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Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut

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Abstract

Bacteria communicate and coordinate their behaviour at the intra- and interspecies levels by producing and sensing diverse extracellular small molecules called autoinducers. Autoinducer 2 (AI-2) is produced and detected by a variety of bacteria and thus plays an important role in interspecies communication and chemotaxis. Although AI-2 is a major autoinducer molecule present in the mammalian gut and can influence the composition of the murine gut microbiota, its role in bacteria–bacteria and bacteria–host interactions during gut colonization remains unclear. Combining competitive infections in C57BL/6 mice with microscopy and bioinformatic approaches, we show that chemotaxis (cheY) and AI-2 signalling (via lsrB) promote gut colonization by Escherichia coli, which is in turn connected to the ability of the bacteria to utilize fructoselysine (frl operon). We further show that the genomic diversity of E. coli strains with respect to AI-2 signalling allows ecological niche segregation and stable co-existence of different E. coli strains in the mammalian gut.

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Fig. 1: Chemotaxis provides E. coli with a fitness advantage in competitive mouse infections.
Fig. 2: Chemotaxis towards AI-2 promotes colonization and mediates co-existence of E. coli strains in the gut.
Fig. 3: Co-occurrence analysis of lsrB/lsrG and lsrB/frlA genes in E. coli genomes.
Fig. 4: Competitive infection experiments demonstrating a functional link between fructoselysine utilization and LsrB in E. coli Z1331.
Fig. 5: Fructoselysine is an attractant sensed by the Trg chemoreceptor.
Fig. 6: Effect of fructoselysine on lsr and frl operon expression in E. coli Z1331.

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Data availability

The publicly available E. coli genome database and the associated files (annotations, phylogenetic tree) used and reprocessed in the present study can be found under: https://microbiology.figshare.com/articles/dataset/A_comprehensive_and_high-quality_collection_of_E_coli_genomes_and_their_genes/13270073. Any additional data can be requested from the corresponding author. Source data are available for Figs. 1–5 and Extended Data Figs. 1–10.

Code availability

Customized code used to produce the results presented in the present study is available at https://github.com/lukasmalfi/E_Coli.

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Acknowledgements

We thank K. Xavier (Instituto Gulbenkian de Ciência, Oeiras, Portugal) for generously providing the E. coli ARO071 strain and for helpful discussions. We also thank the EPIC RCHCI staff for support of the animal work. L.L. is supported by a grant (no. LA 4572/1-1) from the Deutsche Forschungsgemeinschaft. This work has been further funded by grants from the Swiss National Science Foundation (SNF; grant nos. 310030B_173338 and 310030_192567, NCCR Microbiomes) to W.-D.H. V.S. acknowledges support by the Hessian Ministry of Higher Education, Research, and the Arts–LOEWE research cluster ‘Diffusible Signals’ subproject A1. J.W.L. was supported by a grant (no. NRF-2019R1A6A3A03031885) from the National Research Foundation, Republic of Korea. C.v.M. is supported by the Swiss NSF (grant no. 310030_192569). C.L.D. and J.P. are supported by a grant (no. SNF 205321L_10724) from the Swiss NSF.

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Authors and Affiliations

  1. Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland

    Leanid Laganenka, Cora Lisbeth Dieterich, Lea Fuchs, Jörn Piel & Wolf-Dietrich Hardt

  2. Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany

    Jae-Woo Lee & Victor Sourjik

  3. Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland

    Lukas Malfertheiner & Christian von Mering

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  1. Leanid Laganenka
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Contributions

L.L., W.-D.H. and V.S. conceived and designed the experiments. L.L. and J.-W.L. performed the experiments. L.M. and C.v.M. performed bioinformatic analysis. C.L.D., L.F. and J.P. synthesized fructoselysine. All authors contributed to data analysis and writing of the manuscript.

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Correspondence to Wolf-Dietrich Hardt.

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Extended data

Extended Data Fig. 1 E. coli Z1331 colonizes ampicillin-pretreated SPF mice without causing inflammation.

a, c.f.u. of E. coli Z1331 WT (yidX-bla, ampr) detected in faeces (F) and caecal content (CC) of ampicillin-pretreated SPF mice at different time points of a 72 h infection. Lines indicate median values (mice n = 9, from ≥2 independent animal experiments). The slight drop of fecal E. coli densities between 48 h and 72 h.p.i. is likely due to the regrowth of microbiota. Dashed line indicates the detection limit. b, Lipocalin-2 levels in faeces (F) and caecal content (CC) of E. coli-infected mice as measured by ELISA. Lines represent median values (mice n = 5, from ≥2 independent animal experiments). Dashed line indicates approximate threshold of lipocalin-2 concentration marking a shift from non-inflamed to the inflamed gut, as observed in the streptomycin mouse model for Salmonella diarrhea. Note that gut colonization by wild type S. Typhimurium yields lipocalin-2 levels of 104 ng/g faeces during full-blown gut inflammation1. c, Competitive indices (C.I.) for chemotaxis-deficient ΔcheY strains from different phylogroups in competition against the respective WT strains in SPF ampicillin-pretreated mice. F, faeces. CC, caecal content. Lines indicate median values (minimum mice n = 5, at least two independent replicates). Dashed line indicates C.I. value of 1.

