GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

A novel Gordonia sp. PS3 isolated from the gut of Galleria mellonella larvae: Mechanism of polystyrene biodegradation and environmental toxicological evaluation

Plastic pollution is a global concern, with polystyrene (PS) being a major source of plastic waste. In this study, a PS-degrading bacterial strain, Gordonia sp. PS3, was isolated from the gut of Galleria mellonella larvae. After 40 days, strain PS3 exhibited a 33.59 ± 1.12 % degradation rate of PS-microplastics (PS-MPs). The biodegradation mechanism of PS by strain PS3 was investigated using genomics, molecular docking, and metabolomics. Degradation resulted in a significant decrease in molecular weight, disappearance of characteristic aromatic peaks, and the appearance of new functional groups (e.g., hydroxyl and carbonyl), indicating oxidative depolymerization and enhanced hydrophilicity. Four key enzymes involved in PS degradation were identified, with alkane 1-monooxygenase initiating cleavage of C-C bonds in PS and cytochrome P450 monooxygenase catalyzing oxidation of the aromatic ring. Metabolomics analysis revealed upregulation of proline, branched-chain amino acids, and polyamines, indicating oxidative stress response and energy acquisition during PS degradation. The PS degradation products showed no significant adverse effects on Arabidopsis thaliana growth, and PS residues were less harmful to G. mellonella larvae than untreated PS-MPs. This study presents a novel strain for PS biodegradation and provides new insights into the microbial degradation mechanism of PS and the safety of its degradation products.

Identification and Biological Characteristics of Rare Pathogen Comamonas kerstersii in the First Case of Gallbladder Puncture Fluid

Comamonas kerstersii is an environmental microorganism, and clinical infections caused by this species are rare. In this study, the strain CXZJT123 was isolated from gallbladder puncture fluid and identified using a comprehensive approach including morphological observation, mass spectrometry, biochemical identification, 16S rRNA sequencing, and whole-genome sequencing. The morphological characteristics of CXZJT123 were consistent with the Comamonas. Mass spectrometry initially identified the strain as Comamonas aquatica, while biochemical assays demonstrated key features aligning with the Comamonas genus. Phylogenetic analysis of 16S rRNA sequences placed CXZJT123 in the same clade as C. kerstersii (NR 025530.1). Whole-genome sequencing followed by gene annotation using the Non-Redundant Protein Database (NR) revealed the highest gene homology with C. kerstersii. Further genomic analysis using the Virulence Factors of Pathogenic Bacteria (VFDB) and the Comprehensive Antibiotic Research Database (CARD) identified the presence of virulence genes, including those encoding flagella (flg series) and biofilm formation (pil series), as well as antibiotic resistance genes such as macB, arlR, and evgS. This study presents the first reported isolation of C. kerstersii isolated from gallbladder puncture fluid. The findings contribute valuable insights into the identification, genomic characteristics, and potential pathogenicity of C. kerstersii, providing a useful reference for the diagnosis and management of related infections.

Complete genome sequence of the Listeria innocua lytic bacteriophage LIS04

The Listeria innocua American Type Culture Collection 51742-specific phage LIS04, isolated from paddy water, belongs to Caudoviricetes class. Phage LIS04 has a 181,606 bp double-stranded DNA with 37.09% guanine-cytosine content and 217 predicted open reading frames. Genomic analysis confirmed its lytic cycle and low similarity to known phages.

A novel thermostable lytic phage vB_EF_Enf3_CCASU-2024-3 against clinical Enterococcus faecium and Enterococcus faecalis

Enterococci, Gram-positive bacteria, have become a major concern in healthcare settings due to their significant virulence and antibiotic resistance. This research focuses on isolating, phenotypic, and genotypic analysis of enterococci-specific lytic phages to be used as potential candidates in combating multidrug-resistant (MDR) Enterococcus clinical isolates. The virulence of Enterococcus isolates was analyzed by testing for gelatinase and biofilm formation. The phage(s) was isolated from a sewage sample, then purified, propagated, and physiochemically analyzed. The phage was examined using transmission electron microscopy, and the whole genome sequence (WGS) was performed. Sixety-five clinical enterococci including, 27 (41.5%), 33 (50.7%) 3 (4.6%), and 2 (3%) E. faecalis, E. faecium, E. avium, and E. durans, respectively were isolated. Linezolid, teicoplanin, chloramphenicol, and vancomycin exhibited the lowest resistance. Twenty-five (38.5%) isolates were both gelatinase- and biofilm-producers. A novel lytic vB_EF_Enf3 phage belonging to Caudoviricetes class, characterized by an icosahedral head with a diameter of 100 ± 5 nm and a tail measuring 70 ± 5 nm in length was isolated. The phage demonstrated good thermal stability, and viability across various pH levels and exhibited a broad- spectrum of activity against E. faecium and E. faecalis. The vB_EF_Enf3 phage (36,202 bp length) harbored 36 open reading frames (ORFs) with a GC content of 34.4% (GenBank accession, PP747318). In conclusion, a novel thermostable lytic bacteriophage vB_EF_Enf3, belonging to class Caudoviricetes, was isolated from sewage showing broad-spectrum potent lytic activity against E. faecium and E. faecalis and maintained stability under various extreme conditions, including temperature, and pH fluctuations.

