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At least 19 recordsLinked to original sources
PubMed2026

Extensive hidden prophage diversity in Enterobacter species reveals host specificity and local distribution.

Bacteriophages are key drivers of bacterial evolution, particularly through their integration as prophages within host genomes. However, the diversity and host specificity of prophages in relevant pathogens such as Enterobacter species remain poorly characterized. In this study, we revealed the diversity of prophages, mapped their distribution and explored their relationships with their bacterial hosts. We analysed 3,661 prophage sequences identified from the genomes of 20 different Enterobacter species. This analysis uncovered an extensive hidden diversity, comprising 1,617 phage genera and 2,423 phage species - nearly 80% of which were singletons - highlighting an exceptionally rich prophage landscape. We found substantial variation in prophage species richness across host species and isolation sources, with Enterobacter kobei and environmental isolates exhibiting the highest richness. Prophage populations showed strong host specificity and limited cross-species transmission. Moreover, prophages exhibited geographic structuring and significant congruence between host and prophage phylogenies, as well as with the ecological lifestyles of their bacterial hosts. Although we found phages of the same species infecting different host species, these events were infrequent. Finally, bacterial genomes encoded diverse defence systems, mainly PDC-S07, RM type I-II and gabija, whereas only 8.9% of prophages encoded anti-defence systems, mostly anti-CBASS and anti-RM. Overall, this study provides new insights into the diversity of Enterobacter prophages and underscores their ecological and clinical relevance in shaping host adaptation and phage-host dynamics.

Prophages↗
PubMed2025

Development and application of a novel beta-tubulin genotyping tool reveals host-specific transmission cluster in Balantioides coli.

Balantioides coli is a zoonotic ciliated protozoan that infects humans and other mammals. Conventional and ITS-based genotyping approaches have limitations that hinder precise molecular epidemiological investigations. The objective of this study was to develop a new β-tubulin gene-based approach to enhance the detection and genotyping of B. coli. We performed single-cell isolation and whole-genome sequencing on two B. coli isolates from pigs and two from guinea pigs. We then used the β-tubulin gene sequences to design PCR primers for the new genotyping assay. We validated the assay using 56 ITS-confirmed B. coli-positive fecal DNA samples from pigs, cattle, sheep, and guinea pigs. Phylogenetic analyses were conducted using both β-tubulin and ITS sequences. The β-tubulin-based nested PCR assay exhibited 100% detection efficiency and greater specificity than ITS-based methods. Phylogenetic analysis of the β-tubulin gene sequences classified B. coli into three genotypes (I-III). Genotype III appears to be specific to guinea pigs. Genotypes I and II were found across multiple hosts, indicating potential cross-species transmission. Of the five full-length B. coli β-tubulin sequences obtained in this study, 264 polymorphic sites (19.8%) were identified, including both synonymous and non-synonymous mutations. Frequent recombination events within the β-tubulin locus were detected, indicating substantial genetic diversity. Therefore, the β-tubulin gene is a robust marker for genotyping and epidemiological studies of B. coli. The novel nested PCR assay overcomes the limitations of ITS-based methods and has produced data revealing previously unrecognized genetic diversity and host specificity patterns of B. coli.

Tubulin↗
PubMed2024

Impact of effluent parameters and vancomycin concentration on vancomycin resistant Escherichia coli and its host specific bacteriophage lytic activity in hospital effluent.

Vancomycin resistance in bacteria has been classified under high priority category by World Health Organization (WHO) and its presence in hospital effluent is reported to be increasing owing to excess antibiotics use. Among various strategies, bacteriophage has been recently considered as a promising biological agent for combating such antimicrobial resistant bacteria (ARB). However, the influence of effluent's properties on phage-ARB interaction in actual hospital effluent is not completely understood. The present works intends to study this influence of hospital effluent and its parameters on the interaction between vancomycin resistant E. coli (VRE) and its host specific bacteriophage. The isolated VRE was identified by 16S rRNA sequencing, matrix-assisted laser desorption/ionization-time of flight (MALDI - TOF) and whole genome sequencing. The infectivity of phage onto host bacteria was investigated using electron microscopic techniques, dynamic light scattering (DLS), spectrofluorophotometer and confirmed using double agar overlay method. The monovalency and polyvalency of isolated phage against various bacterial species were determined. The phage morphology was identical to T7 phage belonging to Podoviridae. The phage lysis was maximum at pH 7 (90.2%), 37 °C (91.6%) and vancomycin concentration of 50 μg/mL in both synthetic media (89.13%) and effluent (100%). At a maximum vancomycin concentration of 100 μg/mL, decrease in Ca, K, Mg and P (up to 19.70, 14.18, 28, and 15.82% respectively) concentration in effluent was observed due to phage infectivity when compared to control. The whole genome sequencing was performed and the bioinformatics analysis presented the role of mdfA gene encoding the efflux pump in causing vancomycin resistance in E. coli. It also depicted the presence of multiple genes responsible for mercury, cobalt, zinc and cadmium resistance in VRE. These results clearly indicate that bacteriophage mediated combating of VRE is possible in actual hospital effluent and can be used as one of the treatment methods.

