Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.

Salmonella, a prominent foodborne pathogen, has posed enduring challenges to the advancement of food safety and global public health. The escalating concern over antibiotic misuse, resulting in the excessive presence of drug residues in animal-derived food products, necessitates urgent exploration of alternative strategies for Salmonella control. Bacteriophages emerge as promising green biocontrol agents against pathogenic bacteria. This study delineates the identification of two novel virulent Salmonella phages, namely phage vB_SalS_ABTNLsp11241 (referred to as sp11241) and phage 8-19 (referred to as 8-19). Both phages exhibited efficient infectivity against Salmonella enterica serotype Enteritidis (SE). Furthermore, this study evaluated the effectiveness of two phages to control SE in three different foods (whole chicken eggs, raw chicken meat, and lettuce) at different MOIs (1, 100, and 10000) at 4°C. It\'s worth noting that sp11241 and 8-19 achieved complete elimination of SE on eggs after 3 h and 6 h at MOI = 100, and after 2 h and 5 h at MOI = 10000, respectively. After 12 h of treatment with sp11241, a maximum reduction of 3.17 log10 CFU/mL in SE was achieved on raw chicken meat, and a maximum reduction of 3.00 log10 CFU/mL was achieved on lettuce. Phage 8-19 has the same effect on lettuce as sp11241, but is slightly less effective than sp11241 on chicken meat (a maximum 2.69 log10 CFU/mL reduction). In conclusion, sp11241 and 8-19 exhibit considerable potential for controlling Salmonella contamination in food at a low temperature and represent viable candidates as green antibacterial agents for food applications.

Relationships between bacterial taxa are traditionally defined using 16S rRNA nucleotide similarity or average nucleotide identity. Improvements in sequencing technology provide additional pairwise information on genome sequences, which may provide valuable information on genomic relationships. Mapping orthologous gene locations between genome pairs, known as synteny, is typically implemented in the discovery of new species and has not been systematically applied to bacterial genomes. Using a data set of 378 bacterial genomes, we developed and tested a new measure of synteny similarity between a pair of genomes, which was scaled onto 16S rRNA distance using covariance matrices. Based on the input gene functions used (i.e., core, antibiotic resistance, and virulence), we observed varying topological arrangements of bacterial relationship networks by applying (i) complete linkage hierarchical clustering and (ii) K-nearest neighbor graph structures to synteny-scaled 16S data. Our metric improved clustering quality comparatively to state-of-the-art average nucleotide identity metrics while preserving clustering assignments for the highest similarity relationships. Our findings indicate that syntenic relationships provide more granular and interpretable relationships for within-genera taxa compared to pairwise similarity measures, particularly in functional contexts.
OBJECTIVE: Given the prevalence and necessity of the 16S rRNA measure in bacterial identification and analysis, this additional analysis adds a functional and synteny-based layer to the identification of relatives and clustering of bacteria genomes. It is also of computational interest to model the bacterial genome as a graph structure, which presents new avenues of genomic analysis for bacteria and their closely related strains and species.

Elizabethkingia anophelis MSU001, isolated from Anopheles stephensi in the laboratory, was characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF/MS), biochemical testing, and genome sequencing. Average nucleotide identity analysis revealed 99% identity with the type species E. anophelis R26. Phylogenetic placement showed that it formed a clade with other mosquito-associated strains and departed from a clade of clinical isolates. Comparative genome analyses further showed that it shared at least 98.6% of genes with mosquito-associated isolates (except E. anophelis As1), while it shared at most 88.8% of common genes with clinical isolates. Metabolites from MSU001 significantly inhibited growth of E. coli but not the mosquito gut symbionts Serratia marcescens and Asaia sp. W12. Insect-associated E. anophelis carried unique glycoside hydrolase (GH) and auxiliary activities (AAs) encoding genes distinct from those of clinical isolates, indicating their potential role in reshaping chitin structure and other components involved in larval development or formation of the peritrophic matrix. Like other Elizabethkingia, MSU001 also carried abundant genes encoding two-component system proteins (51), transcription factor proteins (188), and DNA-binding proteins (13). E. anophelis MSU001 contains a repertoire of antibiotic resistance genes and several virulence factors. Its potential for opportunistic infections in humans should be further evaluated prior to implementation as a paratransgenesis agent (by transgenesis of a symbiont of the vector).

This work aimed to study the genome organization and the metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, a promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with very high salinity. The strain genome contains a linear chromosome 5,968,715 bp long and has no plasmids. The genome contains 5331 coding sequences among which 2139 (40.1%) are functionally annotated. Biosynthetic gene clusters (BGCs) of secondary metabolites exhibiting antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, and ansamycin) were identified in the genome. The most efficient period of SCPM-O-B-9993 strain cultivation was 72 h: during this period, the culture went from the exponential to the stationary growth phase as well as exhibited excellent phytostimulatory properties and antiviral activity against the cucumber mosaic virus in tomatoes under laboratory conditions. The Streptomyces carpaticus SCPM-OB-9993 strain is a biotechnologically promising producer of secondary metabolites exhibiting antiviral and phytostimulatory properties.

Mycobacterium virus Maravista, a member of the family Gracegardnervirianae and species Cheoctovirus, is an F1 cluster phage that infects Mycobacterium smegmatis mc²155. The Maravista genome has 61.3% GC content, is 60,140 bp in length, and encodes 104 putative genes. Maravista encodes two putative glycosyltransferases, suggesting glycosylation of its capsid protein.

This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.

Uropathogenic Escherichia coli (UPEC) remains the main etiological agent of urinary tract infections affecting females and males. The draft genome sequence of three strains of UPEC isolated from senior citizens and pregnant women in the state of Puebla, Mexico, is reported here.

Streptomyces sp. F41 is a potent insecticidal metabolite producing actinomycetes isolated from the topsoil, and the complete genome sequence was determined. The genome consists of 8,343,496 bp, with 7,221 genes and a GC content of 71.84%.

BACKGROUND: Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences.
RESULTS: Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24.
CONCLUSIONS: Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
CONCLUSIONS: This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.