Diversity and genomics of bacteriome-associated symbionts in treehopper Darthula hardwickii (Hemiptera: Aetalionidae) and implications of their nutritional functions

Symbionts play important roles in insect nutritional ecology, and the phylogenies of some vertically transmitted symbionts mirror the host phylogeny. Here we report the diversity, distribution, transmission, and potential functions of symbionts harbored in the aetalionid treehopper Darthula hardwickii (Aetalionidae) using multiple methods and compare the potential functions of its obligate symbiont Karelsulcia with that of the related aetalionid Aetalion reticulatum. D. hardwickii harbors Karelsulcia in bacteriomes, a yeast-like fungal symbiont (YLS) in fat bodies, and Tisiphia in both the bacteriomes and fat bodies. Karelsulcia and YLS are vertically transmitted to the ovaries but do not cluster to form a "symbiont ball" in terminal oocytes, as is the case in other auchenorrhynchan insects. YLS harbored in D. hardwickii represents the first known instance of a fungal symbiont being associated with treehoppers. Phylogenetic analysis revealed that Aetalionidae are derived from within Membracidae. Gene truncation and absence were revealed in the tryptophan biosynthetic pathway of Karelsulcia from D. hardwickii, suggesting this symbiont is no longer capable of providing this essential amino acid (EAA) to its host. Tryptophan is presumed to be supplied to D. hardwickii by YLS since tryptophan-related genes are either absent or degraded in Karelsulcia and Tisiphia. No truncated genes were found in Karelsulcia from A. reticulatum, but it has lost genes related to the synthesis of other EAAs, as in some leafhoppers. This study sheds new light on the diversity and functions of the nutritional endosymbionts of Membracoidea and processes that may have precipitated symbiont replacement in this diverse insect lineage.IMPORTANCESymbionts in sap-feeding insects play important roles related to nutrition of their hosts, which may change through evolutionary time and vary across host and symbiont lineages. This comparative genomic study indicates that, compared to the related symbionts of other leaf- and treehoppers, the Karelsulcia symbiont of the treehopper Darthula hardwickii has lost the ability to provide the EAA tryptophan to its host. This function is apparently being performed by a coexisting yeast-like symbiont (YLS). This is the first report of a YLS in a species of treehopper, which suggests that the processes involved in symbiont replacement in treehoppers are similar to those observed in other sap-sucking auchenorrhynchan insects. Phylogenetic analyses of Karelsulcia lineages of Membracoidea largely mirror the host insect phylogeny but suggest that Aetalionidae may have originated from Membracidae, in contrast to some recent phylogenies based on the genomic data from the host insects.

Gracilibacillus pellucidus sp. nov., a moderately halophilic bacterium isolated from saline soil in Xinjiang province, China

A motile, Gram-positive, moderately halophilic, catalase-positive and oxidase-negative, obligate aerobic, slender rod-shaped bacterium, strain S3-1-1T was isolated from the plant rhizosphere soil in saline soil of Xinjiang Uygur Autonomous Region. Strain S3-1-1T grew in the presence of 1-21% NaCl and at pH 7.0-9.0, with optimum growth at 3% NaCl and pH 7.5. It grew at 16-45 °C, with optimum growth at 40 °C.Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S3-1-1T should be placed within the genus Gracilibacillus and formed a separate branch. It exhibited highest similarities to Gracilibacillus ureilyticus MF38T (sequence similarity 97.7%), Gracilibacillus massiliensis Awa-1T (sequence similarity 97.5%), Gracilibacillus xinjiangensis J2T (sequence similarity 97.4%) and Gracilibacillus salitolerans SCU50T (sequence similarity 97.4%). Genomic comparisons revealed that strain S3-1-1T shares closest phylogenetic relationships with Gracilibacillus saliphilus YIM 91119T (ANI 77.4%, AAI 78.4%), Gracilibacillus thailandensis TP2-8T (ANI 77.2%, AAI 78.3%), and Gracilibacillus salitolerans SCU50T (ANI 77.3%, AAI 78.1%). However, the digital DNA-DNA hybridization (19.3-22.1%), average nucleotide identity (71.1-77.4%), and average amino acid identity (66.9-78.6%) values all fell below the recommended thresholds for species delineation, supporting its novel taxonomic status. The major cellular fatty acids were anteiso-C15:0, C16:0, iso-C15:0, and anteiso-C17:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and aminophospholipids. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics, S3-1-1T represented a novel species of the genus Gracilibacillus, for which the name Gracilibacillus pellucidus sp. nov. is proposed, with S3-1-1T (= JCM 36422T = GDMCC 1.4017T) as the type strain.

