Public Health Agency of Canada

Author Of 1 Presentation

Microbiome Oral Presentation

PS10.03 - Functional survey of the pediatric multiple sclerosis microbiome        

Speakers
Presentation Number
PS10.03
Presentation Topic
Microbiome
Lecture Time
09:45 - 09:57

Abstract

Background

Metagenomic sequencing reveals the functional potential of the gut microbiome, and may explain how the gut microbiome influences pediatric-onset multiple sclerosis (MS) risk.

Objectives

To examine the gut microbiome functional potential by metagenomic analysis of stool samples from pediatric MS cases and controls using a case-control design.

Methods

Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network who provided a stool sample and were not exposed to antibiotics or corticosteroids 30 days prior were included for study. All MS cases met McDonald criteria, had symptom onset <18 years of age and had either no prior disease-modifying drug (DMD) exposure or were exposed to beta-interferon or glatiramer acetate only. Twenty MS cases were matched to 20 non-affected controls by sex, age (± 3 years), stool consistency (Bristol Stool Scale, BSS) and, when possible, by race. Shotgun metagenomic reads were generated using the Illumina NextSeq platform and assembled using MEGAHIT. Metabolic pathway analysis was used to compare the gut microbiome between cases and controls, as well as cases by DMD status (DMD naïve vs DMD exposed MS cases vs controls). Gene ontology classifications were used to assess α-diversity and differential abundance analyses (based on the negative binomial distribution) reported as age-adjusted log-fold change (LFC) in relative abundance, 95% confidence intervals (CI), and false discovery rate adjusted p-values.

Results

The MS cases were aged 13.6 mean years at symptom onset. On average, MS cases and controls were 16.1 and 15.4 years old at the time of stool collection and 80% of each group were girls. MS cases and controls were similar for body mass index (median: 22.8 and 21.0, respectively), stool consistency (BSS types 1-2: n=4, types 3-5: n=16, for both MS and controls) and race (Caucasian: 11 and 9, respectively). Eight MS cases were DMD naïve. Richness of gene ontology classifications did not differ by disease status or DMD status (all p>0.4). However, differential analysis of metabolic pathways indicated that the relative abundance of tryptophan degradation (via the kynurenine pathway; LFC 13; 95%CI: 8–19; p<0.0005) and cresol degradation (LFC 19; 95%CI: 13–25; p<0.0001) pathways were enriched for MS cases vs controls. Differences by DMD status were also observed, e.g., choline biosynthesis was enriched in DMD exposed vs naïve MS cases (LFC 21; 95%CI: 12–29; p<0.0001).

Conclusions

We observed differences in the functional potential of the gut microbiome of young individuals with MS relative to controls at various metabolic pathways, including enrichment of pathways related to tryptophan and metabolism of industrial chemicals. DMD exposure affected findings, with enrichment of pathways involved in promoting CNS remyelination (e.g., choline).

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Author Of 2 Presentations

Biomarkers and Bioinformatics Poster Presentation

P0171 - The gut mycobiome in pediatric multiple sclerosis: establishing a bioinformatics pipeline (ID 876)

Speakers
Presentation Number
P0171
Presentation Topic
Biomarkers and Bioinformatics

Abstract

Background

Studies examining the role of the microbiota in multiple sclerosis (MS) often focus on the gut bacteria; few have considered a potential role of gut mycobiota. Methods for evaluating gut mycobiota are lacking and require systematic evaluation of sequencing protocols, reference databases, and bioinformatics pipelines to properly investigate possible gut mycobiome influences on MS.

Objectives

We set out to evaluate the performance of different sequencing conditions and analytical approaches for characterizing the gut mycobiome in a cohort of healthy individuals and cases with monophasic acquired demyelinating syndrome (mono ADS) or pediatric-onset MS.

Methods

We first assessed a mock-community control pool of known, staggered quantities of 19 defined fungal organisms. We then assessed 201 stool samples obtained from our cohort of 52 healthy individuals, 49 individuals with mono ADS, and 46 participants with pediatric-onset MS. The fungal internal transcribed spacer (ITS) 2 region was sequenced using the Illumina® MiSeq platform. Varying concentrations of PhiX Control v3 Library spike-in were tested to address low-complexity amplicon sequencing. Generated sequences were characterized by the UNITE database—a curated collection of eukaryotic ITS sequences—in conjunction with three distinct fungal sequence analysis pipelines: LotuS, mothur, and PIPITS.

