Changes in gut microbiota in the acute phase after spinal cord injury correlate with severity of the lesion

Abstract

After spinal cord injury (SCI), patients face many physical and psychological issues including intestinal dysfunction and comorbidities, strongly affecting quality of life. The gut microbiota has recently been suggested to influence the course of the disease in these patients. However, to date only two studies have profiled the gut microbiota in SCI patients, months after a traumatic injury. Here we characterized the gut microbiota in a large Italian SCI population, within a short time from a not only traumatic injury. Feces were collected within the first week at the rehabilitation center (no later than 60 days after SCI), and profiled by 16S rRNA gene-based next-generation sequencing. Microbial profiles were compared to those publicly available of healthy age- and gender-matched Italians, and correlated to patient metadata, including type of SCI, spinal unit location, nutrition and concomitant antibiotic therapies. The gut microbiota of SCI patients shows distinct dysbiotic signatures, i.e. increase in potentially pathogenic, pro-inflammatory and mucus-degrading bacteria, and depletion of short-chain fatty acid producers. While robust to most host variables, such dysbiosis varies by lesion level and completeness, with the most neurologically impaired patients showing an even more unbalanced microbial profile. The SCI-related gut microbiome dysbiosis is very likely secondary to injury and closely related to the degree of completeness and severity of the lesion, regardless of etiology and time interval. This microbial layout could variously contribute to increased gut permeability and inflammation, potentially predisposing patients to the onset of severe comorbidities.

Figure 1

Diversity of the gut microbiota of SCI patients as compared to healthy controls. (A) Box plots showing the distribution of alpha diversity values, according to the inverse Simpson index in SCI patients as compared to age- and sex-matched healthy Italian controls. (B) Principal Coordinates Analysis based on Bray–Curtis distances between the genus-level microbial profiles of SCI patients and healthy controls. A significant separation was found (p = 0.001, permutation test with pseudo-F ratios).

Figure 2

Compositional structure of the gut microbiota in SCI. Pie charts showing the average relative abundance of the most abundant phyla (A) and families (B) in SCI patients as compared to age- and sex-matched healthy Italian controls. Only taxa with relative abundance > 0.1% in at least 20 samples for phyla and > 0.01% in at least 30 samples for families are shown. (C) Box plots showing the distribution of the relative abundance values of discriminant genera between SCI patients and healthy controls, according to Random Forests. p < 0.001, Wilcoxon rank sum test.

Figure 3

Enterotype-like groups in SCI patients. (A) Principal Coordinates Analysis of enterotype clusters in SCI patients. Three enterotypes were identified by using the Jensen-Shannon divergence distance metric. The ellipse covers 67% of the samples belonging to a cluster. The silhouette coefficient is shown at the top right. (B) Box plots showing the distribution of the relative abundance values of discriminant genera among the three enterotype-like groups. p < 0.001, Kruskal–Wallis test.

Figure 4

The gut microbiota dysbiosis in SCI patients is stable over time. Principal Coordinates Analysis based on Bray–Curtis distances between the genus-level microbial profiles of SCI patients according to the time interval between injury and fecal sampling (≤ 15 days, between 16 and 30 days, over 30 days). No significant segregation was found (p > 0.05, permutation test with pseudo-F ratios).

Figure 5

The gut microbiota profiles of SCI patients stratify by AIS score and severity of injury. Principal Coordinates Analysis based on Bray–Curtis distances between the genus-level microbial profiles of SCI patients according to AIS score (A) and SCI severity (B). A significant separation by both covariates was found (p ≤ 0.04, permutation test with pseudo-F ratios). More severity, AIS score A or B and neurological level of lesion between C1 to C6 and C7 to T6; less severity, AIS score A or B and lesion level between T7 and L5, and AIS score C or D and every neurological level of lesion. Box plots showing the distribution of the relative abundance values of discriminatory genera by AIS score (C) and SCI severity (D). p ≤ 0.05, Wilcoxon rank sum test.

Figure 6

Impact of antibiotics administration on the gut microbiota of SCI patients. (A) Principal Coordinates Analysis based on Bray–Curtis distances between the genus-level microbial profiles of SCI patients according to antibiotics administration and timing (i.e., no antibiotic therapy, and therapy in the 3 days or between 4 and 10 days before fecal sampling). A significant separation among groups was found (p = 0.001, permutation test with pseudo-F ratios). (B) Box plots showing the distribution of the relative abundance values of discriminant genera. p ≤ 0.05, Kruskal–Wallis test.