Complete genome sequence and comparative analysis of Bacillus velezensis Lzh-5, a fungal antagonistic and plant growth-promoting strain

BACKGROUND

Plant diseases significantly and persistently impair product quality and yield across the globe. Employing antagonistic microorganisms represents an environmentally friendly and cost-effective approach to pathogen management. In this study, Bacillus velezensis Lzh-5 was explored to understand the molecular underpinnings of its antagonistic activity and plant growth-promoting properties.

RESULTS

We present the basic genomic profile of B. velezensis Lzh-5. Whole-genome analysis revealed that Lzh-5 possesses a 4,015,817 bp circular chromosome with a GC content of 46.0%, and an 8,933 bp circular plasmid with a GC content of 40.5%. A total of 3,998 genes were predicted, of which 3,881 (97.07%) are coding DNA sequences (CDSs). Through phylogenomic and comparative genomic analyses, strain Lzh-5 was confirmed as B. velezensis. The Lzh-5 genome harbors genes for cell wall-degrading enzymes. Additionally, 13 gene clusters responsible for secondary metabolite production were identified. Notably, a unique cluster (cluster 2) coding for an unknown compound was found exclusively in strain Lzh-5. Genes associated with plant growth enhancement, such as those involved in chemotaxis, motility, biofilm formation, phytohormone production, nitrogen fixation, phosphate solubilization, glycine betaine biosynthesis, and acetoin and 2,3-butanediol synthesis, were also identified.

CONCLUSION

The basic characteristics of strain Lzh-5 genome were delineated through whole-genome sequencing. Our analysis indicates that the Lzh-5 genome encompasses various genes that promote plant growth, induce systemic resistance, and antagonize pathogens. Compared to other strains, several unique gene clusters in Lzh-5 may contribute to the discovery of novel bioactive compounds and offer a broader antagonistic spectrum. This investigation elucidates the antifungal and plant growth-promoting mechanisms of B. velezensis Lzh-5 at a genetic level, providing a theoretical foundation for further application in agricultural production.

Isolation and characterization of virulent bacteriophages and controlling Salmonella Enteritidis biofilms on chicken meat

Salmonella is a prominent zoonotic pathogen that continues to represent a large threat to food safety and public health worldwide. Concurrently, the inappropriate use of antibiotics has led to the development of antibiotic-resistant strains of Salmonella, highlighting the urgent need for new approaches to manage these bacteria. In this context, virulent bacteriophages are increasingly recognized as a potential and effective biological control method against Salmonella. This study identifies two newly isolated virulent Salmonella phages, phage vB_SalD_ABTNLS3 (S3 for short) and phage 2-3 (2-3 for short). Both phages exhibited effectiveness in preventing biofilm formation and reducing biofilm. S3 and 2-3 could maximize the inhibition of more than 70% and 91% of biofilm formation after 48 h of treatment, and maximize the removal of more than 59% and 96% of mature biofilm after 3 h and 5 h, respectively. Based on these, our study assessed the efficacy of 2-3 in controlling Salmonella enterica serotype Enteritidis (SE) on raw chicken meat at 4°C with varying MOIs, including 1, 100, and 10,000. The maximum reduction observed in SE on chicken meat was 1.15 log10 CFU/mL following a 12-h treatment with the 2-3, a significant decrease of more than 92% compared to the initial levels present in the experiment (MOI = 10,000). In conclusion, our phages performed well in controlling biofilm and disinfecting refrigerated food at 4°C, suggesting their potential as biological agents to reduce Salmonella contamination in the food industry.

