e coli host strain  (DSMZ)

Journal: Materials Today Bio

Article Title: Living probiotics-loaded wound matrices prepared by microchip electrospinning

doi: 10.1016/j.mtbio.2025.102403

Figure Lengend Snippet: A. Schematic illustration of microchip electrospinning set-up together with the scanning electron microscopy (SEM) micrograph of obtained electrospun (ES) living probiotics-loaded fiber matrix and confocal fluorescence microscopy (CFM) micrograph where the bacteria are shown in red within fibers and fibers in green, samples stained using FM 4–64 and SYTO 9, respectively; B. Polydimethylsiloxane (PDMS) chip design, the microfluidic chip (PDMS) included two inlet channels (inlet #1 and inlet #2) — inlet #1 connected to a syringe with the PLC/PEO polymer solution and inlet #2 to a syringe containing the agarose-bacterial dispersion. These channels converged into a common outlet channel, which was connected to a metal needle (21G). The electrospinning voltage was applied to the needle tip, and fibers were collected on a grounded collector plate at a distance of 13 cm. Flow direction is pointed out with an arrow. C - microcapsule with labelled E. coli BW25113 micrograph. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: Gram-positive and gram-negative pathogenic bacteria isolated from wounds, namely E. coli DSM 1103, S. aureus DSM 2569, P. aeruginosa DSM 1117, S. epidermidis DSM 28319 (DSMZ, Germany), were used to assess the antimicrobial activity of probiotic bacteria (e.g.

Techniques: MicroChIP Assay, Electron Microscopy, Probiotics, Fluorescence, Microscopy, Bacteria, Staining, Polymer, Dispersion

Journal: Materials Today Bio

Article Title: Living probiotics-loaded wound matrices prepared by microchip electrospinning

doi: 10.1016/j.mtbio.2025.102403

Figure Lengend Snippet: Viability and functionality (including antimicrobial activity) of probiotic bacteria within electrospun fiber matrices. A. Bromocresol purple indicator incorporated into M17 agarose plates was used to visualize the decrease of pH in the surrounding medium caused by probiotic ( L. rhamnosus Fibro 2)-loaded fiber matrices electrospun directly onto glass discs. The color change of the media due to acidification is shown at different time points: B. 24 h, C . 48 h, D . 72 h. E. Schematics of agar overlay assay setup. F. Agar overlay assay using 6 mm diameter fiber matrix discs with and without different probiotic bacteria namely ( L. plantarum Fibro 1 and L. rhamnosus Fibro 2). Initial concentration of pathogenic bacteria in the soft agar was 10 6 CFU/mL. G. Schematics illustrating the L. rhamnosus Fibro 2-loaded fiber matrix disc, cut from the entire sample and placed on MRS base agar. The antimicrobial activity against E. coli DSM 1103 was assessed using the agar overlay assay immediately after electrospinning, as well as after 24 h and 4 months. Key : red dashed circles indicate zones of inhibition, representing the activity of probiotic bacteria against relevant pathogenic bacteria. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: Gram-positive and gram-negative pathogenic bacteria isolated from wounds, namely E. coli DSM 1103, S. aureus DSM 2569, P. aeruginosa DSM 1117, S. epidermidis DSM 28319 (DSMZ, Germany), were used to assess the antimicrobial activity of probiotic bacteria (e.g.

Techniques: Activity Assay, Bacteria, Overlay Assay, Concentration Assay, Inhibition

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A ) Comparison between the genomic region containing trg gene in E. coli MG1655 and the corresponding region in the B2 phylogroup of E. coli , represented by UTI89, based on the NCBI and MiST4.0. Genes are labeled with the names of their products, including truncated Trg-like signaling protein (Tls) instead of Trg in the B2 phylogroup. Besides the truncation of trg , deletion of the shaded genomic region in the B2 phylogroup resulted in the loss of the divergently transcribed gene mokB that is unrelated to motility. ( B ) Structural models of the full-length Trg (left) and of Tls (right), constructed using AlphaFold3. The C-terminal part common between Trg and Tls is marked in yellow. A Tls-specific short N-terminal amino acid sequence (TlsN) in marked in red. Methylation sites of Trg and corresponding residues in Tls are labeled in blue. Trg is shown in its functional dimeric form. Although the oligomeric state of Tls is unknown, the prediction for a dimeric structure is shown by analogy with Trg. ( C ) Presence of Tls in the completely sequenced E. coli genomes, isolates from the ECOR collection, and E. coli S13. The phylogenetic tree is based on the trg nucleotide sequences and strains are colored according to previously established phylotypes. Tree scale is 0.01 substitutions per site. Tls with the conserved TlsN sequence MNVRIVLLS is present in the majority of the B2 phylogroup E. coli strains. ECOR65 has intact trg nucleotide sequence, and E. coli strain 536 and ECOR64 have frameshift in trg nucleotide sequence. An asterisk denotes Tls variant that carries the N-terminal sequence MRFSQFNHSLLS (TlsN*).

