CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional patent application no.

62/152,478, filed April 24, 2015, the disclosure of which is incorporated herein by reference. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under contract no. R01 GM103593 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD The present disclosure relates generally to anti-infective agents, and more specifically to use of secreted antigen A (SagA) as an anti-infective agent, as well as

recombinant microorganisms and food products expressing heterologous SagA and/or SagA- generated metabolites.

BACKGROUND The intestinal microbiome mediates host resistance to enteric pathogens, but the underlying protection mechanisms of individual bacterial species have remained elusive (Buffie, C. G. & Pamer, E. G. Nat Rev Immunol 13, 790-801 (2013). For example, commensal strains of Enterococcus faecium can inhibit the virulence of several bacterial pathogens, but whether E. faecium directly targets pathogens or modulates host immunity is unknown (Tannock, G. W. & Cook, G. The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. 101- 132 (ASM Press, 2002). Because enteric pathogens are responsible for gastroenteritis, but can also cause life threatening infections, there is an ongoing and unmet need for improved compositions and methods that can be used to inhibit their growth. The present disclosure meets these needs.

SUMMARY

The present disclosure is based in part on the discovery that Enterococcus faecium heterologous secreted antigen A (SagA)-produced peptidoglycan fragments are protective against enteric bacterial infections. Further, E. faecium-SagA protection is conserved and is transferable to other bacteria. As a consequence, bacteria that are engineered to heterologously express SagA can confer the same protective function against pathogenic bacteria as E. faecium. Furthermore, the protective effect can be elicited using E. faecium culture supernatant that contains peptidoglycan fragments produced by SagA activity. Aspects of the disclosure are demonstrated in both C. elegans and in mice and it is therefore expected that the present compositions and methods are applicable for use with a variety of animals, and against multiple types of pathogenic bacteria. Accordingly, in one aspect the disclosure provides modified bacteria that are engineered to express heterologous SagA, wherein the modified bacteria are for use in prophylaxis and/or therapy of enteric bacterial infections. The disclosure includes a proviso that the modified bacteria are not E. coli. In certain embodiments the modified bacteria may be selected from different types of bacteria that are suitable for use in nutraceutical, pharmaceutical, probiotic, and food based products and delivery methods, and such products and methods are also aspects of the disclosure. In non-limiting examples the modified bacteria are gram positive bacteria, such as Lactobacillus bacteria, and in particular may be L. plantarum, L. casei or L. acidophilus. Combinations of such bacteria, with or without other types of bacteria whether modified or unmodified, are included. In certain implementations the modified bacteria which express heterologous SagA are present in a gastrointestinal system of an animal, including but not limited to those in humans and non-human mammals.

The disclosure includes a variety of products for human or non-human animal consumption that comprise live modified bacteria. Such products include but are not limited to dairy products, such as yogurt, and drinkable dairy products. In a related aspect the modified bacteria are provided as a probiotic formulation.

In one approach the disclosure includes a method comprising introducing into an individual modified bacteria of that express and secrete heterologous SagA. The modified bacteria can be introduced into the individual as a component of a food product, a probiotic formulation, or a pharmaceutical formulation. In certain approaches the modified bacteria are introduced into an individual who is at risk for contracting an enteric bacterial infection, or the modified bacteria are given to an individual who has an enteric bacterial infection, and subsequently the pathogenicity of the bacteria is reduced. Generally the modified bacteria are introduced into the gastrointestinal system of the individual.

The disclosure provides isolated peptidoglycan fragment preparations made by a process comprising the steps of exposing a composition comprising peptidoglycan to an isolated or recombinant SagA, or to modified bacteria expressing a heterologous SagA, allowing SagA to generate the peptidoglycan fragments, and separating the peptidoglycan fragments from the composition to obtain the isolated peptidoglycan fragments or a preparation comprising them.

DESCRIPTION OF THE FIGURES

Figure 1. Enterococcus faecium induces host resistance to S. Typhimurium. (A) Schematic of pulsed infection assay. Animals were treated on bacterial lawns for 1 day or in liquid wells for 2 hours before infection with S. Typhimurium for 1 day. Animals were then transferred onto E. coli OP50 plates for the remainder of the assay, and survival was scored. (B) Survival curve showing E. faecium-mediated inhibition of S. Typhimurium pathogenesis (p<10- 10). The legend indicates treatment-infection. Control worms were fed E. coli OP50 for both the treatment and infection stages of the assay. For all C. elegans survival curves, significance was calculated by log-rank test with Bonferroni correction for multiple comparisons. Data points represent mean survival from 90 worms. (C) Fluorescence images of C. elegans infected with S. Typhimurium expressing plasmid-encoded mcherry (mcherryStm) at day 3 post-infection. The dotted lines indicate an outline of the worm body. Scale bar = 100 μπι. (D) S. Typhimurium CFUs measured in C. elegans throughout the infection assay. Data points represent average CFUs from 5 worms ± standard deviation of two independent experiments. The dotted line indicates detection limit. The background shading represents stage of the treatment-infection assay. Green indicates treatment, red indicates infection, and grey indicates E. coli OP50 feeding. (E) Electron microscopy of transverse sections of C. elegans (top), and magnification of intestinal region (bottom) at day 4 post-infection. The intestinal microvilli are highlighted blue; the intestinal lumen is highlighted red. In the top middle panel, the top arrow indicates bacteria that have breached the epithelial barrier, and the bottom arrow indicates loss of overall turgidity. Scale bar (top row) = 5 μηι. Scale bar (bottom row) = 200 nm. Abbreviations: E. coli OP50 (OP); S. Typhimurium (Stm); E. faecium (Efm).

Figure 2. E. faecium SagA is sufficient for inducing host resistance to S.

Typhimurium. (A) Survival curve showing that both E. faecium culture supernatant (Efm, sup) (p<10-6) and live E. faecium culture (Efm, live) (p<10-7) can inhibit S. Typhimurium-induced death. OP50 culture supernatant (OP, sup) is not protective (p=l). (B) Summary of proteins identified in E. faecium culture supernatant by mass spectrometry with at least 10 peptide spectrum matches (PSMs). Proteins involved in peptidoglycan remodeling are in red. The x- axis represents arbitrary protein number. (C) Fluorescence images of C. elegans treated for 1 day with wild-type E. faecium or E. faecium expressing mcherry under the SagA promoter

(psagA:mcherry). The dotted lines indicate an outline of the worm body. Scale bar = 200 μηι. (D) Coomassie stained SDS-PAGE of culture supernatants and SagA-His6 purifications from E. faecium Com 15 (Efm) a d E. coli BL21-RJL(DE3) (Ec). (E) Survival curve showing that SagA- His6 purified from either E. coli BL21-RJL(DE3) (SagA, Ec) (p<10-10) or E. faecium Coml5 (SagA, Efm) (p<10-10) is sufficient to inhibit S. Typhimurium pathogenesis. Abbreviations: E. coli OP50 (OP); S. Typhimurium (Stm); E. faecium (Efm).

Figure 3. E. faecium-SagA protection is conserved, transferable to other bacteria and requires tol-1 signaling. (A) Schematic showing insertion of SagA-His6 into the E. faecalis OG1RF chromosome to generate E.faecalis-sagA. CAT = chloramphenicol resistance gene. For comparison, a schematic of the SagA locus in E. faecium Coml5 is shown underneath. (B) Stain- free imaging and anti-His6 Western blot (WB) of E. faecalis and E. faecalis-sagA culture supematants. Arrow indicates protein band corresponding to SagA mobility in SDS-PAGE. (C) Survival curve from a continuous infection assay showing that E. faecalis-sagA inhibits

Salmonella pathogenesis (p<10-10) similarly to E. faecium (p=l). (D) Survival curve from a continuous infection assay showing that E. faecalis-sagA (p=0.053) does not inhibit S.

Typhimurium pathogenesis in tol-1 (nr2033). Abbreviations: E. coli OP50 (OP); B. subtilis (Bs); S. Typhimurium (Stm); E. faecium (Efm), E. faecalis (Efl).

Figure 4. Enzymatic activity of SagA is required for inducing host resistance through Tol-1 signaling. (A) Schematic of SagA domain organization. The signal sequence is yellow, the predicted coiled-coil (CC) domain is orange, and the NlpC/p60 type hydrolase domain is blue. Active site residues in the hydrolase domain are in red type. Amino acid number is as indicated. (B) Survival curve showing that SagA inhibits S. Typhimurium pathogenesis (p<10-10) while an active site mutant (AS) and C-terminal truncation mutant (Ctrunc) do not (p=0.42 and 0.98 respectively). (C) OD600 of E. coli BL21-RIL(DE3) expressing SagA, the active site mutant, or SagA-SS under an IPTG-inducible promoter. Measurements were taken 1 hour post-induction and normalized to the OD600 of a mock-induced non-expressing BL21- RIL(DE3) culture. Bars represent mean ± s.e.m. from three independent experiments.

Significance was calculated by unpaired t test. For **, p < 0.01. (D) Survival curve showing that 5-kDa MWCO column filtered E. coli culture supematants expressing SagA-His6 (Ec, sagA-FT) inhibit S. Typhimurium pathogenesis (p<10-4), while filtered E. coli culture supematants expressing the active site mutant (Ec, AS-FT) do not (p=l). (E) Survival curve showing that purified E. coli peptidogly can treated with SagA (PG, SagA) can inhibit S. Typhimurium pathogenesis (p<10-10), while E. coli peptidoglycan treated with the active site mutant (PG, AS) cannot (p=l). (F) ANTS visualization of E. coli culture supematants expressing SagA-His6 or the active site mutant. Samples were filtered through 10-kDa MWCO columns, dried, ANTS labeled, separated by native PAGE, then visualized by UV. ANTS-labeled synthetic fragments MDP, GlcNAc, MurNAc, and MurNAc-L- Ala were run for comparison. A sugar-less pentapeptide (Ala-D-Glu-Lys-Ala-Ala (PP)) was run to show specificity of the UV signal. (G) ANTS visualization of peptidoglycan fragments in E. faecium (Coml 5), E. faecium-sagA (Com 15 transformed with SagA expression plasmidj, E. faecalis (OGIRF), and E. faecalis-sagA culture supernatants. (H) Survival curves showing that treatment with MurNAc (p<10-5) or MurNAc-L-Ala (p<10-10) can inhibit S. Typhimurium pathogenesis, while MDP (p=l) and GlcNAc (p=l) are not protective. (I) Survival curve showing that MurNAc (p=l) and MurNAc- Ala (p=0.61) do not inhibit S. Typhimurium pathogenesis in tol-l(nr2033) animals. Abbreviations: E. coli OP50 (OP); S. Typhimurium (Stm).

Figure 5. Characterization of E. faecium-m diat d protection. (A) Images of C. elegans 1 day post-infection. Scale bar = 1mm. (B) Survival curve showing comparable activity of Efm strains NCTC 7171 and DO. (C) Pulsed treatment-infection assay showing E. faecium treatment inhibits E. coli OP50 pathogenesis. (D) Survival curve showing that Efm NCTC 7171 can protect C. elegans from E. faecalis V583 (Efl) pathogenesis. (E) Survival curve showing comparable pathogenicity of mcherry-^. Typhimurium (mchStm) to wild-type S. Typhimurium (Stm). (F) Enter ococcus CFUs measured in C. elegans throughout the pulsed treatment-infection assay. Background shading represents stage of the pulsed treatment-infection assay. Green indicated treatment, red indicates infection, and grey indicates E. coli OP50 feeding. The data points represent average CFUs from 5 worms ± standard deviation from two independent experiments. The dotted line indicates detection limit. For (B) through (F), data points represent mean ± s.d. for 3 plates of 30 worms each.

Abbreviations: E. coli OP50 (OP); S. typhimurium (Stm); E. faecium (Efm), E.faecalis (Efl).

Figure 6. Protein from E. faecium culture supernatant is protective. (A)

Proteinase-K- treated E. faecium culture supernatant (Efm,sup,protK) loses activity compared to untreated E. faecium culture supernatant (Efm,sup). Untreated media (BHI) and proteinase- K-treated media (BHI,protK) are inactive. (B) Trichloroacetic acid (TCA) precipitated E. faecium culture supernatant (Efm,sup,TCA) loses activity. Untreated media (BHI) and TCA precipitated media (BHI, TCA) are inactive. (C) 10 kDa MWCO column filtered E. faecium culture supernatant (Efm, sup,FT) is inactive. Untreated media (BHI) and 10 kDa MWCO column filtered media (BHI,FT) are inactive. (D) Coomassie stained SDS-PAGE of E.

faecium Coml5 culture supernatant subsequently digested for mass spectrometry analysis presented in Table 1 and Fig. 2B. (E) Stain-free imaging of E. faecium culture supernatants from various E. faecium strains separated by SDS-PAGE. Arrow indicates protein band corresponding to typical SagA migration. For (A) through (C), data points represent mean ± s.d. for 3 plates of 30 worms each. Abbreviations: E. coli OP50 (OP); S. typhimurium (Stm); E. faecium (Efm).

Figure 7. Characterization of SagA from E. faecium and E. coli. (A) Coomassie staining and glycoprotein-staining of E. faecium Com 15 culture supernatant. The arrows indicate protein bands excised for mass spectrometry analysis presented in Table 2. The blue arrow indicates a protein band corresponding to typical SagA migration. (B) SDS-PAGE of culture supernatants and SagA-His ₆ purifications from E. faecium Com 15 (Efm) and E. coli BL21-RIL(DE3) (Ec). Samples were visualized by Coomassie staining, glycoprotein-staining, and anti-His6 Western blot (WB) as indicated. SagA is glycosylated in E. faecium but not E. coli.

Figure 8. Secretome profiling of E. faecium, E. faecalis, and E. faecalis-sagA. (A)

Predicted domain architecture of three proteins in the E. faecalis OG1RF genome with significant alignment to SagA. By Needleman-Wunsch global alignment, F2MNS9 has 35.1% sequence identity and 50.6% sequence similarity to SagA; F2MNY6 has 35.6% identity and 54.5% similarity, and F2MN84 has 14.5% identity and 24.2% similarity. Amino acid number is as indicated, and putative catalytic residues are indicated in red bold type.

F2MNY6 lacks any putative catalytic residues in its NlpC/p60 like domain, and F2MN84 lacks a predicted coiled- coil domain. As indicated in Fig. 9A, both SagA and F2MNS9 are located after the mreCD operon in the chromosome. (B) Stain-free imaging and anti-His6 Western blot (WB) of culture supernatants from E. faecium Com 15 (Efm), E. faecalis OG1RF (Efl), and E. faecalis-sagA (EiisagA). Parallel samples were trypsin digested in- solution for mass spectrometry analysis presented in (B) through (E), and Tables 3 and 4. (C) Summary of proteins identified by mass spectrometry from E. faecalis OG1RE culture supernatant. Proteins shown were identified with at least 2 unique peptides. Proteins involved in cell-wall remodeling are highlighted in red. on the y-axis is peptide spectrum matches (PSMs); on the x-axis is arbitrary protein number. For the list of proteins identified, see Table 3. (D) Summary of proteins identified by mass spectrometry from E. faecalis-sagA culture supernatant. Proteins shown were identified with at least 2 unique peptides. Proteins involved in cell-wall remodeling are highlighted in red. For the list of proteins identified, see Table 4. (E) Summary of proteins identified by mass spectrometry from E. faecium Com 15 culture supernatant. Proteins shown were identified with at least 2 unique peptides. Proteins involved in cell-wall remodeling are highlighted in red. For the list of proteins identified, see Table 5. (F) Venn diagram comparing the proteins identified by mass spectrometry after in-gel trypsin digestion (blue) (See Fig. 2B, Table 1) versus in-solution trypsin digestion (red) (See Fig. 9E, Table 4). Proteins identified in both samples are indicated in the overlap (grey). Proteins included in this graph were identified with at least 2 unique peptides, and at least lO PSMs. Figure 9. Growth rate of E. faecalis-sagA. Growth curves of E. faecalis (Efl) and E. faecalis- sagA (EflsagA). Cm+ and Cm- indicate ± 10 μg/mL chloramphenicol.

Figure 10. Characterization of E. faecalis-sagA. (A) Schematic of a treatment- continuous Salmonella infection assay. Animals were treated for 1 day on BHI agar with E. faecium, E. faecalis, or E. faecalis-sagA, then transferred to NGM agar plates for infection with Salmonella for the remainder of the assay and survival was scored. Control animals were fed E. coli OP50 throughout the assay. (B) Salmonella and Enterococcus CFUs measured in

C. elegans throughout the continuous infection assay. Data points represent average CFUs from 5 worms ± standard deviation of two independent experiments. The dotted line indicates detection limit. The background shading indicates stages of the treatment-continuous infection.

Green indicates treatment and red indicates infection. (C) Survival curve showing that E. faecalis-sagA is less pathogenic than E. faecalis in a continuous E. faecalis infection assay.

Data points represent mean ± standard deviation for 3 plates of 30 worms each. Abbreviations: E. coli OP50 (OP); S. typhimurium (Stm); E. faecium (Efm); E. faecalis (Efl); E. faecalis-sagA

(EflsagA).

