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Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary "arms race" dynamics.

Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, as drivers of gut bacterial composition, can affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore direct interactions between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. Analysis of 1,086 bifidobacterial genomes reveals the presence of complex systems that prevent viral invasion, with 34 defense systems and 56 subtypes detected, including several different CRISPR-Cas systems. CRISPR spacers target almost three-quarters of bifidobacteria-derived prophages, indicating dynamic interactions. At least one prophage is present in ∼67% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. These prophages encode various defense and anti-defense systems, such as anti-CRISPR genes and restriction-modification mechanisms. Overall, this investigation reveals that coevolutionary "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.

Prophages

Effect of temperature on motility and chemotaxis of Escherichia coli.

The swimming velocity of Escherichia coli at various constant temperatures was found to increase with increasing temperature. The frequency of tumbling had a peak at 34 degrees C and was very low both at 20 and at 39 degrees C. The swimming tracks near the surface of a slide glass showed curves, and the curvature increased the temperature. When the temperature of a bacterial suspension was suddenly changed, a transient change of the tumbling frequency was observed. A temperature drop induced a temporary increase in the tumbling frequency, and a quick rise of temperature, on the other hand, resulted in a temporary suppression of the tumbling. These dynamic responses to sudden changes of temperature was not observed in the smoothly swimming nonchemotactic strains bearing the mutations cheA and cheC and also in a mutant with the metF mutation under a smooth swimming condition.

Chemotaxis

Demonstration of enterobacterial common antigen by bacterial agglutination.

Potent antisera against the enterobacterial common antigen (ECA) agglutinate R bacteria of the Enterobacteriaceae family that possess unimpaired R-core structures of the Escherichia coli R1 or E. coli R4 core type. In these strains, known to be ECA immunogenic, ECA is most probably linked to the lipopolysaccharide R core. R mutants of other core types (e.g., Salmonella Ra, E. coli R2 or R3) or R mutants with incomplete core structures of the E. coli R1 type, as well as an rfaL mutant deficient in the O-translocase system, agglutinate to a much lesser extent or not at all. All the later mutants are nonimmunogenic; they possess the ECA in a free form, not linked to the R core. None of the S forms tested from many different enterobacterial genera was found to be agglutinable with the ECA antiserum. The dynamics of the ECA agglutinin formation in rabbits parallels the ECA hemagglutinin formation, indicating that the same antibody class might be involved in bacterial agglutination and hemagglutination.

Agglutination

[Antibacterial activity of rifampicin against the causative agents of suppurative, septic diseases].

The antibacterial activity of rifampicin was studied in comparison with other antibiotics with respect to clinical strains isolated from cases with various purulent inflammatory processes caused by Staphylococcus, E. coli, Ps. aeruginose, Proteus. The aim of the study was to define the role of rifampicin in the treatment of the above infections. No rifampicin resistant strains were found among staphylococci belonging to the phenotype carrying the determinants of resistance to 2-8 antibiotics. Rifampicin was less active against gramnegative organisms. High heterogeneity of the microbial population of rifampicin was shown with respect to all microbial strains tested. The rate of the spontaneous mutants was high. The average rate of the mutants was 1-7.7-10-8. The studies on the dynamics of the rifampicin resistance increase in the strains of Staphylococci, E. Coli, Ps. aeruginosa and Proteus showed that the resistance increased after 1-2 passages, which means that one-stage mutation was characteristic rifampicin.

Anti-Bacterial Agents

The activity of polymyxins against Escherichia coli in an in-vitro model of the urinary bladder.

The activities against a strain of Escherichia coli of polymyxin B, colistin (polymyxin E) and their sulphomethyl derivatives sulphomyxin and colistin sulphomethate have been examined in an in-vitro model of the urinary bladder under conditions similar to those that may operate in the therapeutic situation. In the dynamic conditions of the model, polymyxins exhibited a reduced activity against E. coli in comparison with activity against exponentially growing cultures in a static system. Nevertheless, long-term suppression of bacterial growth was achieved with levels of polymyxin B and colistin that can be attained during therapy, whereas sulphomethylpolymyxins had little effect on bacterial growth even on prolonged exposure.

Bacteriolysis

Nation-wide survey of antibiotic resistance by means of a computer. Analysis of 200.000 strains of problem bacteria isolated in 1973.