Source data

Extended Data Fig. 2 E. coli Z1331 ΔcheY has no colonization defect in single-strain infection.

a, c.f.u. of E. coli Z1331 WT and ΔcheY detected in faeces (F) and caecal content (CC) of ampicillin-pretreated SPF mice at different time points of a 72 h infection. Lines indicate median values (mice n = 4, two independent replicates). b, Number of aggregates formed by WT and ΔcheY cells in a single-strain infection normalized to the number of detected cells in a tissue section as seen below (two-tailed Mann-Whitney test, **P < 0.005). Lines indicate median values (image sample n = 11, tissue sections from two independent experiments were analyzed). c, Caecal tissue sections of mice infected either with E. coli WT (mCherry-positive, shown in orange) or ΔcheY (GFP-positive, shown in green) at 72 h.p.i. Actin filaments (red) and DNA (blue) were stained with phalloidin and DAPI, respectively. Scale bars, 50 µm. d, An example of image segmentation and analysis of bacterial aggregates (as seen above) using ImageJ. Detected particles are indicated in red, with aggregates (at least 50 px2 in size) outlined in yellow. Particles of non-bacterial origin (food fibers etc, as seen in ΔcheY panel) were manually excluded from analysis. Scale bars, 50 µm.

Source data

Extended Data Fig. 3 Increased luminal AI-2 levels abolish fitness advantage of wild-type E. coli in ΔlsrB/WT competitive infection.

a, AI-2 levels of AI-2 in faeces of SPF mice before (SPF Amp−) and 24 h after (SPF Amp+) treatment with 20 mg ampicillin. Mean fluorescence of a plasmid-based AI-2 reporter strain was measured by flow cytometry and plotted in arbitrary units (a.u.). Lines indicate median values (mice n = 4, at least two independent replicates). P values were calculated using two-tailed Mann-Whitney test (*P < 0.05). b, AI-2 levels of AI-2 in faeces (F) of SPF ampicillin-pretreated mice infected with E. coli Z1331 WT (-ARO071) or with 1:1 mix of E. coli Z1331 WT and E. coli ARO071. Mean fluorescence of a plasmid-based AI-2 reporter strain was measured by flow cytometry and plotted in arbitrary units (a.u.). Lines indicate median values (mice n = 6, at least two independent replicates). P values were calculated using two-tailed Mann-Whitney test (**P < 0.005). c, c.f.u. data for the experiment shown in Fig. 2d. F, faeces, CC, caecal content. Lines indicate median values (mice n = 6, at least two independent replicates). P values were calculated using two-tailed Mann-Whitney test (**P < 0.005; ns, not significant). The dashed line indicates the detection limit. Note that the total c.f.u. loads can differ between caecum and faeces due to yet unidentified reasons.

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Extended Data Fig. 4 Competitive indices (C.I.) for ΔlsrB strains of lsr-positive E. coli W3110 and 8550 in competition against the respective WT strains in SPF ampicillin-pretreated mice.

F, faeces. CC, caecal content. Lines indicate median values (minimum mice n = 5, at least two independent replicates). Dashed line indicates C.I. value of 1.

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Extended Data Fig. 5 CheY and LsrB belong to the same regulatory pathway.

E. coli Z1331 ΔcheY and ΔcheY ΔlsrB knockout strains were competed against the wild-type strain. Additionally competitive indices (C.I.) of ΔlsrB and ΔcheY mutants were analyzed in ΔcheY and ΔlsrB backgrounds, respectively. F, faeces, CC, caecal content. Lines indicate median values (minimum mice n = 5, from at least two independent infection experiments). P values were analyzed using two-tailed Mann-Whitney test (**P < 0.005; *P < 0.05; ns, not significant).