Figure 11. E. faecium protection in C. elegans mutants. Survival curves assaying E. faecium- mediated protection in (A) pmk-l(km25) (B) dbl-l(nk3) (C) daf-2(el370);daf- 16(mgDf47) (D) daf-16(mu86) and (E) npr-l(ad609) . For survival curves with error bars, each condition was tested with 3 plates of 30 worms each, and data points represent mean ± standard deviation. For curves without error bars, each condition was tested with one plate of 30 worms. Abbreviations: E. coli OP50 (OP); S. typhimurium (Stm); E. faecium (Efm).

Figure 12. SagA does not affect SPI-1 type III protein secretion in S.

typhimurium. (A) Fluorescence imaging of C. elegans treated with SagA or the active site mutant, then infected with Salmonella expressing mcherry (mchStm) at day 5 post-infection. The dotted lines indicate an outline of the worm body. Scale bar = 200 μπι. (B) Salmonella CFUs measured in C. elegans at indicated time points from an average of 10-20 worms ± standard deviation. The dotted line indicates detection limit. (C) SagA does not affect SPI-1 secretion in culture. Salmonella cultures were grown in LB + 10 μg/ml BSA, SagA, or the active site mutant. PBS indicates control treatment. AinvA is a Salmonella mutant that does not secrete effectors in culture. (D) Growth curves of Salmonella in LB media + 10 μg/ml SagA or BSA. Abbreviations: E. coli OP50 (OP);S. typhimurium (Stm).

Figure 13. Characterization of SagA enzymatic activity in E. coli. (A) Growth curves of E. coli BL21-RIL(DE3) in LB media + 10 μg/ml SagA or BSA. (B) Growth curves of E. coli BL21- RIL(DE3) expressing SagA, the active site mutant (AS), or SagA lacking a signal sequence (Sag- SS) under an IPTG-inducible promoter. The dotted line indicates time of IPTG induction. (C) anti-His6 Western blots of cell lysate or culture supernatant from E. coli BL21-RIL(DE3) expressing SagA, the active site mutant, or Sag-SS after IPTG induction. SagA-SS is mostly retained in the cell lysates, while SagA and the active site mutant are secreted.

Figure 14. Characterization of SagA peptidoglycan hydrolases activity. (A)

Removal of SagA-His6 from column filtrate. Coomassie staining and anti-His6 WB of E. coli culture supernatants expressing SagA-His6 or the active site mutant. Supernatant was filtered through a 5-kDa MWCO column. Unfiltered supernatant (Full), column concentrate (C), and column flow- through (FT) are as indicated. (B) ANTS visualization of purified E. coli peptidoglycan (PG) digested with lysozyme and either SagA or the active site mutant.

Figure 15. Model of SagA protective activity. E. faecium (green cocci) secretes SagA (blue pac-man) in the intestinal lumen. SagA hydrolyzes E. coli peptidoglycan (PG) into smaller fragments. SagA-generated PG fragments stimulate an immune response that leads to the inhibition of intestinal pathogenesis (red bacilli). The dashed arrows indicate processes require tol-1 in C. elegans.

Figure 16. E. faecium enhances pathogen resistance and intestinal epithelial barrier integrity. (A-C) C57BL/6 mice were orally gavaged with streptomycin and given 10 ⁸ colony- forming units (CFU) E. faecalis or E. faecium 4h before (b.i.) or 24h after (a.i.) oral infection with 10 ⁶ CFU S. Typhimurium. (A) Weight loss, (B) S. Typhimurium (S. Tm) bacterial burden in feces, and (C) survival are shown. Pooled data from 3 independent experiments, n=6-8 mice/group. (D) Cecum tissue stained with H&E, harvested at 48h post-infection (p.i.) from mice given streptomycin and left uninfected or treated before infection as in (A-C).

Representative images, 40X objective, from 1 of 3 independent experiments, n=2-3 mice/group. (E) Ileum, cecum, and colon tissues were harvested and prepared as in (D) and scored for 4 pathology parameters. Pooled combined pathology scores from 3 independent experiments, n=6- 7 mice/group. (F) Intestinal permeability measured by FITC-dextran concentration in the serum 48h p.i. from mice treated before infection as in (A-C). Pooled data from 3 independent experiments, n=7-9 mice/group. (G) S. Tm bacterial burden 48h p.i. in the livers of mice treated before infection as in (A-C). Pooled data from 4 independent experiments, n=l 1-12 mice/group. (H) FISH staining for all bacteria (red, universal 16S probe) and epithelial nuclei (blue,

Hoechst) from intestinal tissues 48h p.i. from mice treated before infection as in A-C).

Representative images, 40X objective, from 1 of 3 independent experiments, n=4-6 mice/group. White arrows indicate bacteria in contact with or invading through the epithelium, and white dashed line designates zone of segregation from bacteria. (A and B) mean±SEM, 2-way

ANOVA, p-value shown comparing E. faecalis to E. faecium b.i., n.s.=not significant. (C) Log- rank analysis, p-value shown comparing E. faecalis to E. faecium b.i. (E) median±range, Mann- Whitney comparing E. faecalis to E. faecium (Wilcoxon for colon, n.d.=none detected, score of zero). (F and G) bar=median, Mann-Whitney comparing E. faecalis to E. faecium. *p<0.05, **p<0.01, ***p<0.001 for all analyses.

Figure 17. E. faecium-inductd expression of Reg3g is required for protection against S. Typhimurium. (A) C57BL/6 mice were orally gavaged with a broad-spectrum antibiotic cocktail of ampicillin, metronidazole, neomycin, and vancomycin (AMNV) daily for 7d prior to gavage with 10 ⁸ CFU E. faecalis or E. faecium. 4d post-colonization, intestinal epithelial cells (IECs) were isolated and analyzed by RQ-PCR for expression of shown genes vs unmanipulated specific pathogen-free (SPF) mice. Representative data from 1 of 3 independent experiments, n=2-3 mice/group. (B) Mice were given a single gavage of streptomycin followed by gavage with 10 ⁸ CFU E. faecium 24h later. At indicated time-points post-colonization, IECs were isolated and analyzed by RQ-PCR. Representative data from 1 of 2 independent experiments, n=2 mice/group. (C-E) Reg3g-I- mice or +/- littermate controls were given AMNV for 7d and colonized with E. faecium (E. fm) prior to oral infection with 10 ⁶ S. Tm. (C) Weight loss, (D) S. Tm bacterial burden in feces, and (E) survival are shown. Pooled data from 4 independent experiments, n=10-12 mice/group. (F) S. Tm bacterial burden 72h p.i. in the livers or (G) mesenteric lymph nodes (mLN) of Reg3g-I- or +/- littermate controls treated before infection as in (C-E). Pooled data from 2 independent experiments, n=5-6 mice/group. (A and B) mean±SEM, 1-way ANOVA with Dunnett's post-test comparing all to antibiotic-only controls. (C and D) mean±SEM, 2-way ANOVA, p-value shown comparing Reg3g-I- E. fm to Reg3g+I- E. fm, n.s.=not significant. (E) Log-rank analysis, p-value shown comparing Reg3g-I- E. fm to Reg3g+I- E. fm. (F and G) bar=median, Wilcoxon (F) and Mann-Whitney (G) comparing Reg3g- l- E. fm to Reg3g+/- E. fm. *p<0.05, **p<0.01, ***p<0.001 for all analyses.

Figure 18. MyD88 and NOD2 are required for AMP induction and E. faecium- mediated protection. (A-C) or Cre ^" ( yDSS®) littermate control mice were injected with tamoxifen 7 days prior to oral gavage with streptomycin. After 24h, mice were gavaged with 10 ⁸ CFU E. fm followed 4h later by oral infection with 10 ⁶ CFU S. Tm. (A) Weight loss, (B) S. Tm bacterial burden in feces, and (C) survival are shown. Pooled data from 3 independent experiments, n=7-l 1 mice/group. (D) Mice were treated and colonized as in (A-C). At 4 and 72h post-colonization (p.c), IECs were isolated and analyzed by RQ-PCR for expression of shown genes. Pooled data from 2 independent experiments, n=2-4 mice/group. (E- G) Nod2-l- mice or +/- littermate controls were gavaged with streptomycin 24h prior to gavage with 10 ⁸ CFU E. fin followed 4h later by oral infection with 10 ⁶ CFU S. Tm. (E) Weight loss, (F) S. Tm bacterial burden in feces, and (G) survival are shown. Pooled data from 4 independent experiments, n=9-12 mice/group. (H) Mice were treated and colonized as in (E-G). At 4 and 72h post-colonization (p.c), IECs were isolated and analyzed by RQ-PCR for expression of shown genes. Pooled data from 2 independent experiments, n=2-4 mice/group. (A, B, E, and F) mean±SEM, 2-way ANOVA, p-value shown comparing E. ^w-colonized deficient to sufficient controls, n.s.=not significant. (C and G) Log-rank analysis, p-value shown comparing E. fin- colonized deficient to sufficient controls. (D and H) mean±SEM, 1-way ANOVA with Dunnett's post-test comparing all to streptomycin-only controls. *p<0.05 and ***p<0.001 for all analyses.

Figure 19. The E. faecium protein SagA is sufficient to enhance pathogen resistance against S. Typhimurium and improve host intestinal barrier function. (A-C) Germ-free (GF) C57BL/6 mice were orally gavaged with 10 ⁸ CFU E. faecalis (E. fs), E. faecalis expressing sagA (E. fs-sagA) or E. faecium (E. fin) Id before oral infection with 10 ² CFU S. Tm. (A)

Weight loss, (B) S. Tm bacterial burden in feces, and (C) survival are shown. Pooled data from 4 independent experiments, n=10-14 mice/group. (D) Mice were given a single gavage of streptomycin followed 24h later by gavage with 10 ⁸ CFXJ E. fin, E. fs, or E. fs-sagA. At 72h post- colonization, IECs were isolated and analyzed by RQ-PCR. Pooled data from 2 independent experiments, n=2-4 mice/group. (E-G) Mice were given AMNV for 14d and colonized with 10 ⁸ CFU L. plantarum harboring an empty plasmid vector (L. pl-wector) or a sagA plasmid (L. pl- sagA) or 10 ⁸ CFU E. fin prior to oral infection with 10 ⁶ S. Tm. (E) Weight loss, (F) S. Tm bacterial burden in feces, and (G) survival are shown. Pooled data from 2 independent experiments, n=2-5 mice/group. (H) FISH staining for all bacteria (red, universal 16S probe) and epithelial nuclei (blue, Hoechst) from intestinal tissues 48h p.i. from mice treated before infection as in (E-G). Representative images, 45X objective, from 1 of 2 independent experiments, n=2 mice/group. White arrows indicate bacteria in contact with or invading through the epithelium, and white dashed line designates zone of segregation from bacteria. (A, B, E, and F) mean±SEM, 2-way ANOVA, p-value shown comparing sagA -expressing E. fs or L. i to WT or vector controls, respectively, n.s.=not significant. (C and G) Log-rank analysis, p- value shown comparing sagA-expressing E. fi or L. pi to WT or vector controls, respectively. (D) mean±SEM, 1-way ANOVA with Dunnett' s post-test comparing all to streptomycin-only controls. *p<0.05, **p<0.01, ***p<0.001 for all analyses. Figure 20. E. faecium is protective in mono-colonized gnotobiotic mice. Germ-free (GF) C57BL/6 mice were orally gavaged with 10 ⁸ CFU E. faecalis or E. faecium 7d before oral infection with 10 ² CFU S. Tm. (A) Weight loss, (B) S. Tm bacterial burden in feces, and (C) survival are shown. Pooled data from 4 independent experiments, n=12 mice/group. (A and B) mean±SEM, 2-way ANOVA, p-value shown comparing E. faecalis to E. faecium. (C) Log-rank analysis, p-value shown comparing E. faecalis to E. faecium. **p<0.01 and ***p<0.001 for all analyses.

Figure 21. E. faecium is protective in broad-spectrum antibiotic-treated mice.

C57BL/6 mice were orally gavaged with a broad-spectrum antibiotic cocktail of ampicillin, metronidazole, neomycin, and vancomycin (AMNV) daily for 7d prior to gavage with 10 ⁸ CFU E. faecalis or E. faecium or PBS, followed by infection with 10 ⁶ S. Tm. (A) Weight loss, (B) S. Tm bacterial burden in feces, and (C) survival are shown. Pooled data from 4 independent experiments, n=14 mice/group. (A and B) mean±SEM, 2-way ANOVA, p-value shown comparing E. faecalis to E. faecium. (C) Log-rank analysis, p-value shown comparing E.

faecalis to E. faecium . * p<0.05.

Figure 22. E. faecium-m diat d protection does not require an adaptive immune response. (A and B) C57BL/6 mice were gavaged with a broad-spectrum antibiotic cocktail of ampicillin, metronidazole, neomycin, and vancomycin (AMNV) daily for 7d prior to gavage with 10 ⁸ CFU E. faecium. 5d post-colonization, intraepithelial lymphocytes were isolated and analyzed by flow cytometry for (A) relative frequency of shown subpopulations and (B) cytokine profile. Pooled data from 2 independent experiments, n=2-5 mice/group. (C) Ragl-I- mice were gavaged with AMNV daily for 7d prior to gavage with 10 ⁸ CFU E. faecalis or E. faecium or PBS, followed by infection with 10 ⁶ S. Tm. Pooled data from 4 independent experiments, n=13-14 mice/group. (C) Log-rank analysis, p-value shown comparing E. faecalis to E. faecium. *p<0.05.

Figure 23. E. faecium elicits upregulation of antimicrobial peptides (AMPs).

C57BL/6 mice were orally gavaged with a broad-spectrum antibiotic cocktail of ampicillin, metronidazole, neomycin, and vancomycin (AMNV) daily for 7d prior to gavage with 10 ⁸ CFU E. faecalis or E. faecium. 4d post-colonization, intestinal epithelial cells (IECs) were isolated and analyzed by RQ-PCR for expression of shown genes vs unmanipulated specific pathogen- free (SPF) mice. Representative data from 1 of 3 independent experiments, n=2-3 mice/group.

Figure 24. E. faecium is protection is maintained in the absence of MyD88 signaling myeloid cells. LysMAMyd88 or Cre ^" (MyD88 ^m ) littermate control mice were gavaged with streptomycin 24h prior to gavage with 10 ⁸ CFU E. fm followed 4h later by oral infection with 10 ⁶ CFU S. Tm. (A) Weight loss, and (B) survival are shown. Pooled data from 2 independent experiments, n=4-7 mice/group. (A) mean±SEM, 2-way ANOVA, p-value shown comparing E. faecium LysMAMyd88 to E. faecium Cre ^" controls. (B) Log-rank analysis, p-value shown comparing E. faecium LysMAMyd88 to E. faecium Cre ^" controls. *p<0.05 for all analyses.

Figure 25. Lactobacillus plantarum-sagA produces and secretes SagA. L. plantarum expressing a plasmid vector encoding his-tagged sagA were grown to stationary phase, and proteins from the supernatant and lysed cell pellet were analyzed by Western Blot for the presence of the His-tag.

Figure 26. Graphical summary of data demonstrating inhibition of Clostridium difficile pathogenesis in mice given SagA-expressing E.faecium.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure is based in part on our discovery that Enterococcus faecium can inhibit pathogenesis by various strains of bacteria, including Salmonella enterica serovar Typhimurium and Clostridium difficile. Inhibition of pathogenesis is shown in Caenorhabditis elegans, which has historically been used as a model organism to study evolutionarily conserved aspects of innate immunity and microbial pathogenesis, but the inhibition of pathogenesis is also demonstrated in mice. In particular, it is demonstrated that C elegans survival can be dramatically increased by feeding the worms E. faecium prior to infection with S. Typhimurium, as compared to worms fed control bacterial strains, and that this protective effect is

unexpectedly mediated by E. faecium secreted antigen A (SagA). We determined that SagA exhibits peptidoglycan hydrolase activity and generates cell wall fragments which, without intending to be constrained by any particular theory, are believed to activate host immunity to inhibit pathogenesis. We further show that recombinant expression of SagA in non-protective commensal bacteria is sufficient for mediating host protection against pathogenic bacteria, not only in C. elegans, but also in a mouse model, wherein engineered microbes that express heterologous SagA recombinantly can extend survival of the mice after challenge with S.

Typhimurium. Thus, SagA itself, and modified microorganisms which have been engineered to express SagA heterologously, are provided for use in prophylaxis and/or therapy of infections caused by a variety of enteric microbial pathogens. Microorganisms engineered to express SagA are also provided as probiotic microbes. Such microbes include but are not necessarily limited to members of the Lactobacillus genus. The probiotic microbes can be provided as

pharmaceutical or nutraceutical formulations, as components of human or non-human animal food items. Moreover, we demonstrate that introducing SagA producing E. faecium into mice limits Clostridium difficile pathogenesis. The disclosure also includes preparations of cell wall fragments produced by the enzymatic activity of SagA. Thus, the disclosure encompasses or SagA-generated metabolites as further described below.