High-yield bacterial cellulose production from rice bran using a genetically characterized Komagataeibacter europaeus strain

A high-yielding Komagataeibacter europaeus strain, KFET1, was evaluated for its capacity to utilize rice bran as a cost-effective substrate for bacterial cellulose (BC) production. By employing an optimized enzymatic hydrolysis approach, the yield of rice bran-derived BC (RB-BC) reached 15.67 g/L, a 389.06 % improvement over Hestrin-Schramm-derived BC (HS-BC). RB-BC demonstrated superior nanofiber uniformity, rehydration capacity, and thermal stability, confirmed by FTIR, SEM, DSC, X-ray diffraction, and solid-state NMR analyses. Scale-up fermentation in a 15 L bioreactor achieved a BC yield of 20.69 g/L and a sugar conversion rate of 87.85 %. The high BC yield (20.69 g/L) stems from synergistic interactions between the KFET1 strain's enhanced carbohydrate metabolism (264 genes) and enzymatic hydrolysis-driven nutrient release from rice bran. Economic analysis demonstrated a profit of 1166.42 USD/ton for rice bran medium, significantly exceeding values for Hestrin-Schramm (-153.06 USD/ton) and coconut water (906.33 USD/ton), highlighting rice bran's cost-effectiveness. This study provides an efficient and sustainable strategy for converting agricultural by-products into high-value biomaterials, paving the way for industrial-scale BC production.

Sequence analysis of two F1 mycobacteriophages, Deb65 and DocMcStuffins

Isolated from wetland soil, Deb65 and DocMcStuffins are bacteriophages with a siphoviral morphology that infect Mycobacterium smegmatis. Deb65 and DocMcStuffins encode 97 and 91 putative genes, 41 of which are shared. Based on gene content similarity to actinobacteriophages more broadly, both phages are assigned to subcluster F1.

Genome sequences of four A1 subcluster Mycobacterium smegmatis bacteriophages

Payneful, Marchy, Hami1, and Sorpresa are A1 subcluster tailed bacteriophages belonging to the Caudoviricetes class that infect Mycobacterium smegmatis strain mc2155. They are consistent with other A1 subcluster phages based on their genome length and guanine-cytosine content. Their genomes contain six novel open reading frames.

Whole genome sequences of eight Erwinia amylovora phages isolated from South Korea

The gram-negative Enterobacteriaceae Erwinia amylovora is the causative agent of fire blight. Herein, we announce the full genome sequencing and annotation of eight E. amylovora bacteriophages from apple and pear orchards in South Korea, which have remarkable similarity to Erwinia phages previously isolated from the Americas.

Penton blooming, a conserved mechanism of genome delivery used by disparate microviruses

Microviruses are single-stranded DNA viruses infecting bacteria, characterized by T = 1 shells made of single jelly-roll capsid proteins. To understand how microviruses infect their host cells, we have isolated and studied an unusually large microvirus, Ebor. Ebor belongs to the proposed "Tainavirinae" subfamily of Microviridae and infects the model Alphaproteobacterium Rhodobacter capsulatus. Using cryogenic electron microscopy, we show that the enlarged capsid of Ebor is the result of an extended C-terminus of the major capsid protein. The extra packaging space accommodates genes encoding a lytic enzyme and putative methylase, both absent in microviruses with shorter genomes. The capsid is decorated with protrusions at its 3-fold axes, which we show to recognize lipopolysaccharides on the host surface. Cryogenic electron tomography shows that during infection, Ebor attaches to the host cell via five such protrusions. This attachment brings a single pentameric capsomer into close contact with the cell membrane, creating a special vertex through which the genome is ejected. Both subtomogram averaging and single particle analysis identified two intermediates of capsid opening, showing that the interacting penton opens from its center via the separation of individual capsomer subunits. Structural comparison with the model Bullavirinae phage phiX174 suggests that this genome delivery mechanism may be widely present across Microviridae.

IMPORTANCE

Tailless Microviridae bacteriophages are major components of the global virosphere. Notably, microviruses are prominent members of the mammalian gut virome, and certain compositions have been linked to serious health disorders; however, a molecular understanding of how they initiate infection of their host remains poorly characterized. We demonstrate that trimeric protrusions located at the corners of a single microvirus capsomer mediate host cell attachment. This interaction triggers opening of the capsomer, driven by separation of subunits from its center, much like flower petals open during blooming. This extensive opening explains how the genome translocation apparatus, along with the genome itself, is able to exit the capsid. "Penton blooming" likely represents a conserved mechanism shared by diverse viruses possessing similar capsid architectures.

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.