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Extended Data Fig. 6 Self-produced AI-2 enhances gut colonization by E. coli.

a, Experimental scheme of competitive infection in germ-free (GF) mice. C57BL/6 J GF mice were orally infected with 5×107 c.f.u. E. coli W3110 WT and ΔlsrB or ΔlsrB ΔluxS and ΔluxS at a 1:1 ratio. Faeces were collected 24, 48 h.p.i. and mice were euthanized at 72 h.p.i. b, C.I. of non-AI-2 chemotactic ΔlsrB mutant in WT and ΔluxS background strains in the GF mouse infection model. F, faeces, CC, caecal content. Lines indicate median values (mice n = 9, from least two independent experiments). P values were calculated using two-tailed Mann-Whitney test (****P < 0.0001). Dashed line indicates C.I. value of 1. c, Experimental scheme of competitive infection in SPF mice. C57BL/6 J SPF mice were pretreated with 20 mg ampicillin by oral gavage 24 h prior to infection with E. coli W3110 WT and ΔlsrB or ΔlsrB ΔluxS and ΔluxS at 1:1 ratio. Faeces were collected at 24, 48 h.p.i and mice were euthanized at 72 h.p.i. d, C.I. of non-AI-2 chemotactic ΔlsrB mutant in WT and ΔluxS background strains in SPF ampicillin-pretreated mouse infection model. F, faeces, CC, caecal content. Lines indicate median values (minimum mice n = 5, from at least two independent experiments). P values were calculated using two-tailed Mann-Whitney test (**P < 0.005). Dashed line indicates C.I. value of 1.

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Extended Data Fig. 7 Infection of SPF ampicillin-pretreated mice with E. coli 8178 and 8850 does not cause inflammation.

a, H&E staining of caecal tissue of uninfected mice (PBS) and mice infected with 5×107 c.f.u. of E. coli Z1331 WT + 8178 WT and E. coli Z1331 WT + 8850 WT (1:1000 ratio) at 72 h.p.i (as seen in Fig. 4). Scale bar, 50 µm. b, Histopathology analysis of the caecal tissue section as seen above. 3 sections from 2 mice per group were analyzed. c, Lipocalin-2 levels in faeces (F) and caecal content (CC) of E. coli-infected mice as measured by ELISA. Lines represent median values (mice n = 7, at least two independent animal experiments). Dashed line indicates approximate threshold of lipocalin-2 concentration marking a shift from non-inflamed to the inflamed gut. d, Colonization levels of E. coli 8178 in competition experiments with E. coli Z1331 as seen in Fig. 2. Lines indicate median values (mice n = 7, at least two independent replicates). P values were calculated using two-tailed Mann-Whitney test (ns, not significant). e, Colonization levels of E. coli 8850 in competition experiments with E. coli Z1331 as seen in Fig. 2. Lines indicate median values (minimum mice n = 6, at least two independent replicates). P values were calculated using two-tailed Mann-Whitney test (ns, not significant).

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Extended Data Fig. 8 Fructoselysine is an attractant sensed by the Trg chemoreceptor.

Examples of FRET measurements of the response to fructoselysine (reflected by the ratio of YFP/CFP fluorescence) by E. coli W3110 a, wild-type, b, Δtrg, c, Δtsr, d, Δtar, e, Δtap, f, ΔptsI and g, ΔcheA (negative control) knockout strains. Buffer-adapted cells were stimulated with step-like addition and removal of compounds (indicated by downward and upward arrows, respectively). Stimulation with saturating concentration of aspartate or serine, two strong attractants, was used as a positive control. Time traces of fluorescence intensity in the YFP (shown in yellow) and CFP channels (shown in blue) are shown in the right. Opposite changes in two channels indicate specific FRET response. Note that higher concentrations of fructoselysine solution have unspecific effect on fluorescence in both YFP and CFP channels, particularly visible in ΔcheA negative control, but little effect on the YFP/CFP ratio. Residual effect on the YFP/CFP ratio in the negative control was subtracted from all dose-response curves in Fig. 5b.

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Extended Data Fig. 9 LsrB and Tsr belong to the same regulatory pathway.

Competitive indices (C.I.) of E. coli Δtsr and Δtsr ΔlsrB mutant strains vs the wild-type strain E. coli Z1331 in SPF ampicillin-pretreated mice. F, faeces, CC, caecal content. Lines indicate median values (minimum mice n = 6, at least two independent replicates). P values were analyzed using two-tailed Mann-Whitney test (ns, not significant).

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Extended Data Fig. 10 E. coli Z1331 utilizes fructoselysine as a sole carbon source.

E. coli Z1331 WT, ΔfrlA and ΔptsI strains were grown aerobically for 24 h in M9 minimal medium supplemented with either 1% fructoselysine (FL) or 2% arabinose (non-PTS sugar, used as a control for ΔptsI growth) and NH4Cl as a nitrogen source. Mean optical densities are shown, error bars indicate s.d. (sample n = 6, from at least two independent experiments). P values were calculated using two-tailed Mann-Whitney test (**P < 0.005; ns, not significant).

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Supplementary information

Supplementary Information

Supplementary Figs. 1–3 and Information Tables 1 and 2.

Reporting Summary

Supplementary Tables 1 and 2

Supplementary Table 1: Strains and plasmids used in this study. Supplementary Table 2: Correlation analysis of the E. coli lsrB gene.

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Laganenka, L., Lee, JW., Malfertheiner, L. et al. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 8, 204–217 (2023). https://doi.org/10.1038/s41564-022-01286-7

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