In one aspect the present disclosure provides a modified microorganism, wherein the organism expresses a heterologous SagA. A "modified" microorgism means that the

microorganism has been changed relative to its naturally occurring form, such as having been engineered to express a heterologous protein. A "heterologous" SagA protein is a SagA protein that is not normally encoded by the genome of the microorganism. Accordingly, heterologous SagA production involves introducing a SagA-encoding DNA sequence into the microorganism. The modified microorganism comprises a heterologous SagA coding sequence, the expression of which is driven by a promoter operative in the microorganism. The SagA protein can be expressed from any suitable expression vector or other construct introduced into the

microorganism. In embodiments the heterologous SagA is encoded by a plasmid introduced into the modified microorganism, or is encoded by a segment of DNA introduced into a bacterial chromosome. Many reagents and methods for introducing and expressing any heterologous gene in a wide variety of microorganisms are known in the art and are suitable for use with the present invention. In general, the disclosure contemplates microorganisms that are modified to express and secrete heterologous SagA that retains the ability to generate peptidoglycan fragments from a suitable peptidoglycan-containing substrate. In one embodiment, the recombinantly produced SagA protein comprises the E. faecium amino acid sequence:

MKKSLIS AVM VC SMTLT AVASPI AAAADDFD SQIQQQDQKIADLKNQQ AD AQ S QIDALESQVSEINTQAQDLLAKQDTLRQESAQLVKDIADLQERIEKREDTIQKQAREAQ VSNTSSNYIDAVLNADSLADAIGRVQAMTTMVKANNDLMEQQKQDKKAVEDKKAEN D AKLKEL AENQ A ALE S QKGDLL SKQ ADLNVLKT SL A AEQ AT AEDKK ADLNRQK AE AE AEQ ARIREQQRL AEQ ARQQ AAQEK AEKE AREQ AEAE AQ ATQ AS ST AQ S S ASEES SAAQ SSTTEESSSAAQSSTTEESTTAPESSTTEESTTAPESSTTEESTTVPESSTTEESTTVPE SSTT EESTTVPESSTTEESTTVPETSTEESTTPAPTTPSTDQSVDPGNSTGSNATNNTTNTTPT PT PSGSVNGAAIVAEAYKYIGTPYVWGGKDPSGFDCSGFTRYVYLQVTGRDIGGWTVPQE S AGTKIS VSQ AKAGDLLFWGSPGGTYHVAIALGGGQ YIHAPQPGES VKVGS VQWF APD FAVSM (SEQ ID NO: 1), or a sequence that has at least 90% identity to this sequence, provided such non-identical sequences retain NlpC/p60-type hydrolase activity, which is described further below. As can be seen from Figure 4A, the NlpC/p60 hydrolase domain is from amino acid 389 through amino acid 530. In embodiments, other E. faecium SagA sequences are known and would be expected to function in place of Com 15 SagA, the sequence of which is given above. However, other homologues of SagA from non-E. faecium species would not be expected to function for use with the present disclosure.

In embodiments, the SagA protein is modified so that it has, for example, additional or fewer amino acids than in the sequence presented above. In non-limiting examples, the SagA protein is modified to include additional amino acids used for isolation, purification, or detection, including but not necessarily limited to a series of histidine residues at the C-terminus, or a polypeptide sequence that is capable of producing a detectable signal, such as a fluorescent signal.

In embodiments, the disclosure includes modified gram negative bacteria that expresses heterologous SagA protein, with the proviso that the gram negative bacteria do not include Escherichia coli. In embodiments, the disclosure includes modified bacteria that are facultative anaerobes. In embodiments the modified bacteria are gram positive bacteria that expresses heterologous SagA protein. In embodiments the gram positive bacteria are members the Lactobacillus genus, and in particular Lactobacillus species that are active in the production of food products intended for human and/or non-human animal consumption. In non-limiting embodiments the modified bacteria are Lactobacillus species that are active in the production of dairy products, such as yogurt, milk, milk-based creams, ice cream products, and cheese, or fermented drinks, such as wine, cider and beer, or fermented foods, or combinations of the foregoing. In certain embodiments the modified bacteria are L. plantarum, L. casei, L.

acidophilus, L. salivarius, or L. reuteri as well as probiotic strains of Bifidobacterium (i.e. B. longum). Data demonstrating successful heterologous production of SagA in several distinct microorganisms are provided.

In embodiments the disclosure includes combinations of modified bacteria described herein, and further comprises combinations of the modified bacteria with other microorganisms, such as yeasts. Those skilled in the art will recognize that such combinations are useful for production of certain foods.

In another aspect the disclosure comprises a food product comprising a modified bacteria that expresses a heterologous SagA protein. Such products include all of the aforementioned types of food and modified bacteria, and may further include modified E. coli that expresses a heterologous SagA. In embodiments the food product is a dairy product, including but not necessarily limited to yogurt, milk, milk-based creams, and cheese. Use of microorganisms in making foods that intentionally contain live cultures, such as yogurts, are well known in the art and can be adapted for use with the presently provided modified microorganisms. In one aspect the food product is a non-human animal feed, such as food intended for consumption by a bovine, equine, canine, porcine, feline, avian or reptilian animal, or by aquatic animals such as fish. In certain aspects the food product comprises packaging, such as a paper or cardboard carton, plastic container, bottle, bag, etc., that are well known for containing foods. The packaging can provide printed material which includes information that identifies the modified bacteria present in the food product.

In another aspect the disclosure includes a supplement product, such as a nutraceutical product, a dietary supplement, a food ingredient, etc., including but not limited to a probiotic formulation or functional food that contains one or more live modified bacteria as described herein. The supplement product can be provided in the form of, for example, a liquid, capsules, tablets, softgels, powders, freeze-dried compositions, and the like.

In another aspect the disclosure provides a pharmaceutical composition comprising modified microorganisms and/or isolated or purified recombinant SagA as described herein. The pharmaceutical composition can include any suitable diluent, carrier, excipient, buffer, etc., intended for use with the microorganisms for prophylactic and/or therapeutic human or veterinary purposes. Some examples of compositions suitable for preparing pharmaceutical compositions can be found in: Remington: The Science and Practice of Pharmacy (2005) 21st Edition, Philadelphia, PA. Lippincott Williams & Wilkins. Such compositions may also be included in supplement products.

In an embodiment the disclosure includes making modified bacteria that express heterologous SagA for use in inhibiting bacterial infections, or for maintaining or modifying the intestinal flora of an individual. The method comprises introducing into bacteria a heterologous SagA encoding DNA sequence, and culturing the bacteria for use as a probiotic, nutraceutical or pharmaceutical agent. In embodiments, the disclosure comprises such bacterial cultures themselves, and further includes such cultures scaled for use in producing nutraceutical, probiotic and/or pharmaceutical preparations. In embodiments, the cultures are propagated as, for example, a yogurt culture.

In another aspect the present disclosure comprises a composition comprising isolated or purified cell wall fragments generated by SagA. In certain embodiments the disclosure includes isolated and/or purified cell wall fragments (i.e, SagA-generated metabolites) made by a process that comprises exposing a peptidoglycan containing composition of matter, such as gram negative bacteria, or a composition comprising gram negative bacteria cell walls, or another peptidoglycan containing material, to SagA, allowing SagA to generate peptidoglycan fragments, and separating the peptidoglycan fragments from the composition and the SagA to obtain an isolated peptidoglycan fragment preparation. In embodiments the SagA-generated metabolites / peptidoglycan fragment preparation comprise muramyl peptides, i.e.,

muropeptides. Separating the peptidoglycan fragments can be achieved using any suitable approach, including but not necessarily limited to filtration, size exclusion and column-based separation, affinity separation, etc. As is demonstrated in the Examples of this disclosure, peptidoglycan fragments can protect worms and mice from distinct types of bacterial

pathogenesis. Thus, the disclosure provides a process for producing peptidoglycan fragments, and a peptidoglycan fragment preparation comprising or consisting of peptidoglycan fragments produced by that process, wherein such peptidoglycan fragment preparations are useful for the prophylaxis and/or therapy of bacterial infections.

In another aspect the disclosure includes a method comprising introducing into an individual modified bacteria wherein the modified bacteria expresses a heterologous SagA. The modified bacteria can be introduced as a component of a food product, a probiotic formulation, or a pharmaceutical formulation. In an aspect the disclosure includes a method for prophylaxis and/or therapy of a bacterial infection in an individual. The method comprises administering to an individual in need a composition comprising isolated SagA, or a bacterial population wherein at least some members of the population have been modified to produce SagA. In another approach, the composition can comprise peptidoglycan fragments generated by SagA.

Compositions and uses thereof comprising combinations of peptidoglycan fragments generated by SagA, modified bacteria that express SagA and isolated SagA are also encompassed by this disclosure. Compositions of the disclosure may be used prophylactically when they are given to an individual prior to exposure to pathologic bacteria, or within a short time, i.e., several hours, after exposure to pathologic bacteria. Therapeutic approaches comprise administering the engineered bacteria to an individual who has or is suspected of having a bacterial infection, wherein the severity of the infection is lessened subsequent to the administration.

In embodiments, administering a composition to an individual for, for instance, prophylaxis and/or therapy of a bacterial infection according to this disclosure can be performed using any suitable approach. In one embodiment, the composition is consumed by the individual as a probiotic formulation, or as a component of a food item and is thus introduced orally. In another embodiment the composition is administered as a pharmaceutical formulation. The pharmaceutical formulation can be administered using any suitable route, including but not necessarily limited to parenteral, intraperitoneal, intrapulmonary, oral, intra-abdominal, and others. Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, and subcutaneous administration. The amount of modified bacteria, SagA, peptidoglycan fragments, and any other active agent to be included in a composition and/or to be used in the method can be determined by those skilled in the art, given the benefit of the present disclosure. Thus, in one embodiment, an effective amount of a composition is administered. An effective amount can be an amount of the composition that inhibits growth of bacterial cells in the individual, or reduces a sign or symptom of bacterial infection. In embodiments, the individual to whom a composition of the invention is administered has, is suspected of having, or is at risk for development of a bacterial infection. In embodiments, the bacterial infection is an infection by enteric pathogens such as strains of Salmonella, Escherichia coli, Shigella, Campylobacter, Helicobacter, Francisella, Vibrio, Yersinia, Enter ococcus, and pathogenic strains of microbiota. In embodiments, a composition of this disclosure is administered to an individual such that the growth of enteric pathogens in the individual is inhibited, and/or the amount of enteric pathogens is reduced, or the enteric pathogens are eradicated.

Suitable dosages for either therapeutic or prophylactic purposes can be determined by those skilled in the art and will be based, at least in part, on consideration of the individual's age, sex, size, and health, the type of bacterial infection, and other factors as will be apparent to the skilled artisan. In embodiments, a composition of the invention can be administered in combination with an antibiotic.

The following description and specific Example is provided to illustrate the invention, but are not intended to be limiting in any way.

Example 1

This Example uses Caenorhabditis elegans to reconstitute Enterococcus faecium probiotic activity and identify a specific factor that enhances host resistance against enteric pathogens. Through biochemical, proteomic, and genetic approaches, we show that secreted SagA from E. faecium is sufficient to protect animals against Salmonella pathogenesis. Secreted SagA is also protective against other pathogenic microorganisms. Without intending to be constrained by any particular theory, the data show that SagA does not affect pathogen growth or virulence, but instead engages tol-1- dependent signaling to enhance host resistance to enteric pathogens. Biochemical studies demonstrate that the NlpC/p60 peptidoglycan hydrolase activity of SagA is required, and peptidoglycan fragments, i.e., muramyl-peptide fragments, generated by SagA are sufficient to protect C. elegans against Salmonella pathogenesis in a tol-1- dependent manner. This Example thus describes discovery of probiotic factors that can be used to enhance host resistance to pathogens. Such probiotic factors include but are not necessarily limited to SagA, catalytically active fragments of it, and muramyl-peptide fragments generated by SagA.

To facilitate our discovery and characterization of specific protective factors from intestinal bacteria and to develop compositions and methods of using them as described above, we employed C. elegans as a model organism, which has been widely used to study evolutionarily conserved aspects of innate immunity and microbial pathogenesis. We focused on Enterococci lactic acid bacteria that are commonly associated with the intestinal microbiome of diverse animal species ranging from humans to flies. Drug-resistant strains of E. faecium have emerged as nosocomial pathogens, but non-pathogenic strains of E. faecium can attenuate host susceptibility to enteric pathogens, including Salmonella, and have been employed as probiotics in humans and other animals (C. M. Franz, M. Huch, H. Abriouel, W. Holzapfel, A. Galvez, Enterococci as probiotics and their implications in food safety. Int J Food Microbiol 151, 125 (Dec 2, 2011)). Nevertheless, the protection mechanisms of E. faecium are unclear, which limits their utility as probiotics. Interestingly, E. faecium can colonize the C.

elegans intestine without causing apparent disease, which provided a unique opportunity to characterize the protective factors and conserved mechanisms underlying E. faecium probiotic activity. To investigate whether E. faecium can attenuate the pathogenesis of enteric bacteria in C. elegans, we developed a treatment-infection assay with Salmonella enterica serovar Typhimurium (Fig. 1A). S. Typhimurium is a Gram-negative bacterial pathogen with a broad host range that causes persistent intestinal infection and death in C. elegans. In the current disclosure, E. faecium-treated animals appeared less fragile and more motile than control E. coli OP50-treated animals after S. Typhimurium infection (Fig. 5A). Notably, C. elegans survival was increased in animals fed E. faecium prior to infection with S. Typhimurium as compared to animals fed E. coli OP50 or Bacillus subtilis 168 (Fig. IB and Fig. 5B). Multiple strains of E. faecium were able to inhibit S. Typhimurium pathogenesis, including a pig fecal isolate (NCTC 7171), two human fecal isolates (Coml5 and Coml2) (12) (Fig. 5C), and a pathogenic human blood isolate (DO) (X. Qin et al., Complete genome sequence of

Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol 12, 135 (2012)) (Fig. 5D). E. faecium-tr eated animals were also more resistant to the intrinsic pathogenesis of E. coli OP50 (Fig. 5E) as well as pathogenesis caused by the Gram- positive pathogen Enterococcus faecalis strain V583 (A. Garsin et al., A simple model host for identifying Gram-positive virulence factors. Proc Natl Acad Sci USA 98, 10892 (Sep 11, 2001)) (Fig. 5F). These results indicate that despite the genetic variation across the E. faecium strains tested, the mechanism of protection is conserved amongst E. faecium strains and may be active against diverse enteric pathogens.

To evaluate the mechanism of E. faecium-mediated protection, we first analyzed the effect of E. faecium treatment on S. Typhimurium colonization and persistence. Fluorescence imaging of mCherry-^. Typhimurium 3 days post-infection showed comparable S. Typhimurium colonization of animals with or without E. faecium treatment (Fig. 1C and Fig. 5G). Viable S. Typhimurium counts (CFUs) recovered from lysed worms revealed a ~2 log decrease in S. Typhimurium colonization 1 day post-infection in E. faecium-treated S. Typhimurium-infected animals (Fig. ID). However, by 3 days post-infection, S. Typhimurium titer was similar in OP50- and E. faecium-treated S. Typhimurium-infected animals (Fig. ID). To determine if this transient decrease in S. Typhimurium colonization represented direct niche competition early in the assay, we monitored E. faecium CFUs throughout the infection assay (Fig. 5H). While E. faecium initially colonized worms to ~10 ⁵ CFUs/worm, E. faecium numbers decreased to -10- 10 ² per worm 1 day post-infection, demonstrating that the transient decrease in S. Typhimurium colonization was not concomitant with an increase in E. faecium load. Electron microscopy of worm transverse sections 4 days post-infection revealed substantial degradation of the intestinal microvilli in OP50-treated S. Typhimurium-infected animals as compared to uninfected or E. faecium-treated animals (Fig. IE). In OP50-treated S. Typhimurium-infected animals, bacteria had escaped the intestinal lumen and caused extensive tissue damage (Fig. IE, middle panel). In contrast, E. faecium-treated S. Typhimurium-infected animals contained a similar bacterial load to the intestinal lumen and showed no apparent tissue damage (Fig. IE, right panel), indicating improved epithelial barrier integrity. These results demonstrate that E. faecium does not prevent S. Typhimurium colonization or replication in vivo, but may enhance host resistance to pathogens.

We next explored whether specific factors produced by E. faecium were sufficient for protection against S. Typhimurium pathogenesis. Using a liquid-treatment infection assay (Fig. 1 A), we found that E. faecium culture supernatant was as effective as live bacterial cultures in inhibiting S. Typhimurium pathogenesis (Fig. 2A). Activity of the E. faecium supernatant was sensitive to proteinase-K treatment, trichloro-acetic acid precipitation, and 10-kDa size exclusion (Fig. 6A-C), leading us to analyze the protein composition of E. faecium culture supernatant by mass spectrometry (Fig. 6D-E, Table 1). Proteomic analysis of E. faecium culture supernatant revealed a number of secreted proteins and an enrichment of peptidoglycan remodeling factors (Fig. 2B). We focused on secreted antigen A (SagA), the most abundant protein identified in the supernatant (Fig. 2B), which encodes a putative secreted NlpC/p60 peptidoglycan hydrolase that is believed to be essential for E. faecium viability. Fluorescence imaging of animals treated with E. faecium-expressmg mCherry under the sagA promoter (psagA:mcherry) indicates that SagA is expressed by E. faecium during C. elegans colonization (Fig. 2C). To test the protective activity of SagA in C. elegans directly, we expressed and purified recombinant SagA-Hise from both E. coli BL21-RIL(DE3) and E. faecium Com 15 (Fig. 2D and Fig. 7A-B; Table 2). Remarkably, treatment of animals with SagA-His ₆ purified from the culture supernatant of either source was sufficient to inhibit S. Typhimurium pathogenesis (Fig. 2E and Fig. 7C).