Characterization, whole-genome sequence analysis, and protease production of a new thermophilic Bacillus licheniformis strain isolated from Debagh hot spring, Algeria

A new thermophilic strain, designated as Bacillus sp. LMB3902, was isolated from Hammam Debagh, the hottest spring in Algeria (up to 98 °C). This isolate showed high protease production in skim milk media at 55 °C and exhibited significant specific protease activity by using azocasein as a substrate (157.50 U/mg). Through conventional methods, chemotaxonomic characteristics, 16S rRNA gene sequencing, and comparative genomic analysis with the closely related strain Bacillus licheniformis DSM 13 (ATCC 14580 T), the isolate Bacillus sp. LMB3902 was identified as a potentially new strain of Bacillus licheniformis. In addition, the gene functions of Bacillus sp. LMB3902 strain were predicted using the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups, Non-Redundant Protein Sequence Database, Swiss-Prot, and Pfam databases. The results showed that the genome size of Bacillus sp. LMB3902 was 4.279.557 bp, with an average GC content of 46%. The genome contained 4.760 predicted genes, including 8 rRNAs, 78 tRNAs, and 24 sRNAs. A total of 235 protease genes were annotated including 50 proteases with transmembrane helix structures and eight secreted proteases with signal peptides. Additionally, the majority of secondary metabolites found by antiSMASH platform showed low similarity to identified natural products, such as fengicin (53%), lichenysin (57%), and surfactin (34%), suggesting that this strain may encode for novel uncharacterized natural products which can be useful for biotechnological applications. This study is the first report that describes the complete genome sequence, taxono-genomics, and gene annotation as well as protease production of the Bacillus genus in this hydrothermal vent.

Quality control and law exploration of microbial oil production from spent grains fermented by Wickerhamomyces anomalus CY2

Microbial oils are gaining attention as a promising raw material for biodiesel production. However, the high cost of microbial culture media and the elevated cold filter plugging point of the resulting biodiesel hinder their conversion. This study focused on fermenting SGs with added metal ions to regulate microbial oil saturation and enhance biodiesel quality. We investigated the relationship between sugar metabolism and lipid synthesis in the CY2 strain fermentation of SGs, aiming to provide insights into metabolic regulation for the industrial production of microbial oils. The results indicated that the addition of 50 mg/L FeCl3•6H2O to the lipid-producing medium for the CY2 strain significantly enhanced the content of unsaturated fatty acids without compromising the yield of microbial oils. This modification effectively reduced the cold filter plugging point of biodiesel, thereby improving its anti-freezing performance. In the analysis of material metabolism during the fermentation of SGs by the CY2 strain, it was observed that amylase and cellulase activities increased from 24 h to 60 h. The sugar content initially decreased, reaching its lowest point at 36 h, before gradually rising again. Within the first 48 h of fermentation, sugar catabolism in the CY2 strain surpassed lipid synthesis metabolism, leading to rapid microbial growth and reproduction. Subsequently, microbial growth plateaued, with excess carbon sources converted into triglycerides. This study produced high-quality biodiesel from low-cost SGs using Wickerhamomyces anomalus and provided a theoretical basis for metabolic regulation in microbial oil production and industrial fermentation, highlighting significant economic and environmental benefits.

Effect of temperate bacteriophage vB_SauS_S1 on the adaptability and pathogenicity of Staphylococcus aureus ST398

Livestock-associated Staphylococcus aureus ST398 is a highly pathogenic species that causes infections in a wide variety of animals, including humans. The bacteriophage (phage) vB_SauS_S1 was isolated originally using a ST398 strain as its "isolating host", then the spot tests showed it was able to infect 73.33% (22/30) ST398 isolates. Phage S1 was assigned as a temperate phage based on genome analysis and phenotypic validation. Phylogenetic analysis showed that S1 was closely related to temperate phages tp310-2 and SA137ruMSSAST121PVL. Following infection of ST398 by phage S1, the lysogenic strain showed enhanced biofilm forming ability compared to the wildtype strain, and the invasion rate of MAC-T cells increased by 10.39%. The minimum inhibitory concentration showed that phage S1 did not change the antibiotic sensitivity of the lysogen strain, and the virulence of the lysogen strain did not change significantly in the injection models of Galleria mellonella (G. mellonella) and mice. The lysogen demonstrated superinfection immunity and reduced sensitivity to virulent phage infection. Thus, this study contributes to understanding the co-evolutionary relationships between temperate phages and the multi-host zoonotic pathogen S. aureus ST398.