Vancomycin↗
PubMed1979

Mapping of genes determining nonpermissiveness and host-specific restriction to bacteriophages in Bacillus subtilis Marburg.

Bacillus subtilis Marburg is nonpermissive for the multiplication of bacteriophages SP10 and phi NR2. A permissive mutant was derived from the Marburg strain, and the genetic determinants of non-permissiveness were analyzed by PBS1 transduction. The simultaneous presence of two genes as mutant alleles, nonA and nonB, was necessary for permissiveness. The gene nonA is linked very closely to rfm (cotransfer: 95%); nonB is located between dal and purB (cotransfer of nonB and purB6 : 48%). The genetic determinant of host-specific restriction intrinsic to the Marburg strain (hsrM) was found to be identical or very closely linked to nonB. The segregation on nonB and hsrM has never been observed in the course of transduction analysis. The mutation, hsrM1, diminishes the restriction activity, but not the host-controlled modification.

Bacillus subtilis↗
PubMed2026

Comprehensive in silico genomics analysis of global trends and host-specific emergence of aminoglycoside resistance in Staphylococcus aureus: a One-Health perspective.

BACKGROUND: Aminoglycosides remain clinically valuable against Staphylococcus aureus. Aminoglycoside resistance in S. aureus represents a critical One Health concern and is primarily driven by aminoglycoside-modifying enzymes (AMEs), which are frequently plasmid-encoded. Although regional studies have provided valuable insights, the global epidemiology of aminoglycoside resistance determinants remains poorly characterized because comprehensive data integrating human, animal, and environmental reservoirs are still lacking. This study addresses this gap by analyzing over 110,000 S. aureus genomes (2000-2025) to map the global resistome, quantify temporal and host-specific trends, and assess the association between genetic determinants and phenotypic resistance. METHODS: We performed a retrospective One Health meta-analysis of 110,309 S. aureus genomes collected between 2000 and 2025 from 128 countries. Genomes were quality-filtered and aminoglycoside resistance determinants were identified using NCBI AMRFinderPlus (v4.0.23). Multilocus sequence typing and host-source harmonization (Human, Animal, Environment, Unknown) enabled clonal and reservoir stratification. Temporal trends in gene prevalence and resistance burden were modeled with robust regression. Geographic and host-associated structuring of key genes was assessed via &#x3c7;2 and enrichment tests. Machine-learning models (elastic-net, random forests, XGBoost) were benchmarked for minimum inhibitory concentration (MIC) prediction via nested cross-validation, with performance evaluated by mean absolute error, RMSE, and SHAP-based feature importance. All analyses were conducted in R and Python using publicly available, de-identified genomic data. RESULTS: Aminoglycoside resistance-associated genes were dominated by modifying enzyme determinants, with ant(6)-Ia, ant(9)-Ia, aph(3')-IIIa, sat4, aadD1, and aac(6')-Ie/aph(2'')-Ia occurring in 14-22% of isolates worldwide. Temporal analysis revealed significant declines in several major determinants, most notably ant(9)-Ia (-2.22 percentage points per year, p&#x2009;<&#x2009;0.001), whereas apmA exhibited a non-significant decreasing trend in animal isolates. Host structuring was marked: human clinical isolates concentrated common determinants, while animal and environmental isolates harbored rare alleles (apmA, spw, str, spd). Geographic mapping confirmed near-universal distribution of common genes but focal restriction of rare ones. Publicly available phenotypic data indicated strong activity of amikacin, whereas gentamicin showed a distinct resistant subpopulation that closely corresponded with AME gene carriage. Genotype-phenotype analyses demonstrated strong concordance, with gene-rich complements predicting resistant MIC strata and absence of determinants predicting susceptibility. Analysis across different gene classes revealed frequent co-occurrence of aminoglycoside resistance genes with determinants from other classes, such as mecA, blaZ, and MLS_B, embedding them within multidrug-resistant (MDR) genomic contexts. CONCLUSION: Over 25&#xa0;years, the prevalence of aminoglycoside resistance-associated genes in S. aureus has declined for several common determinants, while rare veterinary-linked alleles are emerging in animal isolates. Strong genotype-phenotype concordance supports genomic prediction for gentamicin and amikacin, where MIC data are available, although phenotypic confirmation remains essential. The frequent co-occurrence of aminoglycoside resistance genes with other antimicrobial resistance determinants indicates their integration within co-occurrence patterns of MDR genes, defined here as clusters of co-occurring resistance genes often carried on shared mobile genetic elements. These patterns highlight the need for integrated One Health surveillance combining clinical, veterinary, and environmental monitoring with plasmid-context resolution to anticipate emerging threats.

