Differences in faecal microbiome composition between adult patients with UCD and PKU and healthy control subjects

C Timmer; M Davids; M Nieuwdorp; J H M Levels; J G Langendonk; M Breederveld; N Ahmadi Mozafari; M Langeveld

doi:10.1016/j.ymgmr.2021.100794

Differences in faecal microbiome composition between adult patients with UCD and PKU and healthy control subjects

Mol Genet Metab Rep. 2021 Sep 8:29:100794. doi: 10.1016/j.ymgmr.2021.100794. eCollection 2021 Dec.

Authors

C Timmer¹, M Davids², M Nieuwdorp², J H M Levels², J G Langendonk³, M Breederveld³, N Ahmadi Mozafari³, M Langeveld¹

Affiliations

¹ Department of Dietetics and Nutritional science and Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
² Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
³ Department of Dietetics and Department of Internal Medicine, Center of Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Erasmus MC, Rotterdam, the Netherlands.

Abstract

Urea cycle disorders (UCDs) are a group of rare inherited metabolic diseases causing hyperammonemic encephalopathy. Despite intensive dietary and pharmacological therapy, outcome is poor in a subset of UCD patients. Reducing ammonia production by changing faecal microbiome in UCD is an attractive treatment approach. We compared faecal microbiome composition of 10 UCD patients, 10 healthy control subjects and 10 phenylketonuria (PKU) patients. PKU patients on a low protein diet were included to differentiate between the effect of a low protein diet and the UCD itself on microbial composition. Participants were asked to collect a faecal sample and to fill out a 24 h dietary journal. DNA was extracted from faecal material, taxonomy was assigned and microbiome data was analyzed, with a focus on microbiota involved in ammonia metabolism.In this study we show an altered faecal microbiome in UCD patients, different from both PKU and healthy controls. UCD patients on dietary and pharmacological treatment had a less diverse faecal microbiome, and the faecal microbiome of PKU patients on a protein restricted diet with amino acid supplementation showed reduced richness compared to healthy adults without a specific diet. The differences in the microbiome composition of UCD patients compared to healthy controls were in part related to lactulose use. Other genomic process encodings involved in ammonia metabolism, did not seem to differ. Since manipulation of the microbiome is possible, this could be a potential treatment modality. We propose as a first next step, to study the impact of these faecal microbiome alterations on metabolic stability.

Take home message: The faecal microbiome of UCD patients was less diverse compared to PKU patients and even more compared to healthy controls.

Keywords: 16S rRNA, taxonomic marker genes, common to all bacteria; ADI, Arginine Deimination. Bacteria derive energy from the deamination of arginine to citrulline and citrulline cleavage to ornithine plus carbamoyl phosphate. The latter is then converted into ATP and carbon dioxide, or used for pyrimidine biosynthesis. This route also generates two moles of ammonia (one from the arginine-citrulline conversion, the second from carbamoyl phosphate hydrolysis); ARG1d, arginase 1 (ARG1) deficiency; ASLd, argininosuccinate lyase (ASL) deficiency; ASSd, argininosuccinate synthetase (ASS) deficiency; ASV, Amplified Sequence Variant. A specific nucleotide sequence representing a bacterial lineage; Alpha Diversity, the species diversity in a microbial sample. Used to represent the taxonomic diversities of individual samples; Ammonium scavengers, agents developed for the reduction of blood ammonia concentration used for the treatment of patients with urea cycle disorders. Sodiumbenzoate and phenylbutyrate are ammonium scavengers; BCAA, branched chain amino acids: isoleucine, leucine and valine; DEGs, differentially expressed genes; DESeq, an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression; EAA supplement, essential amino acids supplement containing L-histidine, L-isoleucine, L-leucine, l-lysine, L-methionine, L-phenylalanine, L-threonine, L-tryptofaan and L-valine with optional L-cystine and L-tyrosine added (depending on what product is used); FPD, Faiths Phylogenetic Diversity, alpha diversity metric accounting for genetic diversity; Faecal; Genus, a taxonomic rank; Gut; Hyperammonemia; Metagenome, microbiome collective genome; Microbiome; OTCd, ornithine transcarbamylase deficiency; PCoA, Principal Coordinate Analysis. PCoA is aimed at graphically representing a resemblance matrix between p elements (individuals, variables, objects, among others). By using PCoA we can visualize individual and/or group differences. Individual differences can be used to show outliers; PFAA, precursor free amino acid supplement, in this case phenylalanine free; PKU, Phenylketonuria; Phenylketonuria; Proteolytic capacity, the capacity to break proteins down into smaller polypeptides or amino acids. In this study: enzymes involved in protein degradation; RT-qPCR, real-time quantitative polymerase chain reaction; Sodium BPA, sodium phenylbutyrate; UCD, urea cycle defect; Urea cycle defect.