Haptophyte-infecting viruses change the genome condensing proteins of dinoflagellates

Giant viruses are extraordinary members of the virosphere due to their structural complexity and high diversity in gene content. Haptophytes are ecologically important primary producers in the ocean, and all known viruses that infect haptophytes are giant viruses. However, little is known about the specifics of their infection cycles and the responses they trigger in their host cells. Our in-depth electron microscopic, phylogenomic and virion proteomic analyses of two haptophyte-infecting giant viruses, Haptolina ericina virus RF02 (HeV RF02) and Prymnesium kappa virus RF02 (PkV RF02), unravel their large capacity for host manipulation and arsenals that function during the infection cycle from virus entry to release. The virus infection induces significant morphological changes in the host cell that is manipulated to build a virus proliferation factory. Both viruses' genomes encode a putative nucleoprotein (dinoflagellate/viral nucleoprotein; DVNP), which was also found in the virion proteome of PkV RF02. Phylogenetic analysis suggests that DVNPs are widespread in marine giant metaviromes. Furthermore, the analysis shows that the dinoflagellate homologues were possibly acquired from viruses of the order Imitervirales. These findings enhance our understanding of how viruses impact the biology of microalgae, providing insights into evolutionary biology, ecosystem dynamics, and nutrient cycling in the ocean.

Anellovirus species in the serum of acute febrile patients from Mato Grosso, central Western Brazil, 2019

The Anelloviridae family is one of the most diverse group of viruses within human virome, comprising 155 species distributed across 30 genera, four of which infect humans. Using a metagenomic approach to examine the frequency and diversity of viruses in the serum of patients with acute febrile illness in Mato Grosso during 2019, we identified and characterized two complete, three nearly complete and nine partial anellovirus genomes, including eleven putatively new species. Alphatorquevirus was the most prevalent genus (50%; n = 7), followed by Gammatorquevirus (35.7%; n = 5) and Betatorquevirus (14.3%; n = 2), consistent with global reports showing its dominance within Anelloviridae. Additionally, 65% of genomes were recovered from children, supporting higher anellovirus diversity and load in younger individuals.

Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland

Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in Acanthamoeba castellanii from a composting soil sample in Jyväskylä, Central Finland. Its genome shares similarities with other marseilleviruses. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus life cycle. We reconstructed the Jyvaskylavirus particle to 6.3 Å resolution using cryo-electron microscopy. The ~2500 Å diameter virion displays structural similarities to other Marseilleviridae giant viruses. The capsid comprises of 9240 copies of the major capsid protein, encoded by open reading frame (ORF) 184, which possesses a double jellyroll fold arranged in trimers forming pseudo-hexameric capsomers. Below the capsid shell, the internal membrane vesicle encloses the genome. Through cross-structural and -sequence comparisons with other Marseilleviridae using AI-based software in model building and prediction, we elucidated ORF142 as the penton protein, which plugs the 12 vertices of the capsid. Five additional ORFs were identified, with models predicted and fitted into densities that either cap the capsomers externally or stabilize them internally. The isolation of Jyvaskylavirus suggests that these viruses may be widespread in the boreal environment and provide structural insights extendable to other marseilleviruses.

Genomic, Probiotic, and Functional Properties of Bacteroides dorei RX2020 Isolated from Gut Microbiota

BACKGROUND/OBJECTIVES

Gut microbiota is essential for maintaining host immune homeostasis and has been confirmed to be closely related to some intestinal and extraintestinal diseases. Bacteroides, as the dominant bacterial genus in the human gut, has attracted great attention due to its excellent metabolic activity, but there are few studies on Bacteroides dorei species. In our previous study, a gut commensal strain, Bacteroides dorei RX2020 (B. dorei), was isolated from healthy human feces and exhibited superior flavonoid metabolic activity, prompting further analysis of its uncharacterized genomic features, probiotic potential, safety, and immunomodulatory activity.

RESULTS

The results showed that B. dorei exhibited intrinsic probiotic functionalities with preserved genomic and phenotypic stability, demonstrated safety profiles in murine models through in vivo assessments, and conferred antagonistic activity against enteric foodborne pathogens via competitive exclusion. The strain also demonstrated abundant metabolic activity and was involved in the metabolism of tryptophan and bile acids (BAs). Moreover, B. dorei can promote the production of IFNβ by dendritic cells (DCs) to inhibit the replication of influenza virus in epithelial cells, which may be achieved by regulating host metabolism.

CONCLUSIONS

This study reveals the potential of B. dorei as next-generation probiotics (NGPs), contributing to a broader understanding and application of these novel probiotics in health and disease management.

Unveiling the complete genome sequence of Paenibacillus taichungensis: genomic features and biocontrol potential

OBJECTIVES

The genus Paenibacillus encompasses a diverse group of Gram-positive bacteria with significant biotechnological potential. However, the research data and application cases of Paenibacillus taichungensis were still poorly understood. In this study, we isolated a P. taichungensis strain BB507, which demonstrated antibacterial effect on Ralstonia solanacearum species complex, and provided data and analysis of its complete genome.