Analysis of sequenced E. faecium strains suggests they all encode a sagA ortholog in their genomes. In contrast, sequenced E. faecalis strains do not encode a clear sagA ortholog in their genomes and have not been reported to inhibit S. Typhimurium

pathogenesis. For example, E. faecalis OG1RF encodes three putative NlpC/p60-type peptidoglycan hydrolases (Uniprot accession: F2MNS9, F2MN84, F2MNY6) with less than 40 percent protein sequence identity to SagA (Fig. 8A). F2MNS9 and F2MN84 are predicted NlpC/p60-type hydrolases, whereas F2MNY6 lacks the conserved amino acid residues predicted for catalytic activity (Fig. 8 A). To determine if sagA expression is sufficient to confer protective activity, we inserted sagA-hise into the chromosome of E. faecalis OG1RF to generate E. faecalis-sagA (Fig. 3 A). In culture, SagA-His6 was expressed and secreted by E. faecalis-sagA (Fig. 3B), marginally affecting bacterial growth (Fig. 9). Proteomic analysis of E. faecalis OG1RF, E. faecalis-sagA, and E. faecium culture supernatants revealed less relative secreted SagA in E. faecalis-sagA culture supernatant as compared to E. faecium culture supernatant (Fig. 8B-F; Tables 3, 4). We detected only F2MNY6 in E. faecalis OG1RF culture supernatant (Fig. 9C), suggesting that, unlike E. faecium, E. faecalis does not secrete high levels of active NlpC/p60-type peptidoglycan hydrolases. In a continuous infection assay (Fig. 10A), treatment of C. elegans with E. faecalis-sagA attenuated S. Typhimurium pathogenesis comparably to E. faecium, while treatment with wild-type E. faecalis was not protective (Fig. 3C). S. Typhimurium load was similar in animals across all infected conditions, indicating that treatment with E. faecalis-sagA does not inhibit S. Typhimurium colonization or replication in vivo (Fig. 10B). In addition, SagA expression also counteracted the intrinsic pathogenesis of E. faecalis OG1RF (8) (Fig. IOC). These results demonstrate that the protective activity conferred by sagA expression is transferable to other bacterial species.

The protective activity of E. faecium against multiple enteric pathogens indicated that SagA may engage host pathways to limit pathogenesis. In response to intestinal infection, C. elegans mounts both general and pathogen-specific immune responses, which can lead to behavioral changes as well as the expression of antimicrobial and stress response effectors. The C. elegans innate immune system comprises both constitutive and induced signaling pathways, many with homology to mammalian pathways. Literature regarding C. elegans immunity-associated mutants indicates no major roles for the p38 MAPK/Pmk-1 pathway, the TGF-P-like/Dbl-l pathway, the insulin-like receptor/Daf-2 pathway, or the Npr- 1 mediated pathogen avoidance pathway in E. faecium-mediated protection against S.

Typhimurium infection (Fig. 11). C. elegans encodes one predicted homologue of Toll-like receptor, tol-1 (N. Pujol et al., A reverse genetic analysis of components of the Toll signaling pathway in Caenorhabditis elegans. Curr Biol 11, 809 (Jun 5, 2001)). Although tol-1 is important for development, C. elegans lacking the tol-1 TIR signaling domain [tol-1 (nr 2033)] are viable but exhibit defective pathogen avoidance to S. marsescens and an increased susceptibility to S. Typhimurium infection. We assessed SagA-mediated protection against S. Typhimurium pathogenesis in tol-l(nr2033) animals and found that both E. faecium and E. faecalis-sagA were not protective against continuous S. Typhimurium infection in this mutant background, suggesting that tol-1 signaling is required for SagA-mediated host protection (Fig. 3D). Without intending to be constrained by any particular theory, these results suggest SagA activates innate immune signaling pathways to enhance host resistance to enteric pathogens.

To determine the mechanism by which SagA enhances host resistance, we evaluated the NlpC/p60 hydrolase activity of SagA. SagA contains a type-1 signal sequence, an

uncharacterized N-terminal coiled-coil domain, a linker region of Ser/Thr-rich repeats, and a C- terminal NlpC/p60-type hydrolase domain (M. Firczuk, M. Bochtler, Folds and activities of peptidoglycan amidases. FEMS Microbiol Rev 31, 676 (Nov, 2007)); (Fig. 4A).

Although SagA is suggested to be essential for E. faecium viability, no hydrolase activity has been described. To determine if the NlpC/p60-type hydrolase domain of SagA is required for protection of C. elegans, we generated an active site (AS) mutant as well as a C-terminal NlpC/p60-type hydrolase domain deletion (Ctrunc) mutant of SagA (Fig. 4A). Both of these protein constructs were expressed, secreted, and purified from . coli BL21- RIL(DE3) (Fig. 12A). However, neither of these SagA mutants was able to inhibit S.

Typhimurium pathogenesis, indicating that the NlpC/p60-type hydrolase domain and active site are required for SagA activity (Fig. 4B). Fluorescence imaging of mCherry-^. Typhimurium and CFU measurements from untreated, SagA-treated, and active site mutant-treated infected animals were comparable (Fig. 12B-C), indicating that SagA does not affect S. Typhimurium colonization of C. elegans. In culture, addition of recombinant SagA also had no effect on the growth rate of S. Typhimurium (Fig. 12D) or on the secretion of S. Typhimurium type III protein effectors (Fig. 12E), suggesting that SagA does not directly attenuate S. Typhimurium growth or virulence mechanisms. The addition of recombinant SagA also had no effect on the growth rate of E. coli in culture (Fig. 13 A). However, induction of SagA expression in E. coli led to a decrease in culture optical density (OD) (Fig. 3C, 13B-C), indicating cell lysis. In contrast, expression of the active site mutant or SagA lacking a signal sequence did not induce E. coli cell lysis (Fig. 4C and Fig. 13B-C). These data suggest that while SagA is not bacteriolytic when added exogenously, SagA is a functional hydrolase that can cleave peptidoglycan when appropriately targeted to the periplasm. Collectively, these results demonstrate that the NlpC/p60 domain of SagA has hydrolase activity and is required for enhancing host resistance.

We analyzed whether SagA could hydrolyze peptidoglycan fragments derived from digested bacteria in the C elegans intestine, and whether these fragments may be responsible for enhancing host resistance. We found that the flow-thru from 5 kDa-MWCO column- filtered culture supematants of E. coli expressing SagA, but not the active site mutant, protected C. elegans from S. Typhimurium pathogenesis (Fig. 4D). We confirmed removal of SagA from the column flow-thru by Western blot (Fig. 14A), suggesting that lower molecular weight products of SagA enzymatic activity are sufficient for C. elegans protection. To more directly test if SagA-generated E. coli peptidoglycan fragments can also protect C. elegans from S. Typhimurium pathogenesis, we digested purified E. coli peptidoglycan with lysozyme and either SagA or the active site mutant, then filtered the digests to exclude protein.

C. elegans treated with the SagA peptidoglycan digests survived similarly to SagA- treated animals, whereas active site mutant digests failed to attenuate S. Typhimurium pathogenesis (Fig. 4E). These results suggest that SagA-generated peptidoglycan fragments, and not SagA itself, are responsible for protecting C. elegans from S. Typhimurium

pathogenesis.

To identify the peptidoglycan fragment(s) generated by SagA, we analyzed filtered bacterial culture supematants by ANTS labeling and gel-based profiling using established techniques. From E. coli expressing SagA, we detected a SagA-specific ANTS-labeled product that migrated similarly to the ANTS-labeled synthetic peptidoglycan components MurNAc-L- Ala and GlcNAc, but not to MurNAc-L-Ala-D-Glu (MDP) or MurNAc (Fig. 4F). Analysis of E. faecium and E. faecalis culture supematants revealed E. faecalis-sagA generates an ANTS-labeled product that co- migrates with MurNAc (Fig. 4G). In contrast, 10 kDa- MWCO filtered E. faecium culture supernatant did not yield detectable levels of MurNAc-L- Ala or MurNAc (Fig. 4G) and was not protective when administered to C. elegans (Fig. 6C). However, SagA is secreted at high levels by E. faecium (Fig. 2C and Fig. 8) and may hydrolyze intestinal peptidoglycan fragments in trans. Indeed, digestion of purified E. coli peptidoglycan with lysozyme and SagA, but not the active site mutant, yielded a unique peptidoglycan cleavage product with similar mobility to MurNAc-L-Ala (Fig. 14B), confirming that secreted SagA can cleave peptidoglycan fragments in trans through its

NlpC/p60-type hydrolase activity. We next assessed the activity of MurNAc-L-Ala, GlcNAc, MDP and MurNAc in protecting C. elegans from S. Typhimurium pathogenesis. While treatment of C. elegans with 50 μΜ of MDP or GlcNAc did not inhibit S. Typhimurium pathogenesis, treatment with either MurNAc or MurNAc-L-Ala was sufficient to inhibit S. Typhimurium pathogenesis (Fig. 4H). MurNAc and MurNAc-L-Ala were not protective in tol-l(nr2033) animals (Fig. 41), indicating that tol-1 signaling is required for mediating host protection in response to these peptidoglycan fragments. These data are consistent with peptidoglycan fragments activating innate immunity in mammals, but show MurNAc-L-Ala and MurNAc are the minimal peptidoglycan components that can enhance host resistance in C. elegans through a to/-7-dependent pathway. Nonetheless, a more complex mixture of peptidoglycan fragments is likely required in mammals, as MurNAc alone is insufficient to protect antibiotic-treatment mice from S. Typhimurium pathogenesis.

It will be recognized from the foregoing that the NlpC/p60 hydrolase activity of SagA generates unique peptidoglycan fragments in vivo that activate host immune signaling to enhance epithelial barrier integrity and confine pathogens to the intestinal lumen (Fig. IE), ultimately promoting host resistance to disease (Fig. 15). The analysis of E. faecium in mice suggests its colonization also improves intestinal epithelial barrier integrity to limit S.

Typhimurium pathogenesis in mammals. The protective activity of E. faecium in mice is mediated by SagA expression and without intending to be bound by any particular theory is believed to require the TLR signaling adaptor MyD88, the peptidoglycan pattern

recognition receptor NOD2 and the C-type lectin Regllly. These results together indicate that E. faecium and SagA may function through evolutionarily conserved pathways to enhance epithelial barrier integrity and protect animals from enteric pathogens. This

Example also reveals a previously unappreciated mechanism for secreted NlpC/p60-type peptidoglycan hydrolases and supports the use of these enzymes to enhance the protective activity of exi sting probi oti c s .

The following materials and methods were used to obtain the results discussed in this Example.

Materials and Methods.

Strains. C. elegans were maintained as described (/). C. elegans strains npr- l(ad609), daf-16(mu86), daf-2(e!370); daf-16(mgDf47), pmk-l(km25), dbl-l(nk3), and tol- l(nr2033) were all provided by the Caenorhabditis Genetics Center. E. coli OP50, E. coli DH5a, E. coli BL21-RJL(DE3) (Agilent Technologies), and Salmonella enterica serovar Typhimurium strain IR715 were grown in LB (BD Difco). Enterococcus faecium strains NCTC 7171 (ATCC 19434), Coml5, Coml2, and TX0016 (DO, ATCC BAA- 472), Enterococcus faecalis strains OGIRF (ATCC 47077) and V583 (ATCC 700802), and Bacillus subtilis strain 168 were grown in BHI (BD BBL). When necessary, ampicillin was used at 100 μg/mL, gentamicin was used at 125 μg/mL, and chloramphenicol was used at 25 μg/mL for E. coli, 10 μg/mL for E. faecium, and 8 μg/mL for E. faecalis.

Plasmids described in this study.

SagA hydrolase domain prediction was determined using Phyre 2 software. Coiled coil domain prediction were determined using COILS software. Signal sequence prediction was determined using SignalP v4.1 software.

Name Backbone Description

pET21a-SagA pET21 a (Novagen) Amp ^R , SagA-Hise

Amp ^R , AS-Hise;

pET21a-AS pET21a

C443A, H494A, H506A

Amp ^R , ACterm-Hise;

pET21a-ACterm pET21a

Δ390-529

Amp ^R , SagA-SS-Hise;

pET21a-SagA-SS pET21a

Δ2-27

pAM401

pAM401-SagA Cam ^R , psagA:SagA-His6

(ATCC 37429)

p AM401 -psagA:mcherry pAM401 Cam ^R , psagA:mcherry

pTEX5501ts

pTEX5501ts-OGlRF-sagA Cam ^R , Gen ^R , *see below p67MCl Amp ^R , mcherry

Cloning strategies: All cloning was done in E. coli DH5a. pET21a constructs were transformed into E. coli BL21- RIL (DE3) for expression. pAM401 constructs were

transformed into E. faecium for expression.

pET21a-SagA:

sagA was PCR amplified from the E. faecium Com 15 genome using the following primers:

FW: GGAC4 TA JGAAAAAGAGTTTAAT ATC AGC AGT AATGG (SEQ ID NO:2) RV: GGAC7UG.4GCATGCTGACAGCAAAGTCAGGTGCAAAC (SEQ ID NO:3)

Restriction sites for Ndel and Xhol are italicized. The PCR product was gel purified and subcloned into pGEMTeasy (Promega) for sequencing. Then, an internal Ndel site was mutated using the Quikchange multi-site directed mutagenesis kit (Stratagene) using the following primer:

AAATATATCGGTACTCCtTATGTTTGGGGCGG (SEQ ID NO:4)

The site mutated is indicated in lowercase, resulting in a synonymous mutation in the SagA protein sequence. sagA was then excised from pGEMTeasy with Ndel and Xhol and was ligated into cut pET21a (Novagen). pET21a-AS: pET21a-SagA was mutagenized with the following primers to generate the indicated cysteine to alanine and histidine to alanine mutations in the SagA protein sequence:

C443A: CCAAGTGGATTTGACgcCTCAGGATTCACACG (SEQ ID NO:5)

H494A: TCACCAGGCGGAACTTACgcCGTAGCGATTGC (SEQ ID NO:6)

H506A: GGAGGACAATATATCgcTGCTCCTCAACCAGG (SEQ ID NO:7)

The mutated sites are indicated in lowercase.

pET21a-ACterm: pet21a-SagA was mutagenized with the following primers to insert BamHl sites flanking the hydrolase domain:

AACAGATCAAAGTGT^JCCTGGGAACAGTACTGG (SEQ ID NO: 8)

TGC ACC TGAC TTTGCgGafccC ATGC TC GAGC AC C AC (SEQ ID NO: 9)

The BamHl sites are italicized. The mutated sites are indicated in lowercase. The plasmid was then cut with BamHl and re-ligated to form pET21a-ACterm, resulting in an in- frame excision of residues 390 through 529 in the SagA protein sequence.

pET21a-SagA-SS: SagA-SS was PCR amplified from pET21a-SagA_BamHl (see pAM401-SagA section below) using the following primers:

FW: C ATC ACG4 TA JGGACGATTTTGATTCTC AGAT A (SEQ ID NO: 10)

RV: C ATC ACGG/47UCTTTCGGGCTTTGTTA (SEQ ID NO: 11)

The Ndel and BamHl sites are italicized. This PCR product was cut and ligated back into cut pET21a-SagA_BamHl, resulting in an in-frame excision of residues 2 through 27 in the SagA protein sequence.

pAM401-psagA:mcherry: The promoter region of sagA (psagA) was PCR amplified from the E. faecium Com 15 genome using following primers:

FW: AAAG7UG.4CACGATGGTGGTCCAATTGAT (SEQ ID NO: 12) RV: TTTG47¾JGTCATTCCTCCGACTGGCTTA (SEQ ID NO: 13)

Restriction sites for Sail and Ndel are italicized. The PCR product was gel purified and subcloned into pGEMTeasy for sequencing. psagA was excised with Sail and

Ndel, and ligated into cut pAM401-padd9:mcherry (**see below) to replace paad9 with psagA. pAM401-SagA:

pET21a-SagA was mutagenized to insert a BamHl site after the 6X-His using the following primer to generate pET21a-SagA_BamHl :

TAACAAAGCCCGAAAGG^fccTGAGTTGGCTGCTGC (SEQ ID NO: 14)

The BamHl site is italicized. The mutated sites are indicated in lowercase. sagA-his6 was then excised with Ndel and BamHl, and ligated into cut pAM401-psagA:mcherry to replace mcherry with SagA-His ₆ . pAM401-SagA was transformed into E.faecium Coml5 as described below in this Example.