Results

Taxa identified in our mock-community differed across sequencing conditions but were similar between technical replicates. LotuS correctly classified 7 taxa at species-level, 7 taxa at genus-level, whereas 5 remained unclassified. Mothur correctly identified 5 species-level taxa, 11 genus-level taxa, whereas 3 remained unclassified. Lastly, PIPITS correctly identified only 3 species-level taxa, 12 genus-level, while 4 remained unclassified. We successfully generated sequence data for 112 of 147 (76%) individuals (70 females; 42 males). The mean age at stool sample collection was 17.3 (SD 5.1) years. Of the tested sequencing conditions, a spike-in of 50% PhiX produced the highest-quality reads.

Conclusions

The LotuS pipeline best identified fungal taxa in our mock-community, with optimal resolution to species level. Sequencing read quality was optimal when 50% PhiX was used for sequencing ITS2 amplicon libraries of stool samples. Establishment of this validated sequencing pipeline, confirmed using a mock-community with known fungal identities, will aid characterization of gut mycobiomes for our cohort of individuals with/without pediatric-onset MS.

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Microbiome Poster Presentation

P0679 - The gut microbiota: a case-control study of children with multiple sclerosis, monophasic acquired demyelinating syndromes and unaffected controls (ID 102)

Abstract

Background

The gut microbiota may influence multiple sclerosis (MS) onset. Pediatric MS offers the opportunity to examine pathological processes close to risk acquisition.

Objectives

To examine the gut microbiota from stool samples of persons with pediatric onset MS, or monophasic acquired demyelinating syndromes (ADS) and unaffected controls in a case-control study.

Methods

Persons ≤21 years old with symptom onset <18 years of age with either MS (McDonald criteria) or ADS were eligible, as were unaffected controls with no known neurological or immune-mediated condition (migraine, asthma/allergies were permissible) were enrolled via the Canadian Pediatric Demyelinating Disease Network. Stools were collected between Nov/2015–Mar/2018, shipped on ice, and stored at -80°C. The 16S ribosomal RNA gene (V4 region) was amplified from extracted DNA and sequenced via the Illumina MiSeq platform. Amplicon sequence variants were used to compare the gut microbiota by disease status (MS/ADS/controls). The MS cases were also compared by disease-modifying drug (DMD) status (exposed/naïve). Negative binomial regression was used for genus-level analyses, with rate ratios adjusted (aRR) for age and sex.

Results

Of the 32/41/36 included MS/ADS/control participants, 24/23/21 were girls, averaging age 16.5/13.8/15.1 years at stool sample, respectively. The MS/ADS cases were 14.0/6.9 years at symptom onset. The 3 groups (MS/ADS/controls) were relatively similar for: body mass index (median: 22.8/19.7/19.9), presence of constipation (number of participants with a Bristol Stool Scale score of 1 or 2=8/9/7) and diet (% caloric intake for fat (median)=34/35/34 and for fibre (median)=9/10/11 g/day). Nine MS cases (28%) were DMD naïve. Gut microbiota diversity (alpha and beta) did not differ by disease (MS/ADS/controls), or DMD status (all p>0.1), while taxa-level findings did. For example, relative abundance of the Proteobacteria, Sutterella was depleted for MS cases vs controls and MS vs ADS cases (aRR:0.13;95%CI:0.03–0.59 and 0.21;95%CI:0.05–0.98), but did not differ for the ADS cases vs controls or by DMD status for the MS cases (all p>0.1). Several of the butyrate-producing genera within the Clostridia class (Firmicutes phylum) —Ruminococcaceae UCG−003, Lachnospiraceae UCG−008 and UCG−004—exhibited similar patterns.

Conclusions

Gut microbiota diversity was similar for individuals with pediatric MS relative to either monophasic ADS or unaffected controls. However, at the taxa-level, differences were observed which differentiated the MS cases from the monophasic ADS cases and controls.

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