DATA DESCRIPTION

Strain BB507 was isolated from a pine rhizosphere in Meizhou city, Guangdong province of China, and showed antibacterial activity against Ralstonia solanacearum species complex. Complete genome was sequenced using Illumina NovaSeq (second-generation) and Oxford Nanopore (third-generation) platforms. The genome of BB507 comprised of a 6,974,531 bp circular chromosome and a 352,197 bp circular plasmid, encoding a total of 6,649 gene with an average gene length of 950 bp, 103 transfer RNAs, 2 sRNAs, and 36 rRNAs. Three candidate CRISPRs, 6 genomic islands and 14 prophages were predicted. The bacterial orthologous average nucleotide identity (OAT) and the type genome server (TYGS) analysis highlighted the strain BB507 was clustered into a subgroup with P. taichungensis. antiSMASH v7.0 predicted the presence of 10 secondary metabolite gene clusters in the genome. These findings will serve as a useful resource for further research in industrial and agricultural biotechnology.

Complete genome sequences of Rhodococcus equi phages CoffeeBean, Dorin, Francesca, Madraxi, and Tonitrus

We report genomes of five phages isolated using the actinobacterium Rhodococcus equi NRRL B-16538 . Based on gene content similarity, one phage is assigned to actinobacteriphage cluster CF, one to cluster CR, two to cluster CG, and one that cannot be assigned to any existing cluster. The latter encodes a five-gene thymine hypermodification system.

Complete genome sequence of Vreelandella sp. SM1641, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Southwest Indian Ocean

Vreelandella sp. SM1641 was isolated from the hydrothermal vent sediment of the southwest Indian Ocean at a water depth of 2519 m. The complete genome sequence of strain SM1641 was analyzed to understand its metabolic capacities and biosynthesis potential of natural products in this study. The genome of strain SM1641 consists of a circular chromosome and two plasmids. The length of the circular chromosome was 4,731,121 bp with GC content of 54.46 mol%, and the length of plasmid A was 302,095 bp with GC content of 54.95 mol%, and the length of plasmid B was 8857 bp with GC content of 46.31 mol%. Genomic data showed that strain SM1641 had several gene clusters involved in the synthesis of exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) synthesis. SM1641 also has a variety of genes that respond to osmotic stress, heat shock, cold shock, oxidative stress, and heavy metal stress, which plays a critical role in bacterial adaptation to hydrothermal environments. Therefore, genome sequencing and data mining of strain SM1641 are helpful to further understand the molecular mechanism of Vreelandella adapting to the deep-sea hydrothermal environment, and provide a basis for further experimental exploration.

Genomic analysis of Isoptericola halotolerans SM2308 reveals its potential involved in fucoidan degradation

Marine bacteria play important roles in the degradation and recycling of algal polysaccharides. However, the marine bacteria involved in fucoidan degradation and their degradation pathways remain poorly understood. Here, we report the complete genome sequence of Isoptericola halotolerans SM2308, isolated from a brown algal sample collected from an intertidal zone of the Yellow Sea in China. The genome of strain SM2308 consists of a single circular chromosome of 4,011,455 bp with a high GC content of 72.70 %. Strain SM2308 exhibited rapid growth on fucoidan as the sole carbon source, indicating its capacity to degrade fucoidan. Gene annotation and metabolic pathway analyses showed that strain SM2308 possesses a complete pathway for utilizing fucoidan, including the extracellular breakdown of polymeric fucoidan into smaller fucooligosaccharides/fucose by fucoidanases, the transmembrane transport of fucooligosaccharides/fucose into the cytoplasm by an ABC transporter, and the intracellular fucose catabolism via a non-phosphorylative pathway. This represents the first genome of an actinobacterium from the order Micrococcales with fucoidan-degrading ability. The genome of Isoptericola halotolerans SM2308 provides insights into the role of actinobacteria in the biogeochemical cycling of fucoidan in marine ecosystems.

