Carbon nutrition of Escherichia coli in the mouse intestine

Abstract

Whole-genome expression profiling revealed Escherichia coli MG1655 genes induced by growth on mucus, conditions designed to mimic nutrient availability in the mammalian intestine. Most were nutritional genes corresponding to catabolic pathways for nutrients found in mucus. We knocked out several pathways and tested the relative fitness of the mutants for colonization of the mouse intestine in competition with their wild-type parent. We found that only mutations in sugar pathways affected colonization, not phospholipid and amino acid catabolism, not gluconeogenesis, not the tricarboxylic acid cycle, and not the pentose phosphate pathway. Gluconate appeared to be a major carbon source used by E. coli MG1655 to colonize, having an impact on both the initiation and maintenance stages. N-acetylglucosamine and N-acetylneuraminic acid appeared to be involved in initiation, but not maintenance. Glucuronate, mannose, fucose, and ribose appeared to be involved in maintenance, but not initiation. The in vitro order of preference for these seven sugars paralleled the relative impact of the corresponding metabolic lesions on colonization: gluconate > N-acetylglucosamine > N-acetylneuraminic acid = glucuronate > mannose > fucose > ribose. The results of this systematic analysis of nutrients used by E. coli MG1655 to colonize the mouse intestine are intriguing in light of the nutrient-niche hypothesis, which states that the ecological niches within the intestine are defined by nutrient availability. Because humans are presumably colonized with different commensal strains, differences in nutrient availability may provide an open niche for infecting E. coli pathogens in some individuals and a barrier to infection in others.

Fig. 1.

Expression profiles of E. coli MG1655 genes involved in catabolism of carbohydrates found in mucus (15). Genes are represented in rows, as indicated to the right, and are grouped by the corresponding sugar degradation pathway. PH1, ratio of early logarithmic phase (OD₆₀₀ = 0.1) cells grown on 10 mg/ml mucus vs. minimal glucose (0.2%); PH2, from the same culture grown to late logarithmic phase (OD₆₀₀ = 0.3); Low, ratio of cells grown to late logarithmic phase (OD₆₀₀ = 0.3) on 5 mg/ml mucus vs. minimal glucose; Cont, ratio of cells grown to late logarithmic phase on chemically defined rich medium (20) vs. minimal glucose. Ratios are displayed colorimetrically: bright red indicates genes with ≥2.5-fold higher expression (≈2 standard deviations) and bright green indicates ≤2.5-fold lower expression in the experimental condition compared with minimal glucose; the colors darken to black to indicate no change in expression. GlcNAc, N-acetylglucosamine; GalNAc, N- acetylgalactosamine; NANA, sialic acid (N-acetylneuraminic acid); GlcNH4, glucosamine. See text for further details.

Fig. 2.

Colonization of the mouse intestine by E. coli MG1655 Str^R Nal^R (wild-type) and mutant derivatives of E. coli MG1655 Str^R, as follows. Sets of three mice were fed one of the following: 10⁵ cfu each of wild-type and MG1655 Str^R Δedd::Km^R (Km^R, kanamycin-resistant) (A); 10⁵ cfu each of wild-type and MG1655 Str^R ΔmanXYZ::Km^R ΔnagE (B); 10⁵ cfu each of wild-type and MG1655 Str^R ΔnanAT::Km^R (C); 10⁵ cfu each of wild-type and MG1655 Str^R ΔfucK::Km^R (D); or 10⁵ cfu each of wild-type and MG1655 Str^R ΔppsA ΔpckA::Cm (E). At the indicated times, fecal samples were homogenized, diluted, and plated as described (13). Bars represent standard error of the log₁₀(mean cfu/g of feces) for each set of three mice.