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• Relationships between protein fermentation and intestinal health were investigated. • Dietary fibres had no impact on particle or liquid-associated bacterial counts. • Among all metabolites, only ammonia appeared to impair intestinal barrier function. • Protein-derived metabolites have not been linked to reduced fecal consistency. • Low-digestible proteins do negatively affect fecal consistency. In vitro and in situ experiments, primarily conducted using human cells, have demonstrated that metabolites produced during protein fermentation can negatively affect intestinal health. However, in vivo research on their impact on intestinal health in pigs remains limited. Furthermore, data from ruminants suggest that the ratio of particle- and liquid-associated bacteria ( PAB and LAB ) may influence the production of protein-derived metabolites. In this experiment, 128 male pigs (mean BW ± SEM; 24 ± 1.5 kg) were assigned to diets using either bovine collagen ( BC ) or zein ( ZE ) as the only, low-digestible, protein source, in the absence ( NFF ) or presence of rapidly ( RFF ) or slowly fermentable fibres ( SFF ), and with titanium dioxide as an indigestible marker. Additionally, two control groups received easily digestible whey protein isolate ( WPI ) with either NFF or SFF. Fecal consistency was monitored daily, and after two weeks, colon digesta samples were analyzed to assess titanium, ammonia, volatile fatty acids, biogenic amines, indolic and phenolic compounds, PAB and LAB. Jejunal and colonic segments were collected to assess intestinal paracellular permeability to 4 kDa FITC- and 40 kDa TRITC-dextran. Results showed that fecal consistency scores declined over time for BC-fed pigs, while they remained relatively constant for WPI. This resulted in lower scores for BC from day 7 onwards (29-46%, P <0.05), regardless of the presence of fibres (protein × fibre P >0.05). Less consistent differences were observed for ZE. No differences were observed in jejunal or colonic permeability between the different protein sources or fibre treatments. Moreover, no correlations were found between protein-derived metabolites and fecal consistency or intestinal barrier function, except for ammonia. Colonic ammonia flow was positively correlated with colonic permeability to 4 kDa- fluorescein isothiocyanate ( FITC )-dextran (proximal colon: r=0.65, P <0.001, distal colon: r=0.59, P <0.001) and 40 kDa- tetramethylrhodamine isothiocyanate ( TRITC )-dextran (proximal colon: r=0.78, P <0.001, distal colon: r=0.71, P <0.001). The total bacterial count in the proximal colon was higher as compared with the distal colon ( P <0.001). The inclusion of fermentable fibres did not alter the abundance or ratio of PAB:LAB. In conclusion, while low-digestible protein sources reduced fecal consistency scores, no causal link was found with protein-derived metabolites. Among all metabolites, only a relation between ammonia flow and impaired intestinal barrier function was confirmed. No evidence that dietary fibres alter the colonic abundance of particle- and liquid-associated bacteria was found.