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Comparison, Labeling, Construct, Sequencing, Methylation, Functional Assay, Variant Assay

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A ) Motility- and chemotaxis-dependent spreading of E. coli S13 and its Δ tls mutant in 0.27% TB soft agar (TBSA). Representative image is shown from three biological replicates. ( B ) Swimming trajectories of E. coli S13 and S13 Δ tls cells close to the glass surface in the microscopy chamber, shown as their projected intensities (white curves on dark background) during 20-s long movies. Representative images are shown from three biological replicates. Scale bars, 50 μm. ( C , D ) Fractions of swimmers ( C ) and swimming speed ( D ) measured in the bulk of the bacterial suspension (middle of the microscopy chamber) via Differential Dynamic Microscopy (DDM) for E. coli S13 and S13 Δ tls cells. Values represent the means and standard deviations of five biological replicates. ( E ) Tumbling bias in the bulk or close to the surface, measured via particle tracking as the averaged fraction of time spent tumbling over 2913 (S13 middle), 4230 (S13 top), 5225 (S13 Δ tls middle) and 5281 (S13 Δ tls top) swimmer trajectories in three biological replicates. ( F , G ) Bacterial growth (OD 600 ) and fluorescence levels of P fliC-gfp reporter normalized by OD 600 in E. coli S13 and its Δ tls mutant ( F ), and in E. coli UTI89 and its Δ tls mutant ( G ). Measurements were performed in a plate reader. Values represent the means and standard deviations of a minimum of three biological replicates. ( H ) Fluorescence levels of P fliC-gfp normalized by OD 600 in E. coli S13 and its Δ tls mutant, both carrying an empty vector pTrc99A, and in S13 Δ tls complemented by expression of Tls from pTrc99A-Tls plasmid induced by indicated concentrations of IPTG. Measurements were performed in the log phase of growth in a plate reader. Values represent the means and standard deviations of four biological replicates, in each case normalized to the reporter activity in the reference strain (S13/pTrc99A). Statistical significance was determined using unpaired two-tailed Student’s t test. The P values are denoted as ns ( P > 0.05), * ( P < 0.05), ** ( P < 0.005), *** ( P < 0.001). (** P = 0.0032 ( C ); *** P = 0.0003 ( D ); * P = 0.0085, * P = 0.0058 ( E ); P values from left to right: *** P = 6.67E-11, *** P = 2.69E-09, *** P = 1.75E-09, *** P = 2.58E-09, *** P = 7.41E-09, *** P = 8.68E-09, *** P = 5.20E-09, *** P = 1.51E-09 ( H ). .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Chemotaxis Assay, Mutagenesis, Microscopy, Suspension, Fluorescence, Plasmid Preparation, Expressing, Activity Assay, Two Tailed Test

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A , B ) Fluorescence levels of P flhD-gfp (class 1), P fliA-gfp (class 2), and P fliC-gfp (class 3) normalized by OD 600 in E. coli S13 and its Δ tls mutant ( A ), or in MG1655 carrying either empty vector pTrc99A or pTrc99A-Tls induced with 15 µM IPTG ( B ). Measurements were performed in the log phase of growth in a plate reader. Values represent the means and standard deviations of a minimum of three biological replicates, in each case normalized to the reporter activity in the respective reference strain (S13 or MG1655/pTrc99A). Statistical significance was determined using an unpaired two-tailed Student’s t test. The P values are denoted as ns ( P > 0.05), * ( P < 0.05), ** ( P < 0.005), *** ( P < 0.001). ( P values from left to right: ns = 0.32, *** P = 3.01E-05, *** P = 6.82E-06 ( A ); ns = 0.54, *** P = 2.03E-05, *** P = 2.15E-06 ( B )). ( C , D ) Flagellar proteins detected in the whole proteome analysis of S13 Δ tls compared to S13 ( C ) or MG1655 expressing Tls from pTrc99A-Tls at 15 µM IPTG induction compared to MG1655/pTrc99A ( D ). Data are from three biological replicates. Statistical significance was determined using moderated t -statistics from the empirical Bayes procedure LIMMA (Kammers et al, ) to calculate P values, followed by adjustment to obtain q values based on the Benjamini–Hochberg method (Benjamini and Hochberg ). Significantly increased or decreased flagellar and chemotaxis proteins are colored according to their gene regulatory class, as indicated. For ( C ), the E. coli UTI89 protein annotation database was used as a reference. For ( D ), although below the statistical threshold, class 1 flagellar protein FlhC was labeled, too. .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Fluorescence, Mutagenesis, Plasmid Preparation, Activity Assay, Two Tailed Test, Expressing, Chemotaxis Assay, Labeling

