Alterations in microbial composition of the gut and urine are associated with many seemingly diverse disorders, affecting the immune system and correspondingly influence the composition of the microbiome (i.e. reciprocal signaling). Individuals with spinal cord injury (SCI) are prone to infections and this could be reflected by changes in the microbiome. Given the paucity in the current literature, there is a need to evaluate urinary tract (UT) and gastrointestinal (GI) microbiota in individuals with chronic SCI.

The aim of this exploratory, feasibility study was to investigate UT and GI microbiota in chronically spinal cord injured individuals in order to identify differences between those with recurrent / chronic infections (YES) and those without (NO). The study was registered at clinicaltrials.gov (NCT02903472) and approved by the local ethics boards of all participating centers, i.e. Zurich (Switzerland), Manhasset (USA), and Fredericton (Canada).
Main inclusion criterion: Individuals with a chronic tetraplegic or paraplegic motor complete (American Spinal Injury Association impairment scale [AIS] A, B) or motor incomplete (AIS C, D) single non-penetrating SCI to the C2-S1 spinal cord, with either recurrent / chronic infections YES or NO, were recruited. Urine and stool samples were scheduled to be obtained approximately 1, 6, and 12 months after enrollment.
DNA sequencing: 16Sv4 amplicons generated from the samples were sequenced, quality-filtered and clustered into 97% similarity operational taxonomic unit (OTUs). Any sample with a read count <1000 was removed the analysis. OTUs were aggregated into each taxonomic rank, and plotted the relative abundance of the most abundant ones. Alpha diversity (Shannon index) was computed and compared between both groups (i.e. infection YES or NO) using analysis of variance (ANOVA). Microbiome composition similarity among samples (Beta diversity) was assessed using permutational ANOVA (PermANOVA). Differential abundance testing was used to identify differentially abundant taxa between both groups. Thus far, we conducted analysis of the urine samples only.

Overall 19 individuals (5 women, 26%, median age 44 years [Q1: 36; Q3: 52] and time post injury 7 years [2.5; 17.5]) were enrolled. Alpha diversity (i.e. Shannon indices shown as mean [SD]) for recurrent / chronic infections YES or NO, were 0.962 [0.735] or 0.677 [0.701], respectively. ANOVA revealed no significant differences (p=0.224) in Alpha diversity between recurrent / chronic infections YES and NO. PermANOVA determined no significant differences (R2=0.0318, P=0.239) in Beta diversity between recurrent / chronic infections YES or NO. Differential abundance testing identified 11 differently abundant (false discovery rate, FDR < 0.05) OTUs, i.e. Phylum / Genus: 1) Proteobacteria / Pseudomonas; 2) Firmicutes / Staphylococcus; 3) Bacteroidota / Prevotellaceae_unclassified; 4)
Actinobacteriota / Corynebacterium; 5) Bacteroidota / Bacteroides; 6) Bacteroidota / Bacteroides; 7) Firmicutes / Faecalibacterium; 8) Bacteroidota / Bacteroides; 9) Actinobacteriota / Micrococcales_unclassified; 10) Actinobacteriota / Bifidobacterium; and 11) Firmicutes / Blautia.

Group-level analysis revealed no significant Alpha and Beta diversity differences between chronically injured individuals with recurrent / chronic infections and those without. However, several differentially abundant OTUs were identified.

To gain more in-depth knowledge about differences of the microbiome between these individuals, we will conduct intra-individual analysis of the urine samples. Furthermore, we will conduct analysis for the participants’ corresponding stool samples including short-chain fatty acids (SCFA) which are known to play an important role in the maintenance of health.