Based on a pilot study performed in 5 District Public Health Laboratories (PHL) in the Slovakia in 1972 (1), the computer system for elaborating the informations concerning the resistance of "problem bacteria" to antibiotics has completely been introduced in 18 PHLs for all-year studies on the resistance to antibiotics in 1973. The results obtained in each PHL and also in total of about 200.000 bacterial strains belonging to 8 of the clinically most important bacterial species were passed on to the corresponding PHL and to the health authorities twice a year. Each PHL elaborated these data being useful and instructive for general practitioners and clinicians in the hospitals of their districts to a commented information on the actual state of effectiveness of individual antibacterial drugs. The multiple spectra of resistance to antibiotics indicating the occurrence of R plasmids in clinical isolates of bacteria and the dynamics for the development of resistance against certain specially monitored "reserved antibiotics" are elaborated at present and will be published in a subsequent communication...

Anti-Bacterial Agents

DURABLE: A Workflow for Determining Corrosion-Driving and Protective Microbial Mechanisms.

Microbiologically influenced corrosion (MIC) threatens global infrastructure, causing billions of dollars in annual losses. Its persistence stems from unresolved mechanisms─particularly the metabolites produced by microorganisms that drive or inhibit corrosion─and the microbial community structures. Progress has been hindered by the absence of systematic workflows to rapidly and accurately identify MIC-relevant microorganisms and their functions. Here, we present DURABLE (Detection of Unique Corrosion Resistant or Accelerating Biologics in a Laboratory Environment), a pipeline that couples high-throughput microbial screening with genomic and metabolic workflows. We applied the DURABLE workflow to six diesel tank samples and revealed fuel-dependent microbial community structures, which showed greater diversity and evenness in bacterial communities than their fungal counterparts. The workflow used carbon steel beads to rapidly screen over 80 bacterial isolates for corrosive activity, reducing assay time to approximately 2 days compared with the conventional 30-day metal coupon test. More than 40 isolates were identified as corrosive. Further testing using mass spectrometry analysis revealed corrosion-associated metabolites, which were further validated using electrochemical assays. Thus, DURABLE achieved a ∼15-fold increase in screening speed and provided a scalable and mechanistic framework for dissecting MIC dynamics. We expect this advance will enable the development of precision mitigation strategies in hydrocarbon fuel infrastructure.

Bacteria

[Dynamics of the changes in the level of antibiotic sensitivity of staphylococci isolated in 1959-1977].

The study of antibiotic sensitivity in staphylococci isolated from the patients in the clinic of the N. N. Burdenko Research Institute of Neurosurgery of the USSR Academy of Medical Sciences in 1977 showed that in this stationary in 1977 predominated cultures resistant to benzylpenicillin. The number of the isolates resistant to streptomycin, levomycetin and erythromycin was high. The percentage of the strains resistant to tetracycline was the least. Still up to 1973 the resistance level to tetracycline among staphylococci was high. Possibly such a dynamics of the changes in the staphylococcal sensitivity to tetracycline was relative and mainly defined by the changes in the system of the results estimation using the paper disc procedure.

Anti-Bacterial Agents

Quantitative RNA modification mapping by mass spectrometry with isobaric tags and nucleobase fragment analysis.

RNA modifications regulate RNA stability, translation, stress responses, and disease processes, yet their function remains poorly understood due to technical limitations in sequence analysis. Here, we present an RNA-specific isobaric tandem mass tagging (RMT) platform for omic-scale quantitative mapping of RNA modifications. The platform combines RNA-specific tags adapted from proteomics with an end-to-end workflow spanning sample preparation through data processing. Validation using synthetic oligonucleotides and total tRNA from Pseudomonas aeruginosa yielded reproducible quantification, with coefficients of variation below 5%. Together with nucleobase fragment analysis, we identified and quantified 24 RNA modifications in PA14 tRNAs, including previously undescribed m2A38 and Gm/Cm39, and assigned their corresponding writer enzymes. Further analyses of tRNAs from writer knockout strains and stressed cells revealed dynamic modification patterns, modification interdependencies, and their potential roles in stress adaptation. This method provides a robust, cost-effective platform for quantitative RNA modification mapping, enabling deeper biological insights.

RNA, Transfer

[Dynamics of accumulation of extracellular proteins of Serratia marcescens and their nuclease activity during cell growth].

