bacterial type strain atcc pseudomonas aeruginosa atcc 27853 bacterial type strain atcc pam1020 wild type  (ATCC)

Journal: Nature Microbiology

Article Title: Deep learning reveals antibiotics in the archaeal proteome

doi: 10.1038/s41564-025-02061-0

Figure Lengend Snippet: The synergistic interactions between pairs of EPs from the same or closely related organisms (phylogenetic pairwise distance ≤8) that showed activity against A. baumannii ATCC 19606 were assessed using checkerboard assays. These assays involved twofold serial dilutions, ranging from 2× MIC to a 1:32 dilution. The histogram shows the FICI values obtained for each pair of EPs. A total of 79 pairs were evaluated. Low FICI values (≤0.5) indicate synergistic interactions, intermediate values (0.5 < FICI ≤ 1) indicate additive effects and higher values (1 < FICI ≤ 2) indicate indifferent interactions. Numbers 1–15 indicate where each pair or group of pairs originates within the archaeal phylogenetic tree.

Article Snippet: We initially selected the bacterial strain A. baumannii American Type Culture Collection (ATCC) 19606, known for its high antibiotic resistance and significant role as an opportunistic nosocomial pathogen with substantial global mortality rates .

Techniques: Activity Assay

Journal: Nature Microbiology

Article Title: Deep learning reveals antibiotics in the archaeal proteome

doi: 10.1038/s41564-025-02061-0

Figure Lengend Snippet: To assess whether archaea EPs act on bacterial membranes, all active peptides against A. baumannii ATCC 19606 were subjected to outer membrane permeabilization and cytoplasmic membrane depolarization assays. a , b , Here we show the two lead permeabilizer and depolarizer archaeasins (see Extended Data Fig. for permeabilization and depolarization results of all archaeasins). The fluorescence probe NPN was used to assess membrane permeabilization ( a ) induced by the tested EPs (Extended Data Fig. ). The fluorescence probe DiSC 3 -5 was used to evaluate membrane depolarization ( b ) caused by archaeasins (Extended Data Fig. ). The shown values represent the relative fluorescence of both probes, with nonlinear fitting compared with the baseline of the untreated control (buffer + bacteria + fluorescence dye) and benchmarked against the antibiotics polymyxin B and levofloxacin. c , Laurdan generalized polarization over time in A. baumannii treated with archaeasins. Generalized polarization values were measured to assess changes in the lipid packing (membrane order) of the cytoplasmic membrane following treatment with the archaeasins that showed greater permeabilization of the outer membrane, archaeasin-21 and archaeasin-22, and greater depolarization of the cytoplasmic membrane, archaeasin-57, and archaeasin-78. Higher generalized polarization values indicate increased membrane rigidity, whereas lower values reflect increased membrane fluidity. Benzyl alcohol was used as a positive control for membrane fluidization, and untreated cells served as a negative control. Data represent a linear regression of the mean of 3 independent experiments over 30 min. d , Haemolytic and cytotoxic concentrations, against RBCs and HEK293T cells, respectively, leading to 50% cell lysis (HC 50 and CC 50 , respectively) were determined by interpolating the dose-response data using a nonlinear regression curve. All experiments were performed in three independent replicates (Extended Data Fig. ). The protein and peptide structures depicted in panels a and b were created with PyMOL Molecular Graphics System, v.3.0 (Schrödinger).

Article Snippet: We initially selected the bacterial strain A. baumannii American Type Culture Collection (ATCC) 19606, known for its high antibiotic resistance and significant role as an opportunistic nosocomial pathogen with substantial global mortality rates .

Techniques: Membrane, Fluorescence, Control, Bacteria, Positive Control, Negative Control, Lysis

Journal: Nature Microbiology

Article Title: Deep learning reveals antibiotics in the archaeal proteome

doi: 10.1038/s41564-025-02061-0

Figure Lengend Snippet: (a-c) Outer membrane permeabilization was assessed using the probe 1-(N-phenylamino)naphthalene (NPN), showing the permeabilization effects of Archaea-encoded encrypted peptides active against A. baumannii ATCC 19606: (a) relative fluorescence, (b) fluorescence intensity, and (c) summary of the relative fluorescence in different time points of the experiment. (d-f) Membrane depolarization assays were performed using the hydrophobic probe 3,3′-dipropylthiadicarbocyanine iodide [DiSC 3 -(5)] on all archaeasins active against A. baumannii ATCC 19606: (d) relative fluorescence, (e) fluorescence intensity, and (f) summary of the relative fluorescence in different time points of the experiment. Polymyxin B served as a positive control, while buffer, buffer with the probe, and buffer with both probe and bacteria were used as baseline controls for fluorescence. Error bars are the standard deviation obtained from the three replicates and relative fluorescence is shown as a non-linear regression of the fluorescence intensity normalized by the untreated control (buffer).

Article Snippet: We initially selected the bacterial strain A. baumannii American Type Culture Collection (ATCC) 19606, known for its high antibiotic resistance and significant role as an opportunistic nosocomial pathogen with substantial global mortality rates .

Techniques: Membrane, Fluorescence, Positive Control, Bacteria, Standard Deviation, Control

Journal: Nature Microbiology

Article Title: Deep learning reveals antibiotics in the archaeal proteome

doi: 10.1038/s41564-025-02061-0

Figure Lengend Snippet: a , Schematic representation of the skin abscess mouse model used to assess the anti-infective activity of archaeasins ( n = 6) against A. baumannii ATCC 19606. b , Archaeasin-2, archaeasin-17 and archaeasin-73, administered at their MIC in a single dose post-infection, inhibited the proliferation of the infection for up to 4 days after treatment compared with the untreated control group. Notably, archaeasin-73 reduced the infection in some mice, showing activity comparable to the control antibiotic, polymyxin B. c , Schematic of the neutropenic thigh infection mouse model, where archaeasins were administered intraperitoneally. Anti-infective activity against A. baumannii ATCC 19606 was evaluated 4 days after intraperitoneal peptide administration ( n = 6). d , At 4 days after intraperitoneal injection (day 8 of the experiment), all archaeasins at their MIC showed a bacteriostatic effect, containing the A. baumannii ATCC 19606 infection, although their activity was less potent than that of polymyxin B and levofloxacin, compared with the untreated control group (Extended Data Fig. ). The limit of detection (LOD) for the CFU quantification is log 10 CFU = 2. Statistical significance in panels b and d was determined using one-way analysis of variance followed by Dunnett’s test; P values are shown in the graphs. In the violin, the centre line represents the mean, the box limits the 1st and 3rd quartiles, and the whiskers (minimum and maximum) represent 1.5× the interquartile range. The solid line inside each box represents the mean value obtained for each group. Panels a and c created with BioRender.com .

Article Snippet: We initially selected the bacterial strain A. baumannii American Type Culture Collection (ATCC) 19606, known for its high antibiotic resistance and significant role as an opportunistic nosocomial pathogen with substantial global mortality rates .

Techniques: Activity Assay, Infection, Control, Injection