^Generating E. faecalis-sagA : pTEX5501ts-OGlRF-sagA:

pTEX5501ts 986 bp of sequence "upstream" (on the minus strand) of the intended SagA insertion site was PCR amplified using the following primers:

FW: AAACGGCCGAGTGGGGCGTGTTATTGAAG (SEQ ID NO: 15)

RV: TTTG7UG/4CGGGTAAGCTTCTCATCGTTTTG (SEQ ID NO: 16)

The Eagl and Sail sites are italicized. 1013 bp of sequence "downstream" (on the minus strand) of the intended SagA insertion site was PCR amplified using the following primers:

FW: AAAC TGCA GTGGAGCCTTGAAGAAAGTTG (SEQ ID NO: 17)

RV: TTTGGZ4CCATTGGCTGCTTTTGTTGCTT (SEQ ID NO: 18)

The Pstl and Kpnl sites are italicized. The upstream and downstream PCR products were subcloned into pGEMTeasy and sequenced, then were excised and ligated into cut pTEX5501ts sequentially. (Note: For the Eagl/Sall double digest of pTEX4401ts, Sail was added first, then Eagl because the restriction sites overlap in the vector, and Eagl can cut more efficiently at the end of a linear DNA fragment). psagA: sagA-hise was excised from pAM401 -SagA with Sail and BamHl and inserted into the cut vector, generating

pTEX5501ts-OGlRF-sagA. OGlRF-sagA- hise was generated using an established protocol. Briefly, OGIRF was transformed with pTEX5501ts-OGlRF-sagA and single recombinants were selected after plasmid curing at 37 °C. Then colonies were passaged at 37 °C and screened for gentamicin sensitivity and chloramphenicol resistance until such a clone was identified. Chromosomal insertion was verified by PCR and sequencing.

**pAM401-paad9:mcherry: paad9:mcherry was designed by us into pUC57. It encodes the synthetic promoter to aad9 flanked by Sail and Ndel restriction sites, driving mcherry flanked by Ndel and BamHl restriction sites. paad9:mcherry was excised from pUC57 with Sail and BamHl and ligated into cut pAM401, inserting into the Tet ^R gene.

Electroporation of Enterococcus: Protocol for preparation of electrocompetent cells and electroporation was adapted from Briefly, Enterococcus were grown for 18 hours in M9YE (M9 media, 0.1% casamino acids, 0.3% yeast extract) + 2% glycine. Cultures were diluted in half with M9YE + 3% glycine, and grown for an additional 3 hours. Cultures were chilled, pelleted, and washed 3 times in sucrose wash buffer (0.625 M sucrose, 1 mM MgCl ₂ , pH 4 with HC1), reducing the original culture volume by 1/2, 1/10, then 1/100 successively with each wash. Finally, cells were aliquoted, flash frozen in liquid nitrogen, and stored at -80 °C. Cells were electroporated in 2 mm cuvettes, 25 μ¥, 400 ohm, 2.5 kV. Cells were allowed to recover for 2 hours at room temperature without shaking in Todd-Hewitt Broth (BD Bacto) then with shaking at 37 °C for an additional 2 hours before plating on selective media.

Protein purification: For E. faecium Coml5 protein expression, plasmid-carrying strains were grown in BHI with appropriate antibiotics overnight. ForE. coli BL21-RIL

(DE3), LB cultures were inoculated with overnight cultures with appropriate antibiotics, grown for 2 hours or until OD ₆ oo ~ 0.4, induced with 1 mM IPTG, then grown for an additional 2 hours. His6-tagged proteins were purified from culture supernatants using Ni-NTA agarose (Qiagen). Native purifications were performed as recommended in the manufacturer's protocol. Purified protein was dialyzed into PBS at 4 °C overnight using 5 kDa or 7 kDa MWCO Slide-a-lyzers (Pierce Protein Biology). Protein concentration was estimated by BCA assay (Pierce Protein Biology) and protein was stored at - 20 °C.

Protein gel methods and Western blotting: Proteins were separated by SDS-PAGE on 4-20% Criterion Tris-HCl or Criterion TGX precast gels (Bio-Rad). Protein was visualized either by Coomassie blue (Bio-Rad) staining or stain-free imaging on a ChemiDoc MP system (Bio-Rad). Glycoproteins were visualized using the Pierce Glycoprotein staining kit (Thermo Scientific) as per the manufacturer's protocol. For Western blotting, proteins were transferred to nitrocellulose membrane. FIRP conjugated polyclonal anti- His ₆ (abeam abl l87) and monoclonal anti-actin (abeam abl4128) were used for His ₆ and actin Western blots

respectively. Western blots were visualized either by developing film or imaging on a

ChemiDoc MP system.

Bacterial growth curves: Growth o/E. coli expressing SagA, AS, or SagA-SS: Cultures were grown as described for protein purification, except that OD ₆ oo was monitored at given time points using a Spectromax M2e spectrophotometer. Growth ofE. coli and S. Typhimurium in the presence ofSagA: LB media was inoculated with overnight cultures 1 : 100. Protein was added at 10 μg/mL and volumes were normalized across all conditions with PBS. OD ₆ oo was measured at given time points.

Growth of GlRF-sagA: BHI media was inoculated with overnight cultures 1 : 100.

Chloramphenicol was added at 10 μg/mL as indicated. OD ₆ oo was measured at given time points.

Salmonella protein secretion assay: For each condition, 2 mL of LB was inoculated with overnight cultures 1 :30. Protein was added to media at 10 μg/mL and volumes were normalized across all conditions with PBS. Cultures were grown for 4 hours, shaking at 37 °C, the pelleted at 7000 g for 5 minutes. 1 mL of culture supernatant was precipitated with trichloro acetic acid (TCA) at a final concentration of 10% overnight at 4 °C. Precipitated proteins were pelleted at 20,800 g for 30 minutes, rinsed 2 times in acetone, then air-dried. Proteins were then separated by SDS-PAGE and visualized by Coomassie staining.

C. elegans infection assays: For each condition, 3 plates of 30 worms each (total 90 worms) were scored, unless otherwise noted. Mean percent survival and standard deviation of the triplicate plates for a representative experiment are shown for extended data figures. Mean percent survival and statistical comparisons by log rank test after Bonferroni correction for multiple comparisons using OASIS software are shown in the figures. E. faecium refers to strain Com 15 unless otherwise noted in the figure legends. Worms were handled using a Leica M60 microscope and imaged using a Leica IC80 HD camera.

Pulsed infection assay: Worms were synchronized using established techniques.

Synchronized young adult worms were washed in S buffer (129 mL 0.05 M K2HPO4, 871 mL 0.05 M KH2PO4, 5.85 g NaCl) and transferred to bacterial lawns grown on 2% agar BHI plates for colonization for 1 day. Then, worms were washed and transferred to lawns of OP50 or IR715 grown on BHI plates for infection for another day. Finally, worms were washed and transferred to lawns of OP50 grown on NGM plates (Day 0). Worms were maintained on OP50-NGM plates and survival was scored using established techniques.

Liquid-treatment pulsed infection assay: Synchronized young adult worms were transferred to 96-well plate wells containing 32% BHI media, culture supernatant, or live cultures. For protein treatments, 10-20 μg/mL of protein in PBS was included in each well. For treatment with peptidoglycan digests, 100 iL of each digest was added to each well. For treatment with defined peptidoglycan fragments, 50 μΜ of each fragment in a mixture of PBS and water was included in each well. MDP, GlcNAc, and MurNAc were purchased from Sigma- Aldrich. MurNAc-L-Ala was synthesized as described below in Scheme SI . After 2 hours, worms were washed and transferred to lawns of IR715 grown on BHI plates for 1 day. Then, worms were washed and transferred to lawns of OP50 grown on NGM plates (Day 0). Worms were maintained on OP50-NGM plates and survival was scored.

Continuous infection assay: Synchronized young adult worms were washed and transferred to bacterial lawns grown on 2% agar BHI plates for colonization for 1 day. Then, worms were washed and transferred to lawns of OP50 or IR715 grown on NGM plates (Day 0). Worms were maintained on OP50 or IR715 NGM plates and survival was scored.

OG1RF pathogenesis assay: This assay was performed using known techniques. Briefly, synchronized young adult worms were washed and transferred to Com 15, OG1RF, or GI ^ -sagA bacterial lawns grown on BHI plates (Day 0). Worms were maintained on Coml5, OG1RF, or GlKP-sagA BHI plates, and survival was scored.

Worm CFU measurements: Protocol for CFU measurements was adapted from previous protocol. Briefly, 5-20 worms were rinsed in drops of S buffer, and allowed to crawl free of bacteria on a sterile plate. These worms were then mechanically lysed in PBS using microtubes and pestles (Kimble-Chase). Serial dilutions of worm homogenate were plated on Salmonella-Shigella agar (BD BBL) or Enterococcosel (BD BBL) agar plates, and plates were incubated at 37 °C overnight.

Treatment of culture supematants: Proteinase K treatment: Culture supernatant or media was digested with 0.1 mg/mL of proteinase K in the presence of 1 mM CaCl ₂ for 2 hours at 37 °C. Then, 1 mM EGTA was added, and digestions were used in the liquid-treatment pulsed infection assay.

Trichloroacetic acid precipitation: Culture supernatant or media was precipitated with TCA (final concentration of 10%) overnight at 4 °C. Precipitated proteins were pelleted and rinsed 2 times in acetone, then air-dried and resuspended in BHI media before use in the liquid-treatment pulsed infection assay.

10-kDa MWCO column filtration: E. faecium culture supernatant or media was filtered through 10-kDa MWCO columns (Vivaspin GE Healthcare), and the flow-thru was used in the liquid- treatment pulsed infection assay.

5-kDa MWCO column filtration of E. coli culture supematants: E. coli BL21- RIL(DE3) expressing SagA-His or AS-His were induced in BHI media instead of LB as described above. Portions of the culture supematants were filtered through 5-kDa MWCO columns (Vivaspin GE Healthcare), and the unfiltered supematants, column concentrate, and column flow-thru were used in the liquid-treatment pulsed infection assay. Peptidoglycan digests:

100 μg of E. coli peptidoglycan (Invivogen) was digested with 20 μg lysozyme (Sigma) and 20μg of SagA-His or AS-His overnight in a mixture of PBS and water at 37 °C. Digests were then filtered through 5-kDa MWCO columns (Vivaspin GE Healthcare), and the flow- thru was used in the liquid-treatment pulsed infection assay.

Synthesis of N-acetylmuramic acid-L-alanine:

(c)

S1-6 S1-5 Scheme SI. Synthesis of the N-acetylmuramic acid-L-alanine. Reagents and conditions:

(a) (S)- 2-chloropropionic acid, NaH, 45 °C, 16 h. (b) Ala-OBn, DIEA, Cl-HOBt, DIC, CH2CI2/DMF, RT, 16 h. (c) Pd(PPh ₃ ) ₄ , AcOH, 40 °C, 16 h. (d) (i) 60% AcOH, 40-50 °C, 1.5 h; (ii) Pd/C, H ₂ , MeOH, RT, 5 h.

Compound Sl-2. SI -2 was synthesized from commercially available N- acetylglucosamine (Sl-1) by following and adapting published protocols.

Compound Sl-3. NaH (0.16 g, 6.67 mmol) was added to a suspension of compound Sl- 2 (0.358 g, 1.02 mmol) in 1,4-dioxane (9 mL). The mixture was stirred at 40 °C for 1 h. (S)-2- chloropropionic acid (0.27 mL, 2.95 mmol) in 1,4-dioxane (3 mL) was added to the reaction mixture dropwise. The mixture was stirred at 45 °C for 16 h. The solvent was removed under vacuum. H2O (20 mL) and 1M HCl( _aq ) (20 mL) was added. The mixture was extracted with CH2CI2 (3 x 25 mL) and the combined organic layers were dried with MgS0 ₄ and concentrated by rotary evaporation. The resulting solid was washed with cold Et20 several times and dried in vacuum to yield Sl-3 as a white solid (95 mg, 22%). Crude compound (Sl-3) was used without further purification. 1H NMR (400 MHz, CD ₃ OD): δ 7.47 (d, J = 4.1 Hz, 2H), 7.37 (d, J = 5.0 Hz, 3H), 5.88 (m, 1H), 5.64 (s, 1H), 5.28 (d, J= 17.2 Hz, 1H), 5.15 (d, J = 10.4 Hz, 1H), 4.63 (d, J= 7.7 Hz, 1H), 4.40 (q, J = 6.9 Hz, 1H), 4.31 (d, J= 4.9 Hz, 1H), 4.28 (t, J = 4.6 Hz, 1H), 4.07 (m, 1H), 3.76 (m, 3H), 3.67 (t, J = 4.2 Hz, 1H), 3.49 (m, 3H), 1.99 (s, 3H), 1.34 (d, J = 6.9 Hz, 3H). ESI-MS [M+H ⁺ ]: m/z calc. for C ₂ iH ₂₈ N0 ₈ ⁺ : 422.1809; found: 422.1807.

Compound Sl-4. L-alanine benzyl ester hydrochloride (68 mg, 0.315 mmol) and N,N- diisopropylethylamine (0.118 mL, 0.677 mmol) were added to a suspension of compound Sl-2 (0.95 mg, 0.225 mmol) in CH ₂ C1 ₂ . 6-Chloro-l-hydroxybenzotriazole (57 mg, 0.336 mmol) in DMF (0.7 mL) was added to the reaction mixture. Ν,Ν'- diisopropylcarbodiimide (45 uL, 0.291 mmol) was added to the reaction mixture. The mixture was stirred at room temperature for 16 h. 1M HCl( _aq ) (40 mL) was added to quench the reaction. The mixture was extracted with CH ₂ C1 ₂ (2x 25 mL) and the combined organic layers were dried with MgS0 ₄ and concentrated by rotary evaporation. The resulting solid was washed with cold MeOH several times and dried in vacuum to yield Sl-4 as a white solid (93 mg, 71%). Crude compound (Sl-4) was used in the next step without further purification. 1H MR (400 MHz, DMSO-d ₆ ): δ 7.41 (m, 10H), 5.84 (m, 1H), 5.69 (s, 1H), 5.25 (dd, J = 17.4, 1.8 Hz, 1H), 5.15 (d, J = 12.8 Hz, 2H), 5.09 (d, 12.6 Hz, 1H),

4.53 (d, J = 8.4 Hz, 1H), 4.31 (t, 7.4 Hz, 1H), 4.23 (m, 2H), 4.04 (m, 2H), 3.80 (m, 2H),

3.65 (t, 8.7 Hz, 2H), 3.42 (m, 1H), 1.79 (s, 3H), 1.34 (d, 7.8 Hz, 3H), 1.21 (d, 6.6 Hz, 3H). ¹³ C MR (600 MHz, DMSO-d ₆ ): δ 172.56, 172.40, 170.27, 138.01, 136.37, 134.93, 129.27, 128.87, 128.61, 128.49, 128.20, 126.32, 116.76, 101.25, 100.58, 80.45, 79.71, 77.70, 69.55, 68.23, 66.41, 66.09, 55.20, 47.97, 23.77, 23.47, 19.32, 17.28. ESI-MS [M+H ⁺ ]: m/z calc. for C3iH39N ₂ 0 ₉ ⁺ : 583.2650; found: 583.2650.

Compound Sl-5. Tetrakis(triphenylphosphine)palladium(0) (95 mg, 0.082 mmol) was added to a suspension of compound Sl-4 (93 mg, 0.160 mmol) in AcOH (1.5 mL). The mixture was stirred at 40 °C for 16 h. The solution was purified by silica gel column chromatography (MeOH/EtOAc/hexanes = 0.5/7/7)) to yield Sl-5 as a light yellow solid (57 mg, 66%). 1H NMR (600 MHz, CD ₃ OD): δ 7.50 (d, J = 4.2 Hz, 2H), 7.34 (m, 8H), 5.65 (s,

1H), 5.21 (d, J = 3.6 Hz, 1H), 5.19 (s, 2H), 4.44 (q, J = 7.2 Hz, 1H), 4.27 (q, J = 6.6 Hz, 1H), 4.21 (dd, J = 10.2, 4.8 Hz, 1H), 4.04 (m, 2H), 3.82 (m, 2H), 3.69 (t, J = 9.6 Hz, 1H), 1.97 (s, 3H), 1.42 (d, J = 7.2 Hz, 3H), 1.31 (d, J = 6.6 Hz, 3H). ¹³ C NMR (600 MHz, CD3OD): δ 174.50, 172.34, 172.20, 137.79, 135.81, 128.52, 128.20, 127.93, 127.86, 127.74, 125.92, 101.40, 101.25, 91.73, 82.08, 77.04, 76.16, 68.73, 66.61, 62.35, 54.21, 21.49, 18.34, 15.91. ESI-MS [M+H ⁺ ]: m/z calc. for C ₂₈ H35N ₂ 09 ⁺ : 543.2337; found: 543.2338.

Compound Sl-6. Compound Sl-5 was suspended in AcOH (0.6 mL) and H ₂ 0 (0.4 mL). The mixture was stirred at 50 °C for 1 h and 40 °C for 30 min. The solvent was removed under vacuum. The resulting solid was dissolved in MeOH (2 mL). 10% palladium on carbon (21 mg) was added to the solution. The mixture was stirred under 1 atm. of H ₂ at room temperature for 5h. After filtration, the solution was concentrated by rotary evaporation. The resulting oil was purified by silica gel column chromatography (MeOH/CHCb = 3 :7 to 4:6) to yield compound Sl-6 (a-anomer). 1H MR (600 MHz, CD ₃ OD): δ 5.13 (d, J = 3.6 Hz, 1H), 4.39 (q, J = 7.2 Hz, 1H), 4.34 (q, J = 6.6 Hz, 1H), 3.94 (dd, J = 10.2, 3.0Hz, 1H), 3.82 (m, 2H), 3.73 (m, 1H), 3.68 (m, 1H), 3.50 (m, 1H), 1.97 (s, 3H), 1.45 (d, J= 7.6 Hz, 3H), 1.41 (d, J = 7.1 Hz, 3H). ¹³ C MR (600 MHz, CD3OD): δ 174.55, 174.36, 172.07, 95.88, 91.15, 79.38, 77.14, 71.83, 70.10, 61.27, 53.96, 21.46, 18.10, 16.27. ESI-MS [M+H ⁺ ]: m/z calc. for Ci ₄ H ₂₅ N ₂ 0 ₉ ⁺ : 365.1555; found: 365.1555.