Serratia marcescens, strain B-10 M-1, liberates an unspecific endonuclease into the extracellular nutrient solution. Two peaks of the enzyme activity were found in the cultural broth during growth of the cells. The dynamics of accumulation of protein fractions in the cultural broth was studied, and the relative electrophoretic mobility of the enzyme-active part of the proteins was established.

Bacterial Proteins

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae

[Enhancement of toxin production and sporogenesis in Cl. tetani 471 cultures under the influence of endogenous metabolites].

A study was made of the dynamics of the population quantity, the delicate morphology of the bacterial cells and the toxin formation in the Cl. tetani 471 cultures grown in fluid nutrient medium with caseine hydrolysate in the industrial 100-litre reactors and under laboratory conditions. Endogenous metabolites contained in the filtrates of the periodic Cl. tetani 471 cultures which reached the phase of accelerated death were capable of enhancement of the toxin formation when introduced in the amount of up to 1 : 100 at the beginning of the exponential growth of the same cultures in the reactors. The growth of the some oligosporogenic strain in the filtrates of the periodic cultures obtained at the beginning of the stationary phase or of the accelerated death phase was characterized by a slower increase in the vegetative cell count, by enhanced spore-formation and by the second, after the initial, increase in the concentration of the microbes partially connected with the spore vegetation.

Clostridium tetani

[Epidemiological and laboratory criteria in the assessment of meningococcus carrier state].

A study was made of the duration of meningococcus carrier state, immunological indices and group-specific properties of meningococci isolated from them. The periods of meningococcus discharge were studied in 738 persons. Three categories of the carrier state were revealed: a single discharge (67% of the carriers), of average duration (up to 4 weeks), and prolonged. Greater indices of group-specific antibodies (in the passive hemagglutination test) were revealed in the carriers with prolonged presence of meningococci in the nasopharynx. Dynamics of immunological indices and periods of the carrier state formation in the foci of infection permitted to characterize the prolonged carrier state as a latent form of meningococcus infection. A study of the group-specific properties in 1845 strains and comparison of the group-specific pattern of the circulating strains with the epidemic situation indicated that meningococci of group A were not only epidemic, but also more virulent.

Adolescent

Pseudomonas aeruginosa mgtC gene is under the control of PhoP and CbrAB regulators, and its expression can be visualized in macrophages.

The MgtC virulence factor is important during the intramacrophage stage in both classical intracellular pathogens, such as Salmonella Typhimurium, and in extracellular bacteria that transiently encounter intracellular environments during infection, such as Pseudomonas aeruginosa. In these different pathogens, mgtC expression is induced in vitro by magnesium ion depletion, a condition reported to mimic the macrophage environment. Here, we developed an unstable GFP reporter system to monitor in real time the transcriptional activation of the P. aeruginosa mgtC promoter. After in vitro validation in magnesium-defined media, this reporter system allowed visualization of the mgtC promoter induction in a subset of bacteria when P. aeruginosa localized inside cultured macrophages. In addition, although rare under our experimental conditions, in vivo activation of the mgtC promoter was observed for the first time within macrophages of live, infected zebrafish larvae, a cutting-edge vertebrate model for real-time imaging. While MgtC regulation in Salmonella is mediated by the magnesium-responsive PhoPQ two-component system, its regulation in P. aeruginosa remained unknown. The use of mutant strains for two-component regulatory systems revealed that the PhoP regulator, but not by its cognate sensor PhoQ, was required to activate P. aeruginosa MgtC expression in vitro. Unexpectedly, CbrAB, a two-component system specific to Pseudomonas species, was also involved in P. aeruginosa MgtC regulation. Both PhoP and CbrB regulatory proteins were found to directly bind the mgtC promoter, supporting a dual transcriptional control. These findings reveal substantial differences in mgtC gene regulation in different bacterial pathogens, reflecting distinct strategies to drive appropriate expression of a shared virulence factor involved in macrophage adaptation.IMPORTANCEThe adaptation of bacterial pathogens to the host intracellular microenvironment requires tight and rapid regulation of specific genes, and investigating the in vivo transcriptional dynamics of such genes is a major challenge. Here, we focused on the expression of mgtC, a gene important for adaptation to the intramacrophage environment in classical intracellular pathogens, such as Salmonella Typhimurium, and bacteria with a transient intracellular lifestyle, such as Pseudomonas aeruginosa. An unstable GFP reporter system was designed to monitor the transcriptional dynamics of P. aeruginosa mgtC. The use of this reporter system in a state-of-the-art vertebrate model for live imaging, the zebrafish embryo, allowed in vivo tracking of P. aeruginosa mgtC promoter activation inside macrophages in a living host. Furthermore, the expression of P. aeruginosa mgtC was found to be regulated through a mechanism distinct from that of Salmonella MgtC, since it involves the PhoP regulatory protein, but not the PhoQ sensor, and the Pseudomonas-specific CbrAB two-component system, reflecting diverse, finely tuned strategies to control a virulence factor shared by several major human pathogens.