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A ) Venn diagram of proteins upregulated in E. coli S13 upon deletion of tls and downregulated in E. coli MG1655 upon expression of Tls from pTrc99A-Tls at 15 µM IPTG induction. ( B ) Venn diagram of proteins downregulated in E. coli S13 upon deletion of tls and upregulated in E. coli MG1655 upon expression of Tls from pTrc99A-Tls at 15 µM IPTG induction. The protein groups shared by both strains are shown below of each Venn diagrams, and all proteins identified in both strains are listed in Appendix Tables – . ( C , D ) The STRING diagram of the clustering of proteins downregulated ( C ) or upregulated ( D ) by Tls in one or both strains. For the downregulated proteins, the clusters of flagellar assembly and chemotaxis, biosynthesis of amino acids, and type 1 fimbriae component and biogenesis are highlighted in red, blue, and green, respectively. For the upregulated proteins, the clusters of ABC transporter, L -threonine metabolism, and organic acid metabolic process are highlighted in yellow, cyan, and orange, respectively. The thickness of the lines indicates the strength of data support in STRING.

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Expressing, Chemotaxis Assay

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A – D ) Fluorescence levels of P fliC-gfp normalized by OD 600 in E. coli S13 or S13 Δ tls cells ( A , B ) or MG1655 cells carrying either empty pTrc99A vector or pTrc99A-Tls expression plasmid induced with 15 µM IPTG ( C , D ). Cells were grown either in liquid TB medium ( A , C ) or on the surface of 0.5% TB agar (TBA) plate ( B , D ). Measurements were performed in the log phase of growth in a plate reader. Values represent the means and standard deviations of a minimum of three biological replicates. Statistical significance was determined using unpaired two-tailed Student’s t test. The P values are denoted as ns ( P > 0.05), * ( P < 0.05), ** ( P < 0.005), *** ( P < 0.001). (*** P = 3.22E-13 ( A ); * P = 0.048 ( B ); *** P = 2.71E-10 ( C ); ns = 0.17 ( D )). ( E , F ) Subcellular localization of Tls-sfGFP fusion protein in MG1655 cells carrying pTrc99A-Tls-sfGFP and grown either in liquid TB medium ( E ) or on 0.5% TBA plate ( F ). Tls-sfGFP expression was induced by 15 µM IPTG. Representative images are shown from three biological replicates. Scale bars, 3 μm. ( G ) Time-dependent changes in subcellular localization of Tls-sfGFP upon reversal of growth conditions. MG1655 cells expressing Tls-sfGFP were grown either in liquid TB medium or on the 0.5% TBA plate for 3.5 h and transferred to the opposite growth condition for the indicated period of time. Quantification of the number of cells showing fluorescence foci formed by Tls-sfGFP was based on microscopy images in Appendix Fig. . For each image, foci were counted in 100 cells from three different images, originating from three biological replicates. Values represent the means and standard deviations. .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Fluorescence, Plasmid Preparation, Expressing, Two Tailed Test, Microscopy