Proteomics: In-gel digestion: 1 mL of culture supernatant was precipitated with TCA as described above, resuspended in loading buffer and separated by SDS-PAGE.

Proteins were processed for in-gel digestion with sequencing grade trypsin (Promega) using known techniques except that dried samples were resuspended in 5% acetonitrile, 2% formic acid in water.

In-solution digestion:

1 mL of culture supernatant was precipitated with TCA as described above, and proteins were digested with 0.2 μg of trypsin in 50 mM ammonium bicarbonate buffer overnight at 37 °C. Samples were dried by speed-vac, then resuspended in 5% acetonitrile, 2% formic acid in water. LC-MS was performed on digested peptides and peptide spectra were analyzed against the E. faecium Com 15 proteome using Mascot v2.3 and Proteome Discoverer software.

8-aminonaphthalene 1,3,6 trisulfonic acid (ANTS) labeling assay:

E. coli supernatants were prepared by inoculating cultures 1 :50 with an overnight culture of E. coli BL21-RIL(DE3) expressing SagA-His6 or AS-His6. Cultures were grown for 2 hours, then induced with 1 mM IPTG, and grown for an additional 2 hours. Enterococcus supernatants were prepared by growing cultures overnight. Cultures were pelleted, and supernatant was filtered through 10 kDa MWCO columns (Millipore Microcon). For peptidoglycan digests, 100 μg of E. coli peptidoglycan wasdigested with 20 μg lysozyme and 20 μg of SagA-His or AS-His overnight in a mixture of PBS and water at 37 °C. Digests were filtered through 10 kDa MWCO columns. Culture supernatants, peptidoglycan digests, and defined peptidoglycan fragments were dried by speed-vac before ANTS labeling. ANTS labeling was using established techniques. ΙΟμΙ of ANTS reaction mix was added to each tube of dried material (1 : 1 mixture of 0.2 M ANTS (in 3 : 17 acetic acid:water): 1 M NaCNBH ₃ (in DMSO)). Reactions were incubated overnight at 37 °C. 0.5-3.5 μL· of the ANTS labeled mixtures were mixed 1 : 1 with 40% glycerol and samples were separated by native PAGE on a hand-cast 37-40% Tris-glycine acrylamide gel (19: 1 polyacrylamide:bisacrylamide, with a 20% acrylamide stack) at 150 V for ~ 3 hours or 80 V for

~ 6 hours. Empty lanes adjacent to sample lanes were loaded with samples of ANTS labeled Ala- D-y-Glu-Lys-D-Ala-D-Ala (Sigma). Remaining lanes were loaded with 20% glycerol. Gels were imaged on the ChemiDoc MP system (Bio-Rad) using the Sybr-safe UV imaging setting.

Epifluorescence:

For imaging of mc erry -Salmonella, worms were treated as described for the pulsed infection assays except worms were infected with S. Typhimurium carrying the plasmid p67MCl . For imaging of E. faecium psagA:mcherry, worms were fed E. faecium carrying the plasmid pAM401-mcherry for 1 day on BHI plates. Worms were mounted as described (18), except that worms were paralyzed in 1 mM tetramisole (Sigma) instead of sodium azide. Worms were imaged on a Nikon Eclipse TS100 and pictures were taken using a Nikon Digital Sight DS-Fil .

Electron Microscopy:

Animals were prepared for electron microscopy using standard methods. Ultrathin serial sections (70 nm) were collected by using a Leica Ultracut UCT Ultramicrotome. Sections at two regions, 120 μιη and 200 μιη away from the head region, were examined for each condition. EM images were acquired using an FEI Tecnai G2 Spirit BioTwin transmission electron microscope operating at 80 kV with a Gatan 4K x 4K digital camera.

Table 1. Proteins identified from E. faecium Com15 culture supernatant by mass spectrometry, after indigestion. Proteins listed have at least 2 unique peptides identified. Proteins involved in peptidoglycan remodeling are shaded. PSM = peptide spectrum match.

C9ASJ4 N-acetylmuramoyl-L-alanine amidase 23 78

C9ATH2 Beta-1 ,4-N-acetylmuramoylhydrolase 16 76

C9AKY1 Periplasmic solute binding protein 21 68

C9AQT6 Periplasmic binding protein 16 63

C9ANP2 N-acetylmuramoyl-L-alanine amidase 10 57

C9APB3 Putative uncharacterized protein 16 56

C9ALQ1 eno Enolase 23 55

C9APJ5 Penicillin-binding protein 23 48

C9AMB1 Sulfatase 20 45

C9ALP8 Glyceraldehyde-3-phosphate dehydrogenase 10 43

C9AQM8 tuf Elongation factor Tu 2 13 41

C9ALW6 Glycosyl transferase 20 41

C9ARZ3 Extracellular solute-binding protein 12 41

C9AMG6 arcA Arginine deiminase 17 39

C9AML5 Amino acid ABC transporter 8 36

C9ASF9 ErfK/YbiS/YcfS/YnhG family protein 16 34

C9AS22 FMN-binding protein 10 34

C9API8 Pyruvate kinase 19 33

C9ALP9 pgk Phosphoglycerate kinase 13 31

C9AMK8 dnaK Chaperone protein DnaK 23 31

C9AMB7 pgi Glucose-6-phosphate isomerase 15 29

C9ALB5 Sulfatase 16 29

C9AMH5 tsf Elongation factor Ts 1 1 27

C9AQB2 Fructose-bisphosphate aldolase class-ll 10 25

C9ARP7 Glycine betaine/L-proline ABC transporter 9 25

C9AP18 D-alanyl-D-alanine carboxypeptidase 10 23

C9APP4 Transcriptional regulator 10 23

C9ANA8 Extracellular solute-binding protein 17 23

C9AL01 Extracellular solute-binding protein 12 21

C9ANQ7 Peptidyl-prolyl cis-trans isomerase 7 20

C9ARQ9 groEL 60 kDa chaperonin 15 19

C9ANB6 Extracellular solute-binding protein 9 19

C9ATA9 ATP-dependent Clp protease 14 18

C9AME5 Iron compound ABC transporter 1 1 18

C9AQM7 fusA Elongation factor G 10 16

C9AS40 ABC transporter substrate binding protein 10 16

C9ANN9 NADH oxidase 10 15

C9AMN8 tig Trigger factor 1 1 14

C9APM7 Phosphoenolpyruvate-protein phosphotransferase 1 1 12

C9AMG7 Ornithine carbamoyltransferase 7 12

C9AP95 Ribosomal protein S1 10 12

C9ARE8 prsA PpiC-type peptidyl-prolyl cis-trans isomerase 8 12

C9ALQ0 tpiA Triosephosphate isomerase 6 12

C9ASG0 Idh L-lactate dehydrogenase 2 8 1 1

C9APR1 Predicted protein 5 1 1

C9AQP2 rplE 50S ribosomal protein L5 4 10

C9ANQ4 Glyceraldehyde-3-phosphate dehydrogenase 7 10

C9APA2 Peptidase M20A 8 10

C9ANB3 Putative uncharacterized protein 5 10

C9AR88 Peptidase S1 6 10

C9APC1 tuf Elongation factor Tu 1 7 9

C9API4 6-phosphogluconate dehydrogenase, decarboxylating 8 9

C9AQB4 Glutamine synthetase 8 9 C9ARL3 rplA 50S ribosomal protein L1 3 3

C9AQN1 rpID 50S ribosomal protein L4 2 3

C9ALV5 UTP-glucose-1 -phosphate uridylyltransferase 2 3

C9ARL4 rplJ 50S ribosomal protein L10 3 3

C9AMD1 Putative uncharacterized protein 2 3

C9APR5 greA Transcription elongation factor greA 2 3

C9AS03 metG Methionyl-tRNA synthetase 2 3

Probable manganese-dependent inorganic

C9AP54 ppaC 2 3 pyrophosphatase

C9ARH5 Aldo/keto reductase 2 3

C9AR84 Glutamyl aminopeptidase 3 3

C9ALL0 Putative uncharacterized protein 3 3

C9AQN6 rpsC 30S ribosomal protein S3 3 3

C9ALV7 Putative uncharacterized protein 3 3

C9ANI8 HD domain-containing protein 3 3

C9AN38 prsA Foldase protein prsA 2 2 3

C9AP35 Putative uncharacterized protein 3 3

C9AQM9 rpsJ Ribosomal protein S10 2 2

C9AMH4 rpsB 30S ribosomal protein S2 2 2

C9AMN9 clpX ATP-dependent CIp protease ATP-binding subunit ClpX 2 2

C9ASA9 gltX Glutamate-tRNA ligase 2 2

C9AQZ1 pnp Polyribonucleotide nucleotidyltransferase 2 2

C9AQP6 rpIR 50S ribosomal protein L18 2 2

C9AL22 M13 family peptidase 2 2

C9ARB8 Predicted protein 2 2

Pyridoxal-phosphate-dependent serine

C9ARX7 glyA 2 2 hydroxymethyltransferase

C9AQ30 ftsZ Cell division protein ftsZ 2 2

C9AP56 Formate acetyltransferase 2 2

C9APC4 2,5-didehydrogluconate reductase 2 2

C9APL6 3-oxoacyl-[acyl-carrier-protein] synthase 2 2 2

C9AQA9 rpmE2 50S ribosomal protein L31 type B 2 2

C9AM29 D-alanyl-D-alanine carboxypeptidase 2 2

C9ASN3 tyrS Tyrosine-tRNA ligase 2 2

C9ANP1 Cysteine synthase 2 2

C9AQ59 rpmA 50S ribosomal protein L27 2 2

C9AQN5 rpIV 50S ribosomal protein L22 2 2

C9AQ61 rplU 50S ribosomal protein L21 2 2

C9APL9 acpP Acyl carrier protein 1 2 2

C9AMM5 Putative uncharacterized protein 2 2

C9ARS4 nadE NH(3)-dependent NAD(+) synthetase 2 2

C9ALC7 Putative uncharacterized protein 2 2

C9AP38 ABC transporter 2 2

C9ASJ8 Putative uncharacterized protein 2 2

C9ALI4 Putative uncharacterized protein 2 2

C9AN28 Predicted protein 2 2

C9ALC4 Lipoprotein YaeC 2 2

C9ASP9 Cell wall surface adhesion protein 2 2

C9APR0 Putative uncharacterized protein 2 2

F2MPG0 eno Enolase 9 22 8 15

F2MR31 Uncharacterized protein 8 16 14 47

F2MQS5 ptsi Phosphoenolpyruvate-protein phosphotransferase 7 16 7 15

F2MPK1 Peptide ABC superfamily ABC transporter, binding 7 15 12 23 protein

F2MNH6 gelE Gelatinase 7 15 9 22

F2MQ41 npr NADH peroxidase 4 15 4 4

F2MNQ3 htrA Serine protease HtrA 4 13 3 4

F2MQL1 rpoC DNA-directed RNA polymerase subunit beta' 7 12 5 7

F2MM76 ABC superfamily ABC transporter, binding protein 6 11 10 23

F2MNH5 sprE SprE protein 4 11 5 20

F2MQ69 ackA Acetate kinase 5 11 5 14

F2MR21 dnaK Chaperone protein DnaK 9 11 8 11

F2MTS3 groEL 60 kDa chaperonin 7 11 7 10

F2MMD6 pepQ Xaa-Pro dipeptidase 4 11 4 9

F2MSU5 Pgi Glucose-6-phosphate isomerase 4 11 4 9

F2MT66 oppA Oligopeptide ABC superfamily ABC transporter, 7 11 6 8 binding protein

F2MRX7 pdhA Pyruvate dehydrogenase complex El component 3 11 2 5 alpha subunit

F2MM98 tuf Elongation factor Tu 7 10 5 6

F2MPU3 Transcriptional regulator 3 9 6 10

F2MQA4 ABC superfamily ABC transporter, binding protein 2 9 4 10

F2MST4 trxA Thioredoxin 2 9 2 10

F2MQC6 glnA Glutamine synthetase 5 9 4 7

F2MN33 ldh L-lactate dehydrogenase 4 9 3 6

F2MR74 ABC superfamily ABC transporter, binding protein 3 8 9 15

F2MRQ5 Iv/.lft Cell wall lvsis protein 1 8

F2MPV9 tyrS Tyrosine-tRNA ligase 5 8 2 7

F2MQH3 ubiD2 UbiD family decarboxylase 6 8 4 6 F2MQK7 dps DNA starvation/stationary phase protection protein 5 8 4 4 Dps

F2MML0 gnd 6-phosphogluconate dehydrogenase, 6 8 2 3 decarboxylating

F2MSU4 gdhA Glutamate dehydrogenase 4 7 6 10

F2MQHS WxL domain surface protein I 3 6

F2MQ03 fbaB Fructose-bisphosphate aldolase 3 7 3 5

F2MRX1 Sugar ABC superfamily ABC transporter, sugar- 5 7 3 5 binding protein

F2MMC3 adk Adenylate kinase 3 7 2 4

F2MQX6 Sulfatase domain protein 5 6 8 15

F2MRL8 glnP Amino acid ABC superfamily ABC transporter, 3 6 4 8 binding/permease protein

F2MRY0 lpd Dihydrolipoyl dehydrogenase 4 6 3 7

F2MN60 fabF 3-oxoacyl-[acyl-carrier-protein] synthase 2 3 6 3 5

F2MMK6 pfkA 6-phosphofructokinase 4 6 3 4

F2MQT2 fruK2 Tagatose-6-phosphate kinase 2 6 2 4

F2MT 3 ndh NADH dehydrogenase 3 6 2 4

F2MMR7 ccpA Catabolite control protein A 4 6 3 3

F2MTG7 hup DNA-binding protein HU 3 6 2 2

F2MM84 deoB Phosphopentomutase 3 5 4 6

F2MRY7 Hydroxymethylglutaryl-CoA synthase 2 5 2 5

F2MTV6 pflB Formate acetyltransferase 4 5 3 4

F2MM91 adh3 Putative alcohol dehydrogenase (NADP(+)) 2 4 3 7

F2MTA8 pta Phosphate acetyltransferase 3 4 3 4

F2MRX8 pdhB Pyruvate dehydrogenase complex El component 3 4 2 2 beta subunit

F2MS34 frr Ribosome-recycling factor 4 4 2 2

F2MS37 rpsB 30S ribosomal protein S2 j - 4 2 2

F2MTE1 Uncharacterized protein 2 3 4 10

F2MRB6 Pheromone cAD 1 lipoprotein 2 3 3 3 F2MT59 aad Aldehyde-alcohol dehydrogenase 2 2 10 18

F2MRB5 Thiamine biosynthesis lipoprotein 2 2 3 5

F2MTQ5 atpA2 ATP synthase subunit alpha 2 2 2 3

F2MU99 ahpC Peroxiredoxin 2 2 2 3

F2MM92 gpmA 2,3-bisphosphoglycerate-dependent 2 2 2 2 phosphoglycerate mutase

F2MNI5 WxL domain surface protein 1 m

F2MNH I Phosphalidvlgh ccrol-me rubra nc-oligosaccharidc 0 1 1 28 glvccrophosphotransfcrasc

F2MMF2 pbpC Penicillin-binding protein C 0 1 t 1

F2MNV6 Chilin-binding prolcin/carboln dralc-binding protein 1 6 m

F2MUF4 penA Penicillin-binding protein 2B 0 1 1 1 i s

F2MRA7 Cell-envelope associated acid phosphatase 1 1 S 8

F2MTN5 pini Mannosc-6-phosphalc isomcrasc 1 1 8

F2MSL7 opuCC Glycine/betaine/carnitine/choline ABC superfamily 0 0 3 7

ABC transporter, binding protein

F2MU67 Transcriptional regulator 0 0 6 6

F2MS22 proS Proline—tRNA ligase 0 0 2 5

F2MMR4 pbp I B Penicillin-binding protein I B 0 1 1 1

F2MMV9 ABC superfamily ABC transporter, substrate- 0 0 3 4 binding protein

xxxxx SagA-His6 0 0 3 4

F2MTQ3 atpD2 ATP synthase subunit beta 0 0 2 4

F2MMX1 pabC Aminodeoxychorismate lyase 0 0 3 3

F2MNF9 Uncharacterized protein 0 0 3 3

F2MQM9 pepV Dipeptidase PepV 0 0 3 3

F2MTH6 Uncharacterized protein 0 0 3 3

F2MP85 dkgB 2,5-diketo-D-gluconate reductase 0 0 2 3

F2MQ25 Uncharacterized protein 0 0 2 3

F2MRN8 Acyltransferase 0 0 2 3 F2MTE4 gap Glyceraldehyde-3 -phosphate dehydrogenase 0 0 2 3