Aminoglycosides↗
PubMedDate not supplied

Impairment of the M-protein and unmasking of a superficial type-specific antigen by proteolytic treatment of influenza A virions with preservation of host-specific antigenicity.

Influenza PR8 particles resulting from strong treatment with caseinase C are spikeless, devoid of neuraminidase and hemagglutinin 1 and 2 glycopeptides, and contain a Schiff-negative polypeptide of about 13,000 molecular weight which exists as traces in intact virions. Their M-protein polypeptide content is reduced to 50% of its original value, but there is no evidence of particle disruption nor of lipid release. They fix complement in the presence of both anti-M-protein antiserum and antiserum raised against a host polysaccharide. During exposure to caseinase C, an antigen is unmasked. It is type-specific and its identity with the M-protein is discussed.

Antigens, Viral↗
PubMed2026

Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.

BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown. RESULTS: We discovered that diatoms exude a C6-sulfated &#x3b1;-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence. CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome. Video Abstract.

Diatoms↗
PubMed1977

Host specificity of a serum marker for hepatitis B: evidence that "e antigen" has the properties of an immunoglobulin.

A family of antigens, referred to collectively as e antigen (eAg), has been detected in sera of some individuals with liver disease who test positive for hepatitis B surface antigen. Studies on eAg partially purified by affinity chromatography on insolubilized antibodies to eAg revealed the following: (i) eAg has the physicochemical and immunologic properties of an immunoglobulin, predominantly of the IgG4 subclass, and (ii) specific antigenic sites, designated as e determinants, differentiate eAg from other immunoglobulins. We suggest that these determinants represent idiotypic determinants on antibodies that are formed in response to hepatitis B virus infection and that block the host's immune surveillance mechanisms by which virus proliferation is stopped.

Chromatography, Affinity↗
PubMed1978

An explanation for the apparent host specificity of Pseudomonas plasmid R91 expression.

Pseudomonas aeruginosa strain 9169 has been reported to contain a plasmid that expresses resistance to carbenicillin (Cb), kanamycin (Km), and tetracycline (Tc) in Escherichia coli but resistance only to Cb in certain Pseudomonas recipients. The triply resistant plasmid in E. coli belonged to incompatibility (Inc) group P or P-1, whereas the singly resistant plasmid in P. aeruginosa was compatible with IncP-1 plasmids and other plasmids of established Inc specificity but incompatible with plasmid pSR1 that is here used to define a new Pseudomonas Inc group P-10. Additional physical and genetic studies showed that strain 9169 contained not one but two plasmids: IncP-1 plasmid R91a, determining the Cb Km Tc phenotype, and IncP-10 plasmid R91, determining Cb that differed in molecular weight and in EcoRI and BamHI restriction endonuclease recognition sites. Plasmid multiplicity rather than host effects on plasmid gene expression can account for differences in the phenotype of strain 9169 transconjugants to E. coli and P. aeruginosa.

Carbenicillin↗
PubMed1978

[The mutual transmission of Staphylococcus aureus between humans and cattle and the environmental adaptation of hemolysin and fibrinolysin formation].

In an ecological investigation in 20 dairy herds of cattle we compared the characteristics of strains isolated from nasal swabs of milkers, from the udder of cows and from cases of mastitis in cows. In 7 herds we found definite strains in the nasal flora of the milkers and in the udder-flora of the cows which only differ in the formation of hemolysin and of fibrinolysin. In the other checked characteristics strains from man and strains from cattle show identical patterns. In 5 herds these strains correspond to the host-specific variety hominis, in 2 herds to the hostspecific--variety bovis. These results refer to an environmental adaptation of the phenotypically detectable formation of hemolysins and fibrinolysin. From the ecological point of view an exchange of strains between man and cattle is likely. The origin of strains which can not be alloted to one ot the known host-specific varieties can be explained by an environmental adaptation. Besides the facts that strains of the host-specific variety bovis occur only very rarely in man and that strains of the host-specific variety hominis occur occasionally in cattle the clinical significance of the reported results has to be clarified by further investigations.

Adaptation, Biological↗
PubMed2026

Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.

Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon&#x2009;=&#x2009;5.90; Simpson&#x2009;=&#x2009;0.98) than in A. cerana (Shannon&#x2009;=&#x2009;4.01; Simpson&#x2009;=&#x2009;0.94; p&#x2009;>&#x2009;0.05), while fungal diversity remained comparable between species (p&#x2009;>&#x2009;0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R2&#x2009;=&#x2009;0.7989, p&#x2009;>&#x2009;0.05) and fungal communities (R2&#x2009;=&#x2009;0.7218, p&#x2009;>&#x2009;0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.

Animals↗
PubMed1976

Two restriction and modification systems in Staphylococcus aureus NCTC8325.

The presence of two distinct host specificities in Staphylococcus aureus strain NCTC8325 was revealed by the isolation of restriction- and modification-deficient mutants. The two host specificity systems, designated S1 and S2, are both active on phage 80mualpha but are not additive in their restricting activity. Restriction-deficient, modification-proficient mutants were invariably affected in both restriction systems. The functional relationship between these two systems is discussed.

DNA, Bacterial↗
PubMed1978

Immunodiffusion studies on Schistosoma mansoni and its host stage specific antigens. 2. Immunoelectrophoresis cross-reactions between hepato-pancreas of Biomphalaria glabrata and Biomphalaria alexandrina.

IMMUNOELECTROPHORESIS was used for studies on immunological cross-reactions between both Schistosoma mansoni (S. m.) intermediate host snails Biomphalaria glabrata and Biomphalaria alexandrina. The preparation of antigens and their corresponding antisera from hepato-pancreas of S. m. infected and non infected snails was described as the homologous reactions of both snails either infected or non infected were rather similar, close immunological relationship between B. glabrata and B. alexandrina could be deduced.

Animals↗
PubMed1975

Inhibition of cellular protein synthesis by simultaneous pretreatment of host cells with fowl plague virus and actinomycin D: a method for studying early protein synthesis of several RNA viruses.

A method is described for analysis of viral protein synthesis early after infection when minute amounts of viral proteins are effectively concealed by large amounts of produced host-specific proteins. The method is superior to a radioimmune assay, since all virus-induced proteins can be measured independent of their immunological reactivity. Host-specific protein synthesis can be suppressed by infection with fowl plague virus. Addition of actinomycin C 1.25 h postinfection does not prevent this suppression, but it does block effectively the formation of fowl plague virus-specific proteins. Such cells synthesize only small amounts of cellular proteins, as revealed by polyacrylamide electrophoresis. They can be superinfected with several different enveloped viruses, however, without significant diminution of virus yeilds. In pretreated cells the eclipse is shortened for Semliki Forest virus, Sindbis virus, and vesicular stomatitis virus, but prolonged for Newcastle disease virus. The onset of protein synthesis, specific for the superinfecting virus, could be clearly demonstrated within 1 h after superinfection. At this time, in cells superinfected with Semliki Forest virus, great amounts of NSP 75 (nonstructural protein; molecular weight, 75 X 10(3)) and reduced amounts of the core protein C could be deomonstrated. The precursor glycoprotein NSP 68 is followed by a new polypeptide, NSP 65: three proteins with molecular weights exceeding 100 X 10(3) were observed which are missing later in the infectious cycle. Similar results were obtained after superinfection with Sindbis virus. The formation of a new polypeptide with a molecular weight of about 80 X 10(3) was detected. After superinfection with vesicular stomatis virus or Newcastle disease virus the formation of new proteins, characteristic for the early stage of infeciton, was not observed.

Cell Line↗
PubMed1978

Immunodiffusion studies on Schistosoma mansoni and its intermediate host stage specific antigens. 3. Immunoelectrophoresis cross-reactions between S. mansoni stages and Biomphalaria sp. hepato-pancreas antigens.

IMMUNOELECTROPHORESIS was applied for cross-wise checking of the different stages in the life cycle of schistosoma mansoni with extracts of hepato-pancreas from its intermediate host snails Biomphalaria glabrata and Biomphalaria alexandrina. Only few fractions were common to non infected snail organ and parasite development stage, while more crossreactions were detected with infected snail hepato - pancreas.

Animals↗
PubMed1978

Immunodiffusion studies on Schistosoma mansoni and its host stage specific antigens. 1. Immunoelectrophoresis cross-reactions between S. mansoni adults and larval stages antigens.

IMMUNOELECTROPHORESIS was applied to evaluate the immunologic relationship between the different stages in the life cycle of Schistosoma mansoni (S.m.). The preparation of antigens and antisera was described. Separated female and male adult worms tested seem to be identical. Eggs, miracidia and cercariae from Biomphalaria glabrata and Biomphalaria alexandrina showed varying degree of cross-reactions. The maximal number of pricipitin arcs was observed, when anti-miracidia-serum was checked against all other S.m. antigens.

Animals↗