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A , B ) Localization of Tls-mCherry or mCherry alone and FlhDC-sfGFP in MG1655 cells grown either in liquid TB medium ( A ) or on 0.5% TBA plate ( B ), as described in Fig. . The mCherry channel, GFP channel, and merged images are shown. Representative images are shown from three biological replicates. Scale bars, 2 μm. ( C ) FRET measurements of complex formation between FlhDC-sfGFP and Tls-mCherry, co-expressed in S13 cells grown either in liquid TB medium or on 0.5% TBA plate, as indicated. Co-expressed mCherry was used as a negative control. FlhDC-sfGFP expression was induced with 0.002% L-arabinose in liquid TB and with 0.004% on 0.5% TBA plate. Tls-mCherry expression was respectively induced with 15 µM or 30 µM IPTG and mCherry expression was respectively induced with 40 µM or 200 µM IPTG. FRET efficiency was determined by acceptor photobleaching in individual cells as described in the Methods. Symbols represent the FRET values in individual cells, measured in three biological replicates (7–33 cells per replicate), with the means and standard deviations being indicated. For liquid-grown cells, the distinction was made between cells that exhibit colocalized foci of Tls-mCherry and FlhDC-sfGFP and those that do not. No colocalized foci were observed in surface-grown cells. Statistical significance was determined using unpaired two-tailed Student’s t test. The P values are denoted as ns ( P > 0.05), * ( P < 0.05), ** ( P < 0.005), *** ( P < 0.001). ( P values from left to right: *** P = 6.76E-27, *** P = 1.41E-12, ns = 0.05). ( D , E ) Localization of mCherry only, or of Tls-mCherry and FlhDC-sfGFP in S13 cells grown either in liquid TB medium ( D ) or on 0.5% TBA plate ( E ), as described in ( C ). The mCherry channel, GFP channel, and merged images are shown. Representative images are shown from two biological replicates. Scale bars, 2 μm. .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Negative Control, Expressing, Two Tailed Test

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A , B ) Graphs depict percent adherence ( A ) and invasion ( B ) for wild-type UTI89 (black), or the isogenic Δ tls mutant (red) using the HTB-9 urothelial tissue culture cell line. Experiments were performed in three biological replicates with four technical replicates in each run. Shown is the percentage of colony-forming units (CFU) formed by adhered or intracellular bacteria from the total bacterial CFU count. The line depicts the geometric mean +/− 95% CI. ( C , D ) Graph depicts urinalysis ( C ) and fecal sample ( D ) titers of UTI89 (black) and the isogenic Δ tls mutant (red) for each mouse collected at 24 h post infection. Urine was collected from each mouse and plated as previously described. Urinalysis is used to track shedding of bacteria from the lumen over time and serves as an indicator for dissemination to the gut. Fecal samples were collected from each mouse to track UPEC proliferation in the gut. To facilitate urinalysis and fecal collection, each mouse was tagged with an identifying ear notch. The same 11–12 mice were tracked in the experiments shown in ( C , D ). Dashed line indicates the clinical threshold for UTI in humans. The line depicts the geometric mean +/− 95% CI. Statistical significance was determined using unpaired two-tailed Mann–Whitney U test. The P values are denoted as ns ( P > 0.05), * ( P < 0.05), ** ( P < 0.005), *** ( P < 0.001). (* P = 0.0372 ( A ); ** P = 0.0014 ( B ); ns = 0.4428 ( C ); ** P = 0.0049 ( D )). ( E ) Competitive index (C.I.) of S13 Δ tls compared to the wild-type S13 strain, determined as the ratio of CFU counts, in the fecal samples (denoted as F) collected at 24 h or 48 h post gavage infection (h.p.i.), and in the cecal content (denoted as CC) at 72 h.p.i. Analyses were performed using 12 mice (individual dots). The line depicts the geometric mean +/− 95% CI, and the dashed line indicates the CI value of 1. .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Mutagenesis, Bacteria, Infection, Two Tailed Test, MANN-WHITNEY

Journal: The EMBO Journal

Article Title: Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli

doi: 10.1038/s44318-025-00595-x

Figure Lengend Snippet: ( A ) Experimental scheme of competitive oral inoculation. C57BL/6J SPF mice were pre-treated with 20 mg of ampicillin by oral gavage 24 h before infection with E. coli (1:1 mix of S13 WT and Δ tls strains). Feces were collected at 24 and 48 h.p.i., and mice were euthanized at 72 h.p.i. ( B ) The CI values of Δ tls in Δ tls /WT competitive infection along the gut at 72 h.p.i. Analyses were performed using 12 mice (individual dots). The line depicts the geometric mean +/− 95% CI. The dashed line indicates the CI value of 1. .

Article Snippet: E. coli S13 , Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) , DSM 10719.

Techniques: Infection