F2MU19 S41A family carboxy-terminal peptidase 0 0 2 3

F2MM97 fusA Elongation factor G 0 0 2 2

F2MNV5 chiC Chitinase CI 0 0 2 2

F2MPG1 tpiA Triosephosphate isomerase 0 0 2 2

F2MSG8 arcA Arginine deiminase 0 0 2 2

F2MT41 glyA Serine hydroxymethyltransferase 0 0 2 2

F2MPW0 Decarboxylase 10 28 0 0

F2MR04 Uncharacterized protein 9 17 0 0

F2MMN0 pstS Phosphate ABC superfamily ABC transporter, 6 13 0 0 binding protein

F2MT47 Fumarate reductase 6 9 0 0

F2MMK7 pyk Pyruvate kinase 5 7 0 0

F2MQL2 φθΒ DNA-directed RNA polymerase subunit beta 4 7 0 0

F2MTJ8 tkt Transketolase 3 7 0 0

F2MMA5 φΙΒ 50S ribosomal protein L2 3 6 0 0

F2MP87 gloA5 Lactoylglutathione lyase 3 6 0 0

F2MQH1 ubiD UbiD family decarboxylase 2 6 0 0

F2MU24 coaC Phosphopantothenoylcysteine decarboxylase 2 6 0 0

F2MRI2 rpll 50S ribosomal protein L9 4 5 0 0

F2MRM7 clpP ATP-dependent Clp protease proteolytic subunit 4 5 0 0

F2MRQ6 leuS Leucine~tRNA ligase 3 5 0 0

F2MMX0 greA Transcription elongation factor GreA 2 5 0 0

F2MNZ2 pep Pyrrolidone-carboxylate peptidase 2 5 0 0

F2MU79 rplK 50S ribosomal protein L 11 2 5 0 0

F2MMN1 aspC2 Aminotransferase 3 4 0 0

F2MQK0 Choline binding protein 3 4 0 0

F2MQK6 φΙΜ 50S ribosomal protein L 13 2 4 0 0

F2MQV8 Gfo/Idh/MocA family oxidoreductase 2 4 0 0 F2MT73 infC Translation initiation factor IF-3 2 4 0 0

F2MMA3 rplD 50S ribosomal protein L4 3 3 0 0

F2MQQ0 prsA Foldase protein PrsA 3 3 0 0

F2MR57 pepS Aminopeptidase PepS 2 3 0 0

F2MSC3 purR Purine operon repressor 2 3 0 0

F2MM66 guaA GMP synthase [glutamine-hydrolyzing] 2 2 0 0

F2MM95 rpsL 30S ribosomal protein S12 2 2 0 0

F2MMA1 rpsJ 30S ribosomal protein S10 2 2 0 0

F2MMA2 rplC 50S ribosomal protein L3 2 2 0 0

F2MMA6 rpsS 30S ribosomal protein S19 2 2 0 0

F2MMA8 rpsC 30S ribosomal protein S3 2 2 0 0

F2MMB9 rpsE 30S ribosomal protein S5 2 2 0 0

F2MMD3 rpmA 50S ribosomal protein L27 2 2 0 0

F2MNV0 pepC Aminopeptidase C 2 2 0 0

F2MPA1 rplS 50S ribosomal protein L 19 2 2 0 0

F2MQT1 fraA PTS family fructose porter, IIABC component 2 2 0 0

F2MRX9 aceF Pyruvate dehydrogenase complex E2, 2 2 0 0 dihydrolipoamide acetyltransferase

F2MTV4 ppaC Probable manganese-dependent inorganic 2 2 0 0 pyrophosphatase

F2MU40 pepF Oligoendopeptidase F 2 2 0 0

F2MUA4 celM M42 family glutamyl aminopeptidase 2 2 0 0

Table 4. Proteins in E. faecium Coml5 culture supernatant identified by mass spectrometry, after in-solution digestion. Proteins listed have at least 2 unique peptides. Proteins involved in cell wall remodeling are highlighted in yellow. PSM = peptide spectrum match.

C9AMB1 Sulfatase 14 39

C9AQT6 Periplasmic binding protein 12 37

C9ARQ9 groEL 60 kDa chaperonin 17 36

C9APJ5 Penicillin-binding protein 16 31

C9API8 Pyruvate kinase 15 31

C9AQM7 fusA Elongation factor G 11 30

C9ATH2 Beta- 1 ,4-N-acetylmuramoylhydrolase 13 29

C9AQM8 tuf Elongation factor Tu 13 27

C9ATA9 ATP-dependent Clp protease 15 26

C9AS94 Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase 11 26

C9AMK8 dnaK Chaperone protein 18 25

C9AMB7 Pgi Glucose-6-phosphate isomerase 11 25

C9ALP9 Pgk Phosphoglycerate kinase 11 24

C9ALP8 Glyceraldehyde-3 -phosphate dehydrogenase 11 23

C9AMG7 Ornithine carbamoyltransferase 10 22

C9AMH5 tsf Elongation factor Ts 12 19

C9APB3 Putative uncharacterized protein 9 18

C9AQB2 Fructose-bisphosphate aldolase class-II 8 18

C9AMN8 tig Trigger factor 10 17

C9APW8 Putative uncharacterized protein 9 17

C9ASN3 tyrS Tyrosine-fRNA ligase 7 17

C9AP18 D-alanyl-D-alanine carboxypeptidase 7 16

C9ASJ4 N-acetylmuramoyl-L-alanine aniidase 9 15

C9AML5 Amino acid ABC transporter 6 15

C9ALB5 Sulfatase 8 14

C9ASF9 ErfK/YbiS YcfS/YnhG family protein 7 14

C9AKY4 Peptidogly can-binding protein LysM 6 14

C9ANA8 Extracellular solute-binding protein 8 13

C9ARE8 prsA Foldase protein PrsA 6 13

C9APM7 Phosphoenolpymvate-protein phosphotransferase 9 12

C9AQN3 ΙΒ 50S ribosomal protein L2 5 12

C9AS40 ABC transporter substrate binding protein 7 11

C9ANB6 Extracellular solute-binding protein 6 11

C9AL01 Extracellular solute-binding protein 5 11

C9ARP7 Glycine betaine L-proline ABC transporter 4 11

C9AQZ1 np Polyribonucleotide nucleotidyltransferase 4 11

C9AQB4 Glutamine synthetase 6 10

C9APW3 Putative uncharacterized protein 5 10

C9APC1 tuf Elongation factor Tu 5 10

C9APP1 Chitin-binding protein 4 10

C9ANY2 Transketolase 4 10

C9ATC6 Uncharacterized protein 3 10

C9A P2 N-acetylmuramoyl-L-alanine amidase 5 9

C9ARY2 Cell wall surface adhesion protein 6 8

C9ATC3 Uncharacterized protein 6 8

C9ALV5 UTP-glucose- 1 -phosphate uridylyltransferase 4 8

C9AQ24 ileS Isoleucine-tRNA ligase 3 8

C9ALL0 Putative uncharacterized protein 6 7

C9ASG0 ldh L-lactate dehydrogenase 5 7

C9AMG6 arcA Arginine deiminase 5 7

C9AQK7 guaA GMP synthase [glutamine-hydrolyzing] 5 7

C9ARS4 nadE NH(3)-dependent NAD(+) synthetase 5 7

C9APR1 Predicted protein 4 7

C9ARL2 φΙΚ 50S ribosomal protein L 11 4 7

C9AS47 Ferritin 4 7 C9ALR9 atpD ATP synthase subunit beta 4 7

C9APW2 Predicted protein 3 7

C9APL9 acpP Acyl carrier protein 3 7

C9ATD5 Intracellular protease 3 7

C9AS03 metG Methionine~tRNA ligase 2 7

C9ANN9 NADH oxidase 2 7

C9AL85 prsA Foldase protein PrsA 6 6

C9AQL4 Basic membrane lipoprotein 5 6

C9AS42 rpoC DNA-directed RNA polymerase subunit beta' 5 6

C9AS49 30S ribosomal protein S9 4 6

C9APA2 Peptidase M20A 4 6

C9ANY3 Pyruvate dehydrogenase 3 6

C9AQP6 φΠ 50S ribosomal protein L 18 3 6

C9AKW7 NAD(FAD)-dependent dehydrogenase 3 6

C9AR84 Glutamyl aminopeptidase 3 6

C9ALQ0 tpiA Triosephosphate isomerase 3 6

C9ALX9 Phosphoglucomutase/phosphomannomutase 3 6

C9ATF4 Citrate lyase alpha subunit 3 6

C9AQP9 rplO 50S ribosomal protein L 15 2 6

C9AN96 Alkyl hydroperoxide reductase 2 6

C9APR5 greA Transcription elongation factor GreA 2 6

C9ALV9 Catabolite control protein A 4 5

C9ASA9 gitx Glutamate~tRNA ligase 4 5

C9ANQ4 Glyceraldehyde-3 -phosphate dehydrogenase 3 5

C9API9 pfkA 6-phosphofructokinase 3 5

C9ASH2 lysS Lysine~tRNA ligase 3 5

C9AQ07 Predicted protein 3 5

C9ANY1 Dihydrolipoamide S-succinyltransferase 2 5

C9ASN4 Putative uncharacterized protein 2 5

C9ARP9 DegV family protein 2 5

C9ARL5 rplL 50S ribosomal protein L7/L12 4 4

C9ARQ8 groES 10 kDa chaperonin 4 4

C9AS41 φθΒ DNA-directed RNA polymerase subunit beta 4 4

C9AQF3 guaB Inosine-5'-monophosphate dehydrogenase 4 4

C9AT02 Uncharacterized protein 3 4

C9AP93 DNA binding protein HU 3 4

C9AMH4 φβΒ 30S ribosomal protein S2 3 4

C9ANQ7 Peptidyl-prolyl cis-trans isomerase 3 4

C9ART9 Sulfatase 3 4

C9AQ23 zwf Glucose-6-phosphate 1 -dehydrogenase 3 4

C9AQM2 gpmA 2,3-bisphosphoglycerate-dependent phosphogly cerate mutase 2 4

C9AL78 Cell wall surface anchor family protein 2 4

C9AQN6 φsC 30S ribosomal protein S3 2 4

C9APL6 3-oxoacyl-[acyl-carrier-protein] synthase 2 2 4

C9APQ3 Superoxide dismutase 2 4

C9AQP1 φΙΧ 50S ribosomal protein L24 2 4

C9AR81 Peptidase M20A 2 4

C9AR88 Peptidase SI 2 4

C9AM29 D-alanyl-D-alanine carboxypeptidase 2 4

C9AP08 xpt Xanthine phosphoribosyltransferase 2 4

C9AKX7 Putative uncharacterized protein 3 3

C9API4 6-phosphogluconate dehydrogenase, decarboxylating 3 3

C9ALU9 Putative uncharacterized protein 3 3

C9AP54 ppaC Probable manganese-dependent inorganic pyrophosphatase 3 3

C9AQR6 Dak phosphatase 3 3 C9APV0 N-acetylmuramoyl-L-alanine amidase 2 3

C9ARH9 Acyltransferase 2 3

C9ANY0 Dihydrolipoyl dehydrogenase 2 3

C9ANP3 Transketolase 2 3

C9AS48 φΙΜ 50S ribosomal protein L 13 2 3

C9APV4 Putative uncharacterized protein 2 3

C9AP95 Ribosomal protein SI 2 3

C9AM30 Putative uncharacterized protein 2 3

C9AQ25 DivIVA protein 2 3

C9ANX7 GTP-binding protein TypA 2 3

C9APW1 Predicted protein 2 3

C9AS27 Cell surface protein (Fragment) 2 3

C9AQ61 φΐυ 50S ribosomal protein L21 2 2

C9AQZ7 φΙΥ 50S ribosomal protein L25 2 2

C9AQQ1 adk Adenylate kinase 2 2

C9ALR7 atpA ATP synthase subunit alpha 2 2

C9ALT5 Sigma 54 modulation protein/ribosomal protein S30EA 2 2

C9AQN4 3 OS ribosomal protein S19 2 2

C9ARJ0 Peptidase M3B 2 2

C9AMQ2 gatB Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B 2 2

Example 2

This Example expands on Example 1, and provides an analysis of how colonization of mice with a human commensal Enterococcus faecium strain affects susceptibility to Salmonella infection. The data demonstrate that E. faecium improves host intestinal epithelial barrier function and limits Salmonella pathogenesis. This protection requires host antimicrobial peptide (AMP) production and innate immune receptor expression in epithelial cells. Ectopic expression of SagA by non-protective bacteria is sufficient to induce AMP expression and confer enhanced activity against Salmonella pathogenesis. This Example demonstrates that a specific factor produced by E. faecium triggers a protective program in the mammalian intestinal epithelium, revealing both host and bacterial mechanisms for commensal bacteria-mediated pathogen resistance.

To analyze protective capacity of E. faecium (human isolate, strain Coml 5), we compared it to E. faecalis (strain OG1RF), in a non-typhoidal Salmonella enterica serotype Typhimurium infection model. Mice treated with a single dose of streptomycin are rendered highly susceptible to S. Typhimurium infection. As expected, streptomycin-treated control and E. faecalis-co\omze& mice showed severe S. Typhimurium-induced pathogenesis, as evidenced by rapid weight loss and mortality within 10 days of infection (Fig. 16A and C). In contrast, streptomycin-treated mice pre-colonized with E. faecium displayed significantly reduced early weight loss and prolonged survival, without changes in pathogen burden over the course of infection (Fig. 16A-C). Of note, administration of E. faecium 24 hours after S. Typhimurium infection also conferred some protective effects, albeit greatly reduced compared to E. faecium administered as little as 4 hours before infection (Fig. 16, A and C), indicating that E. faecium colonization rapidly induces a protective response. Protection was not dependent on secondary effects on the remaining microbiota, as E. faecium was also protective in mono-colonized, S. Typhimurium-infected gnotobiotic mice (Fig. 20A-C) and in mice pre-treated with a broad- spectrum antibiotic cocktail (Fig. 21A-C) from which no bacterial 16S rRNA could be amplified (data not shown). Furthermore, E. faecium did not affect S. Typhimurium proliferation (Fig. 16B) or secretion of type III protein effectors involved in S. Typhimurium invasion of host cells as described in Example 1. These results indicate that E. faecium does not act by bactericidal mechanisms, inhibiting S. Typhimurium virulence, or indirectly modulating the microbiota.

To investigate host mechanisms involved in E. faecium-mediated protection against S. Typhimurium pathogenesis in vivo, we analyzed intestinal lymphocytes after E. faecium colonization. E. faecium colonization did not induce significant changes in the relative frequency or cytokine profile of intestinal intraepithelial lymphocyte subsets (Fig. 22, A and B). In addition, prolonged host survival in response to E. faecium colonization was preserved in Ragl ^{' '} mice, which lack B and T cells (Fig. 22C). Together with the speed of E. faecium 's effects (Fig. 16, A and C), and without intending to be constrained by any particular concept, these data suggest that an adaptive immune response is dispensable for E. faecium-mediated protection. S. Typhimurium produces several effector proteins that disrupt the intestinal epithelium and facilitate bacterial invasion to systemic tissues, such as the liver. We therefore analyzed intestinal tissues at an early time (48 hours) post-infection. Control and E. faecalis-colomzed mice exhibited severe edema, neutrophil infiltration, and destruction of intestinal epithelial integrity upon S. Typhimurium infection, while these effects, particularly epithelial damage, were markedly reduced in E. faecium pre-treated mice (Fig. 16D and E). E. faecium colonization also attenuated S. Typhimurium-induced intestinal paracellular permeability (Fig. 16F), which corresponded to decreased incidence of early invasion of S. Typhimurium into the liver (Fig. 16G). In addition, fluorescence in situ hybridization (FISH) showed improved bacterial segregation from the intestinal epithelium in E. faecium-colomzed mice compared to controls (Fig. 16H), with bacterial contact and invasion into the lamina propria much more apparent in untreated mice. This decreased bacterial contact with the epithelium could be sufficient to limit S. Typhimurium disruption of epithelial tight junctions and invasion of peripheral organs. Taken together, these data indicate that E. faecium does not utilize adaptive immune mechanisms, but rather stimulates protective effects in the intestinal epithelium that are associated with prolonged survival and decreased S. Typhimurium invasion in vivo. Given the preservation of intestinal barrier integrity upon E. faecium colonization, we next examined E. faecium- ^' duced changes in intestinal epithelial cell (IEC) gene expression. In the presence of microbial colonization, IECs produce numerous proteins that function to restrict bacterial contact with the epithelium and prevent bacterial overgrowth, including antimicrobial peptides (AMPs), such as a-defensins (cryptdins in mice) and the C-type lectins Reglli and Regllly, and mucous components like mucins. Expression of many AMP and mucin genes is markedly reduced in response to antibiotic treatment; however, we observed that E. faecium colonization after broad-spectrum antibiotic treatment restored expression to pre-antibiotic levels and increased expression of the C-type lectin Reg3g (Regllly) (Fig. 17A and Fig. 23). The induction of Reg3g above steady-state levels suggests that E. faecium-denved signals are especially capable of prompting expression of certain AMPs. This increase was also present in streptomycin-treated, E. faecium-colomzed mice (Fig. 17B), and consistent with the protection observed against S. Typhimurium infection (Fig. 16, A and C), significant AMP expression was induced as early as 4 hours post-colonization.