Pseudomonas aeruginosa

Studies on Pasteurella multocida. VII. Dynamics and temporal development of local humoral immunity induced by a live avirulent fowl cholera vaccine.

Vaccination of turkeys by administering the CU strain of Pasteurella multocida in drinking water induced local antibodies in the tracheal secretions. Their appearance and persistence were demonstrated by the indirect immunofluorescence technique. Local antibodies were induced by the 10th day and persisted up to the 42nd day postvaccination, whereas none were induced by an oil-adjuvanted bacterin throughout the observation period (56 days). Thus, the CU strain of P. multocida appeared to generate a local humoral immunity in the respiratory system whereas the bacterin did not.

Administration, Oral

[Study of the dynamics of hepataene and pentaene formation by a culture of Streptoverticillium mucoheptinicum strain 44B/1 in the process of biosynthesis].

In the process of growth Streptoverticillium mycoheptinicum, strain 44B/I produced simultaneously a two-component pentaenic antibiotic (mycopenten) and a heptaenic antibiotic (mycoheptin) by the 1st day of cultivation. The ratio of the components remained constant during the whole fermentation process. When grown on the medium with sodium thiosulfate (under conditions of the changed medium potential) the culture produced the heptaen and a mixture of the components with the background absorption of the UV spectrum at 290--360 nm. The ratio of the heptaen and the mixture was also constant during the whole fermentation process.

Anti-Bacterial Agents

Cytoskeletal mechanisms regulating attaching/effacing bacteria interactions with host cells: It takes a village to build the pedestal.

The actin cytoskeleton is a key cellular structure subverted by pathogens to infect and survive in or on host cells. Several pathogenic strains of Escherichia coli, such as enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC), developed a unique mechanism to remodel the actin cytoskeleton that involves the assembly of actin filament-rich pedestals beneath the bacterial attachment sites. Actin pedestal assembly is driven by bacterial effectors injected into the host cells, and this structure is important for EPEC and EHEC colonization. While the interplay between bacterial effectors and the actin polymerization machinery of host cells is well-understood, how other mechanisms of actin filament remodelling regulate pedestal assembly and bacterial attachment are poorly investigated. This review discusses the gaps in our understanding of the complexity of the actin cytoskeletal remodelling during EPEC and EHEC infection. We describe possible roles of actin depolymerizing, crosslinking and motor proteins in pedestal dynamics, and bacterial interactions with the host cells. We also discuss the biological significance of pedestal assembly for bacterial infection.

Humans

The ecology and evolution of microbial immune systems: a look on the wild vibrio side.

Natural populations of vibrio beyond the well-studied pandemic strains of Vibrio cholerae, provide a powerful model for investigating the eco-evolutionary dynamics of microbial immune systems. Their genetic diversity, ecological versatility, ease of culturability and the availability of time-series data enable detailed studies of phage-host interactions in natural contexts. This review synthesizes recent advances in vibriophage research, highlighting key findings and emerging tools. High-throughput assays and genomic tools have offered new perspectives on phage specificity, host range and the evolutionary pressures shaping these interactions. Theoretical frameworks, such as arms race and fluctuating selection dynamics, are informed by empirical data from vibrio-phage systems, with time-series sampling providing crucial insights into their temporal and spatial dynamics. A major finding is the role of mobile genetic elements (MGEs) in encoding bacterial defence systems, which shape phage-host coevolution. Discoveries like the phage satellite PICMI illustrate how MGEs facilitate the transfer of antiviral systems, influencing ecological and evolutionary dynamics. The paradox of generalist vibriophages, rare despite their broad host ranges, is also explored. By integrating experimental approaches with field observations, vibriophage research advances microbial ecology and informs sustainable applications in aquaculture and phage therapy, reinforcing vibrios as a versatile model system.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.

Bacteriophages