Collinsella aerofaciens as a predictive marker of response to probiotic treatment in non-constipated irritable bowel syndrome

Abstract

Probiotics are exploited for adjuvant treatment in IBS, but reliable guidance for selecting the appropriate probiotic to adopt for different forms of IBS is lacking. We aimed to identify markers for recognizing non-constipated (NC) IBS patients that may show significant clinical improvements upon treatment with the probiotic strain Lacticaseibacillus paracasei DG (LDG). To this purpose, we performed a post-hoc analysis of samples collected during a multicenter, double-blind, parallel-group, placebo-controlled trial in which NC-IBS patients were randomized to receive at least 24 billion CFU LDG or placebo capsules b.i.d. for 12 weeks. The primary clinical endpoint was the composite response based on improved abdominal pain and fecal type. The fecal microbiome and serum markers of intestinal (PV1 and zonulin), liver, and kidney functions were investigated. We found that responders (R) in the probiotic arm (25%) differed from non-responders (NR) based on the abundance of 18 bacterial taxa, including the families Coriobacteriaceae, Dorea spp. and Collinsella aerofaciens, which were overrepresented in R patients. These taxa also distinguished R (but not NR) patients from healthy controls. Probiotic intervention significantly reduced the abundance of these bacteria in R, but not in NR. Analogous results emerged for C. aerofaciens from the analysis of data from a previous trial on IBS with the same probiotic. Finally, C. aerofaciens was positively correlated with the plasmalemmal vesicle associated protein-1 (PV-1) and the markers of liver function. In conclusion, LDG is effective on NC-IBS patients with NC-IBS with a greater abundance of potential pathobionts. Among these, C. aerofaciens has emerged as a potential predictor of probiotic efficacy.

Keywords: 16S rRNA gene profiling; Coriobacteriaceae; Dorea; PV-1; diarrhea-predominant IBS; dysbiotic-type IBS; gut-liver axis; mixed-type IBS.

Graphical abstract

Figure 1.

Study scheme (a) and summary of the IBS patients that concluded the PROBE-IBS/2 trial per protocol (PP) in the probiotic arm included in this study (b). NRS, numeric rating scale.

Figure 2.

Fecal bacterial taxa distinguishing responder (R) from non-responder (NR) non-constipated IBS patients. P values, derived from Mann-Whitney tests on CLR-transformed bacterial abundances, are color-coded with red indicating taxa increased in the R group. The heatmap displays mean CLR-transformed abundances of reported taxonomic units. Taxonomic lineage is denoted: p, phylum; c, class; o, order; f, family; g, genus; s, species. Corrections to GreenGenes database nomenclature, based on NCBI Taxonomy, are shown in violet. Taxonomic names in blue were determined via manual BLASTN search in GenBank using corresponding read sequences. The histogram on the right illustrates the contribution of each bacterial taxon to the first two components of the PLSDA biplot in Figure 3, with Roman numerals linking taxa to the PLSDA loading plot. Bold text highlights the 11 bacterial taxa significantly contributing to variability in the PLSDA analysis.

Figure 3.

Biplot of PLS discriminant analysis (PLSDA) with prediction background for responder (R) and non-responder (NR) non-constipated IBS patients (panel a) and for R, NR, and healthy controls (HC) (panel b). Roman numerals in panel a refer to bacterial taxa in figure 2. The percentages indicate the explained variation at each axis. The Receiver Operating Characteristic (ROC) curves of the PLSDA model are shown in supplementary Figure S1.

Figure 4.

Dot plot of the most abundant bacterial taxa found to better discriminate between responders and non-responder patients in the PROBE-IBS/2 trial. HC, healthy controls (n = 100); R and NR, responder and non-responder NC-IBS patients in the PROBE-IBS/2 trial, respectively; other NC-IBS, other non-constipated IBS patients recruited at baseline during the PROBE-IBS/2 trial (n = 161); statistics is according to Mann-Whitney test; *, P < .05; **, P < .01.

Figure 5.

Linear discriminant analysis (LDA) effect size (LEfSe) graphics for responders (R) NC-IBS patients in the probiotic arm. LDA scores indicate taxa significantly (P < 0.05) higher before (V2; negative LDA) or after (V4; positive LDA) probiotic intake. Taxon levels are abbreviated: p, phylum; c, class; o, order; f, family; g, genus; and s, species. Corrections/updates to GreenGenes database nomenclature are marked in violet, while taxonomic names determined through a manual BLASTN search in GenBank using corresponding read sequences are highlighted in blue. Taxon cAVS 254 is identified as the administered probiotic strain (L. paracasei DG; highlighted in green).

Figure 6.

Analysis of data collected during the PROBE-IBS/1 cross-over trial. (a) fecal abundance of the bacterial species collinsella aerofaciens in IBS patients before and after the intake of the probiotic product. IBS-CU, constipated and undefined IBS patients; IBS-DM, diarrhea or mixed IBS patients. Statistics is according to Wilcoxon signed-rank test; *, P < .05; n.S., nonsignificant (P > .05). (b) fecal abundance of C. aerofaciens (on the left) and abdominal pain/discomfort (on the right) in IBS-DM patients during the PROBE-IBS/1 trial. NRS, numeric rating scale used to measure abdominal pain/discomfort. Statistics is according to non-parametric repeated measure ANOVA-Type statistic (RM-ATS). The reported P values indicate significant Time×Treatment interaction. **, P < .01; *, P < .05.

Figure 7.

Correlation analyses between bacterial taxa and serum markers for permeability (panel a) and liver and kidney functionality (panel b). In panel a, correlation analyses were conducted with data from blood samples collected before run-in (visit V1) and fecal samples collected before the probiotic intervention (visit V2), as well as with data from blood and fecal samples collected at the end of the probiotic intervention (visit V4) denoted as V1/V2 and V4, respectively. Only taxa exhibiting consistent significant correlations at both V1/V2 and V4 are displayed. The heatmap represents the τ coefficient of Kendall rank correlation (*, P < .05; **, P < .01; ***, P < .001). Taxonomic lineage is indicated as follows: p, phylum; c, class; o, order; f, family; g, genus; s, species. Corrections/updates to GreenGenes database nomenclature are highlighted in violet, and taxonomic names determined through a manual BLASTN search are in blue. ALT, alanine aminotransferase; AST, aspartate-aminotransferase; Bil, bilirubin; ALP, alkaline phosphatase; BUN, blood urea nitrogen; cr, creatinine.