The expression of Reg3g has been shown to play an important role in excluding bacteria from the epithelial surface, although neither Reglli nor Regllly are bactericidal to S.

Typhimurium. To determine the relevance of the observed increase in expression of Reg3g to E. faecium-mediated protection, we colonized antibiotic-treated Reg^-deficient (Reg3g ^~/~ ) mice and infected them with S. Typhimurium. Absence of Reg3g significantly abrogated E. faecium- mediated protection against S. Typhimurium pathogenesis compared to Reg3g ^+/~ controls (Fig. 17C-E), while un-colonized Reg3g ^~!~ and heterozygous littermate controls were equally susceptible to S. Typhimurium-induced weight loss and mortality. Collectively, these findings signify that E. faecium stimulates IEC expression of relevant AMPs like Reg3g, which is required for faecium-mediated protection against S. Typhimurium pathogenesis.

& Typhimurium dissemination to peripheral organs like the liver can occur by invasion across IECs, disruption of tight junctions, or by unimpeded transport through microfold (M) cells. However, bacteria that are sampled through M cells are likely to be taken up by mononuclear phagocytes in the underlying Peyer's patches (PPs) and transported to the mesenteric lymph nodes (mLN). In Reg3g ^+/~ mice, colonization with E. faecium prevented early S. Typhimurium invasion into the liver, whereas Reg^-deficient mice suffered liver invasion comparable to untreated mice (Fig. 17F). However, translocation of bacteria to the mLN was not affected by colonization or genotype (Fig. 17G). This implies that E. faecium does not affect phagocyte migration or active transport of Salmonella, but rather acts on the level of IEC integrity. Expression of AMPs in the intestinal epithelium is upregulated in response to signaling through a number of pattern recognition receptors (PRRs). Specifically, toll-like receptors (TLRs) and their signaling adapter, MyD88, have are known to be required for IEC expression oiMuc2, Reg3b, and Reg3g. We therefore examined the requirement for MyD88 signaling in E. faecium-mediated protection by generating a tamoxifen-inducible, IEC-specific conditional MyD88 knockout mouse (Villin ^CKERT2 xMyd88 ^m ( VillM4yd88)). We administered tamoxifen to ViWSMyd88 and Cre ^" littermate controls one week prior to streptomycin treatment and followed this with E. faecium colonization and subsequent S. Typhimurium infection. We observed no significant difference in early weight loss or pathogen burden between iVillAMyd88 and Cre ^" mice (Fig. 18, A and B); however, E. faecium-mediated prolonged host survival was abrogated in the absence of epithelial MyD88 expression (Fig. 18C). Furthermore, E. faecium-m ^' duced expression of some AMPs, particularly Defa2 (cryptdin 2) and Reg3g, was impaired in

[VillAMyd88 IECs (Fig. 18D). While macrophages are known to play a major role in S.

Typhimurium pathogenesis and clearance, conditional deletion oiMyD88 in myeloid cells, in particular macrophages, by interbreeding Myd88 ^m with Lyz2 ^Crs mice (LysMAMyd88) still allowed for a significant survival benefit of E. faecium colonization prior to S. Typhimurium infection (Fig. 24A and B). This benefit was evident despite a distinct increase in susceptibility to S. Typhimurium in mice harboring yDSS-deficient myeloid cells. These data indicate that E. faecium-mediated protection requires MyD88 signaling in IECs for improved survival and proper upregulation of Regllly, and they further suggest that E. faecium enhances host epithelial barrier function rather than affecting immune cell responses to S. Typhimurium.

To investigate the contribution of NOD2 to E. faecium-induced protection and AMP expression, we compared the efficacy of E. faecium colonization in streptomycin-treated Nod2- deficient mice (Nod2 ^~/~ ) and heterozygous littermate controls. E. faecium-mediated protection was absent in Nod2r ^/~ animals in terms of early weight loss, pathogen burden, and survival (Fig. 18E-G). While induction of Defa2 and Muc2 expression was mostly maintained, Reg3g upregulation was significantly impaired in Nod2 ^{~ ~} mice (Fig. 18H). Together, these data signify that the signaling adapters and receptors known to contribute to Reg3g and AMP expression, namely MyD88 and NOD2, are required for E. faecium-mediated protection, and corresponding induction of AMP expression by E. faecium is abrogated in the absence of these pathways.

In Example 1 in C. elegans, we identified that E. faecium-deriwed secreted antigen A (SagA) is a secreted NlpC/p60 peptidoglycan hydrolase that is sufficient for protection against S. Typhimurium in worms. Deletion of sagA has been shown to render E. faecium non-viable, and it is encoded in the genomes of all sequenced E. faecium strains; however, sagA is absent in E. faecalis and other known commensal species (K. L. Palmer et al, High-quality draft genome sequences of 28 Enterococcus sp. isolates. J Bacteriol 192, 2469 (May, 2010)). To determine if SagA also mediates protection against S. Typhimurium pathogenesis in mammals, we introduced its expression into our non-protective Enterococcus control, E. faecalis, and used it to mono-col onize gnotobiotic mice prior to S. Typhimurium infection. Similar to E. faecium, E. faecalis-sagA significantly improved early weight loss and survival compared to wild-type E. faecalis, without affecting pathogen burden (Fig. 19A-C). Moreover, both E. faecium and E. faecalis-sagA, but not wild-type E. faecalis, significantly induced expression oiDefal and Reg3g in streptomycin-treated mice (Fig. 19D), indicating that expression of sagA is sufficient to increase AMP expression and attenuate S. Typhimurium pathogenesis.

Although Enterococcus strains have been used as probiotics in livestock, their pathogenic capacity makes them potentially problematic for use in humans. We thus introduced sagA into a known non-pathogenic probiotic, Lactobacillus plantarum (L. M. Dicks, M. Botes, Probiotic lactic acid bacteria in the gastro-intestinal tract: health benefits, safety and mode of action. Benef Microbes 1, 11 (Mar, 2010)), and confirmed that it was expressed and secreted (Fig. 25). Consistent with demonstration of protection using E. faecalis-sagA and E. faecium, sagA -expressing L. plantarum significantly prevented weight loss and improved survival compared to control L. plantarum (Fig. 19E-G). Bacterial segregation from the intestinal epithelium was also maintained in L. plantarum-sagA-colomzed mice relative to the prominent epithelial contact and invasion present in L. plantar um-wector controls (Fig. 19H). These results show that SagA protective activity is transferrable to other probiotic bacteria and can enhance epithelial barrier integrity to limit S. Typhimurium pathogenesis.

The intestinal microbiota may have several beneficial modes of action that can potentially prevent or limit pathogenic infection, including niche competition with pathogenic bacteria, activation of immune cells and augmentation of epithelial barrier function. The present results indicate that commensal E. faecium does not hinder the growth of enteric pathogens in the gut, but instead utilizes a unique secreted peptidoglycan hydrolase, SagA, to increase epithelial expression of AMPs through MyD88 and NOD2 signaling pathways and enhance barrier integrity. These observations are consistent with our studies of E. faecium in C. elegans in Example 1, which also showed improved epithelial barrier integrity and SagA-mediated host resistance to S. Typhimurium pathogenesis. Thus, the results demonstrate a novel and conserved mechanism of pathogen resistance facilitated by bacterial peptidoglycan hydrolases and host pattern recognition receptors. The following is a description of materials and methods used to obtain the data presented in this Example 2.

Animals. C57BL/6J (000664), Lyz2 ^Cve (004781), MyD88 ^m (008888), Nod ^ (005763), Ragl ^{' '} (002216) and Reg3g ^'/' (017480) mice were purchased from Jackson Laboratories and maintained in our facilities. Villin ^CKERT2 mice were developed by Silvie Robine and provided by David Artis. Several of these lines were interbred in our facilities to obtain the final strains described in this disclosure. Genotyping was performed according to the protocols established for the respective strains by Jackson Laboratories. Mice were maintained at the Rockefeller University animal facilities under specific pathogen-free (SPF) or germ-free (GF) conditions. Germ-free mice were obtained from Sarkis Mazmanian and bred and maintained in germ-free isolators in our facilities. Germ-free status was confirmed by plating feces as well as by qPCR analysis (16S rRNA). Mice were used at 8-10 weeks of age for most experiments. Animal care and experimentation were consistent with the NIH guidelines and were approved by the

Institutional Animal Care and Use Committee at the Rockefeller University.

Bacteria. E. faecium (strain Coml 5) was provided by Michael Gilmore, and E. faecalis

(strain OG1RF) and L plantarum (strain WCFS1) were provided by Balfour Sartor. E. faecium and E. faecalis were cultured in BHI broth (BD 237500), S. Typhimurium (strain 14028) was cultured in Luria Broth (LB) and L plantarum was cultured in de Man, Rogosa and Sharpe (MRS) broth. E. faecium, E.faecalis, and L plantarum were grown overnight at 37°C at 230 rpm shaking to stationary phase growth prior to colonization. S. Typhimurium was grown overnight followed by a 3.5h subculture at 37°C at 230 rpm to log phase growth prior to infection.

Colonization and infection of mice. Specific pathogen-free (SPF) mice were gavaged with either a single dose of 20mg streptomycin or a daily dose of AMNV antibiotic cocktail (4mg ampicillin, 2mg metronidazole, 4mg neomycin, and 2mg vancomycin) for 7-14 days as indicated in the figure legends. Bacterial cultures were washed and resuspended in sterile PBS at 10 ⁹ /mL for E. faecium, E.faecalis, and L plantarum or at 10 ⁷ /mL (SPF) or 10 ³ /mL (GF) for S. Typhimurium. Mice were colonized by gavage with lOOuL of the indicated bacterial suspension 4 hours before infection (for streptomycin-treated mice) or 2-7 days before infection (for AMNV and GF gnotobiotic mono-colonized mice). Colonization was followed by infection with S. Typhimurium by oral gavage at the doses indicated above and in the figure legends. Weight loss was monitored from just before infection, and mice were euthanized when they reached 80% baseline weight or when they appeared hunched or moribund, whichever occurred first. Death was not used as an end-point. Colony -forming units (CFU) in the feces were determined by plating 5 serial dilutions of feces suspended in sterile PBS on selective agars: Salmonella Shigella Agar (BD 211597) for S. Typhimurium, Enterococcosel Agar (BD 212205) for E. faecium and E. facealis, and MRS Agar with 8ug/mL chloramphenicol for L. plantarum-wector and -SagA. Resulting quantities were normalized to feces weight.

Pathological scoring. Representative portions of ileum, cecum and colon were fixed in Methacarn (methanol-Carnoy) solution and embedded in paraffin according to standard protocols (see 16S FISH below). 5-μπι sections were mounted on glass slides and stained with hematoxylin and eosin (H&E) for blinded histologic evaluation. Quantitative measures of inflammation were then recorded according to known methods. Briefly, each tissue section was microscopically assessed for the extent of submucosal edema, preservation of epithelial integrity and goblet cell retention (each category scored from 0-3), as well as for polymorphonuclear cell infiltration into the lamina propria (scored from 0-4). The sum of these scores represents the combined pathological score reported for each tissue. Scores >9 are indicative of severe inflammation, while scores of 5-8 are consistent with moderate inflammation. Scores <4 are associated with minimal to mild inflammation and frequently appear histologically normal.

Intestinal permeability and peripheral organ invasion. At 48h post-infection, mice were gavaged with FITC-dextran 4 kDa (600 μg/kg body weight) dissolved in sterile PBS. Serum was harvested by cardiac puncture after 4h, and FITC fluorescence (excitation 488 nm and emission 518 nm) was measured in triplicate on a FLUOstar Omega microplate reader (BMG Labtech) to assess intestinal permeability. Concentration of FITC in serum was determined using a standard curve and expressed as ng/mL serum. To measure invasion, whole livers or mesenteric lymph nodes (mLN) were homogenized in PBS with 0.1% Triton X-100 to release intracellular bacteria. 3 serial dilutions were plated on Salmonella Shigella Agar, and resulting quantities were normalized to organ weight prior to homogenization.

16S FISH. 16S rRNA FISH was performed with a universal probe (EUB388, Cy3- GCTGCCTCCCGTAGGAGT-Cy3) on sections fixed with Methacarn solution according to known techniques. In brief, intestinal tissues (about 1 cm) including intestinal contents were fixed in Methacarn solution (60% methanol, 30% chloroform, 10% glacial acetic acid) for 6 hours at 4°C. After 3 washes with 70% ethanol tissues were embedded in paraffin. 5-μπι sections were cut, mounted on glass slides, and de-paraffinized with xylene and subsequently dehydrated. Probe was diluted (5 ng/μΐ.) in hybridization buffer (0.9 M NaCl, 20 mM Tris-HCl (pH 7.2), 0.1%) SDS) and hybridization was carried out at 50°C for 3 hours. After hybridization, tissues were washed with wash buffer (0.9 M NaCl, 20 mM Tris-HCl (pH 7.2)) and nuclei were stained with Hoechst stain. Tissues were imaged on an Inverted LSM 780 laser scanning confocal microscope (Zeiss). Intestinal cell isolation. Small intestine and large intestine were excised and freed of mesentery and fat. Feces were removed and Peyer's Patches were excised from the small intestine. Both small and large intestine were opened longitudinally and washed in FIBSS, followed by FIBSS + ImM DTT (Sigma-Aldrich). Tissue was cut into 1 cm pieces and incubated with 25 mL of HBSS + 2% FBS + 5mM EDTA for 15 minutes at 37°C at 230 rpm. Supernatant containing intraepithelial lymphocytes was decanted and spun down (for RNA isolation from epithelial cells, see below). Tissue was washed with 10 mL of HBSS + 2% FBS for 15 minutes at 37°C at 230 rpm. The gut tissues were then finely chopped and digested in HBSS + 2% FBS + IX Sodium Pyruvate + 25mM HEPES + 50 μg/mL DNasel + 0.05 mg/mL Collagenase VIII for 40 min. at 37° C at 90 rpm. Cells were separated by discontinuous Percoll gradient (70%/35%) centrifugation. Hematopoietic cells were isolated from the interphase and stained for analysis by flow cytometry.

Antibodies and flow cytometry analysis. Fluorescent-dye-conjugated antibodies were purchased from BD-Pharmingen (anti-CD4, 550954; anti-CD45R, 557683) or eBioscience (anti- CD8aD 56-0081; anti-TCR-β, 47-5961; anti-IFN-γ, 25-7311; anti-TCRy6, 46-5711; anti-CD8 , 46-0083; anti-TNF-a, 17-7321). Flow cytometry data were acquired on an LSR-II flow cytometer (Becton Dickinson) and analyzed using FlowJo software (Tree Star). For analysis of cytokine-secreting cells, cells were incubated in the presence of lOOng/ml PMA (Sigma), 500ng/ml ionomycin (Sigma) and 10μg/ml brefeldin A (BFA) (Sigma) for the 3h prior to staining. Cell populations were first stained with antibodies against cell surface markers, followed by permeabilization in Fix/Perm buffer and intracellular staining in Perm/Wash buffer (BD Pharmingen).

Quantitative PCR. Epithelial cells were resuspended in Trizol (Invitrogen), RNA was isolated according to the manufacturer's protocol, and cDNA was generated using iScript (BioRad). qPCR was performed using Power SYBR Green Master Mix (Agilent) in an ABI 7900HT system. Primers used were:

Mud 3 CTTTGTACTGTGGTGGGAGGA 37 TCAAGCAAGAGCAGCTACCA 38

Mud 7 ATTCAGAGGCCCCAGGTAGT 39 TGGCTAAACACGCTTCTCCT 40

Muc20 CAGGAAGGACATGTGGACAA 41 TTCCTCCTTGTACGGCTGAC 42 eg3g TCCACCTCTGTTGGGTTCAT 43 AAGCTTCCTTCCTGTCCTCC 44

Generation of E. faecalis-sagA and L. plantarum-sagA.

L. plantarum-sagA:

pAM401-SagA was generated as in Example 1 and transformed into L. plantarum WCFS1 by electroporation. Protocol for preparation of electrocompetent cells and

electroporation was adapted from known approaches. Briefly, Lactobacillus were grown for 18 hours in M9YE (M9 media, 0.1% casamino acids, 0.3% yeast extract) + 2% glycine. Cultures were diluted in half with M9YE + 3% glycine, and grown for an additional 3 hours. Cultures were chilled, pelleted, and washed 3 times in sucrose wash buffer (0.625 M sucrose, 1 mM MgC12, pH 4 with HC1), reducing the original culture volume by 1/2, 1/10, then 1/100 successively with each wash. Finally, cells were aliquoted, flash frozen in liquid nitrogen, and stored at -80 °C. Cells were electroporated in 2 mm cuvettes, 25 μΡ, 400 ohm, 2.5 kV. Cells were allowed to recover for 2 hours at room temperature without shaking in MRS broth (BD Bacto), then with shaking at 37°C for another 2 hours before plating on selective media.

E. faecalis-sagA:

E. faecalis-sagA was generated as described in Example 1.

Statistics. Statistical analysis was performed in GraphPad Prism software. Data were analyzed by applying the tests indicated in each figure legend. A P value of less than 0.05 was considered significant.

While the invention has been described through specific embodiments, routine modifications will be apparent to those skilled in the art and such modifications are intended to be within the scope of the present invention.