Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization

Abstract

The enteric pathogen Clostridioides difficile (Cd) is responsible for a toxin-mediated infection that causes more than 200,000 recorded hospitalizations and 13,000 deaths in the United States every year1. However, Cd can colonize the gut in the absence of disease symptoms. Prevalence of asymptomatic colonization by toxigenic Cd in healthy populations is high; asymptomatic carriers are at increased risk of infection compared to noncolonized individuals and may be a reservoir for transmission of Cd infection2,3. Elucidating the molecular mechanisms by which Cd persists in the absence of disease is necessary for understanding pathogenesis and developing refined therapeutic strategies. Here, we show with gut microbiome metatranscriptomic analysis that mice recalcitrant to Cd infection and inflammation exhibit increased community-wide expression of arginine and ornithine metabolic pathways. To query Cd metabolism specifically, we leverage RNA sequencing in gnotobiotic mice infected with two wild-type strains (630 and R20291) and isogenic toxin-deficient mutants of these strains to differentiate inflammation-dependent versus -independent transcriptional states. A single operon encoding oxidative ornithine degradation is consistently upregulated across non-toxigenic Cd strains. Combining untargeted and targeted metabolomics with bacterial and host genetics, we demonstrate that both diet- and host-derived sources of ornithine provide a competitive advantage to Cd, suggesting a mechanism for Cd persistence within a non-inflammatory, healthy gut.

The gut microbial metabolic capacity of microbiome-humanized vs. wild type rodents reveals a likely dual role of intestinal bacteria in hepato-intestinal schistosomiasis

“…For instance, polyamines derived from arginine and ornithine metabolism enhance gut barrier function by inducing overexpression of tight junction proteins and reducing inflammation [ 41 – 43 ]. For these reasons, an enhanced metabolism of these amino acids by the gut microbiome has been linked to a ‘healthy’ gut [ 44 , 45 ]. Given the differences detected between WT vs .…”

“…For instance, polyamines derived from arginine and ornithine metabolism enhance gut barrier function by inducing overexpression of tight junction proteins and reducing inflammation [41][42][43]. For these reasons, an enhanced metabolism of these amino acids by the gut microbiome has been linked to a 'healthy' gut [44,45]. Given the differences detected between WT vs. HMA hosts in infection-associated alterations in arginine/ornithine/polyamine metabolism (S7 Fig and S5 and S6 Tables), caution is warranted when discussing any role(s) of these amino acids and corresponding metabolites in the context of schistosomiasis.…”

Systems biology illuminates alternative metabolic niches in the human gut microbiome

“…Our stable isotope analysis indicated that ornithine is primarily an end product of growth and is relatively inaccessible as a carbon source for E. lenta. However, ornithine is a favorable carbon and/or energy source for numerous other gut microbes (Noronha et al, 2018), including as a substrate for Stickland metabolism by gut bacteria including Clostridioides difficile (Girinathan et al, 2021; Liu et al, 2022; Pruss et al, 2022). Therefore, production of ornithine by E. lenta may promote the growth of other proteolytic bacteria in the surrounding gut ecosystem.…”

Food for thought—The link between Clostridioides difficile metabolism and pathogenesis

“…To date, ornithine has received most attention as a substrate of importance for the maintenance of C . difficile during asymptomatic colonisation of mice [ 24 ]. Ornithine can undergo oxidative Stickland metabolism to yield acetyl-CoA, ammonia, and alanine, involving a cascade of reactions encoded by D-ornithine aminomutase, 2-amino-4-ketopentanoate (AKP), and AKP thiolase [ 58 ].…”

“…Ornithine can undergo oxidative Stickland metabolism to yield acetyl-CoA, ammonia, and alanine, involving a cascade of reactions encoded by D-ornithine aminomutase, 2-amino-4-ketopentanoate (AKP), and AKP thiolase [ 58 ]. Alternatively, it can be converted to proline via ornithine cyclodeaminase before further metabolism to 5-aminovalerate [ 20 , 24 ]. The importance of ornithine as a substrate in supporting growth was confirmed as deletion of genes encoding D-ornithine aminomutase in C .…”