True	All participants were IBD treatment naïve Section `Methods — Participants`, offset 3450
`cohort.ulcerative_colitis_participants`	67	a total of 185 participants (CD = 118; UC = 67) underwent MLI sampling Section `Results — Mucosal luminal aspirate IM characterization`, offset 12300

Data_Assets

Field	Value	Evidence
`data_assets.feature_or_otu_table`	True	subsequently processed into amplicon sequence variants (ASVs) Section `Bioinformatic and statistical analyses — IM`, offset 10400
`data_assets.open_access`	True from source	"inPMC": "Y", "isOpenAccess": "Y", "license": "cc by-nc-nd" Section `publication metadata`, offset —
`data_assets.qc_or_negative_controls_reported`	True	reads ... were filtered to remove primer sequences, read pairs with >1 expected error, denoized ... and the pairs merged Section `Bioinformatic and statistical analyses — IM`, offset 10650
`data_assets.raw_reads`	True	Demultiplexed raw sequencing reads ... were deposited ... under accession PRJNA1062375. Section `Data availability`, offset 19000
`data_assets.taxonomic_table`	True	had their taxonomy assigned against the high quality ribosomal RNA SILVA 132 database Section `Bioinformatic and statistical analyses — IM`, offset 10600

Specimens

Field	Value	Evidence
`specimens.body_site`	terminal ileum, ascending colon, and descending colon	descending colon (DC), ascending colon (AC), and lastly from the TI Section `Methods — MLI aspirate collection`, offset 6400
`specimens.longitudinal_sampling`	False inferred	MLI aspirate sampling ... was performed during their diagnostic colonoscopy Section `Methods — Participants`, offset 3500
`specimens.number_of_samples`	459 from source	ENA sample_count=459 Section `ENA study report`, offset —
`specimens.sample_type`	luminal_aspirate	The intestinal microbiome of mucosal luminal aspirates was profiled Section `study.description`, offset —