A flagella-dependent Burkholderia jumbo phage controls rice seedling rot and steers Burkholderia glumae toward reduced virulence in rice seedlings

Bacteriophages (phages) are being investigated as potential biocontrol agents for the suppression of bacterial diseases in cultivated crops. Jumbo bacteriophages, which possess genomic DNA larger than 200 kbp, generally have a broader host range than other phages and therefore would be useful as biocontrol agents against a wide range of bacterial strains. Thus, the characterization of novel jumbo phages specific for agricultural pathogens would be of importance for the development of phage biocontrol strategies. Herein, we demonstrate that phage S13 requires Burkholderia glumae flagella for its attachment and infection and that loss of B. glumae flagella prevents S13 cellular lysis. As flagella is a known virulence factor, loss of flagella results in a surviving population of B. glumae with reduced virulence. Further experimentation demonstrates that phage S13 can protect rice plants from B. glumae-sponsored destruction in a rice seedling model of infection.IMPORTANCEBacterial plant pathogens threaten many major food crops and inflict large agricultural losses worldwide. B. glumae is a bacterial plant pathogen that causes diseases such as rot, wilt, and blight in several food major crops including rice, tomato, hot pepper, and eggplant. B. glumae infects rice during all developmental stages, causing diseases such as rice seedling rot and bacterial panicle blight (BPB). The B. glumae incidence of rice plant infection is predicted to increase with warming global temperatures, and several different control strategies targeting B. glumae are being explored. These include chemical and antibiotic soil amendment, microbiome manipulation, and the use of partially resistant rice cultivars. However, despite rice growth amelioration, the treatment options for B. glumae plant infections remain limited to cultural practices. Alternatively, phage biocontrol represents a promising new method for eliminating B. glumae from crop soils and improving rice yields.

Biodegradation of S-Triazine Herbicides Under Saline Conditions by Paenarthrobacter ureafaciens PC, a New Halotolerant Bacterial Isolate: Insights into Both the Degradative Pathway and Mechanisms of Tolerance to High Salt Concentrations

In this study, a halotolerant bacterial strain was isolated and identified. This bacterium was confirmed to efficiently degrade s-triazine herbicides under saline conditions. The optimal conditions for the metabolism and growth of this strain were determined through single-factor tests. Furthermore, the biodegradation pathways of prometryne (the target compound) by this strain were proposed based on the detection of possible degradation intermediates and genome sequencing analysis. Additionally, a possible halotolerance mechanisms of this strain were also revealed through screening halotolerance-related genes in its genome. The results demonstrated that a halotolerant bacterial strain (designated PC), which completely degraded 20.00 mg/L prometryne within 12 h under saline conditions (30.0 g/L NaCl), was isolated and identified as Paenarthrobacter ureafaciens. The optimal conditions for the metabolism and growth of the strain PC were identified as follows: yeast extract as the additional carbon source with the concentration of ≥0.1 g/L, NaCl concentration of ≤30.0 g/L, initial pH of 7.0, temperature of 35.0 °C, and shaking speed of ≥160 rpm. Furthermore, the strain PC demonstrated efficient removal of other s-triazine herbicides, including atrazine, ametryne, simetryne, and cyanazine. The strain PC might degrade prometryne through a series of steps, including demethylthiolation, deisopropylamination, deamination, dealkalation, decarboxylation, etc., relying on the relevant functional genes involved in the degradation of s-triazine compounds. Furthermore, the strain PC might tolerate high salinity through the excessive uptake of K+ into cells, intracellular accumulation of compatible solutes, and production of halophilic enzymes. This study is expected to provide a potentially effective halotolerant bacterium for purifying s-triazine pollutants in saline environments.

Comprehensive Phenotypic Characterization and Genomic Analysis Unveil the Probiotic Potential of Bacillus velezensis K12

Bacillus spp. have emerged as pivotal sources of probiotic preparations, garnering considerable attention in recent years owing to their vigorous bacteriostatic activity and antimicrobial resistance. This study aimed to investigate these probiotic characteristics in depth and verify the safety of Bacillus velezensis K12, a strain isolated from broiler intestine. The K12 strain was identified as Bacillus velezensis based on its morphology and 16S rDNA sequence homology analysis. Subsequently, B. velezensis K12 was evaluated for acid resistance, bile salt resistance, gastrointestinal tolerance, drug sensitivity, and antimicrobial activity. Additionally, whole-genome sequencing technology was employed to dissect its genomic components further, aiming to explore its potential applications as a probiotic strain. B. velezensis K12 was sensitive to six antibiotics and had acid tolerance. Furthermore, it showed potent antimicrobial activity against a wide range of pathogenic bacteria, including Escherichia coli (E. coli), Staphylococcus aureus, Salmonella, Clostridium perfringens, Bacillus cereus, and Vibrio parahaemolyticus. The complete genome sequencing of B. velezensis K12 revealed a genomic length of 3,973,105 base pairs containing 4123 coding genes, among which 3973 genes were functionally annotated. The genomic analysis identified genes associated with acid and bile tolerance, adhesion, antioxidants, and secondary metabolite production, whereas no functional genes related to enterotoxins or transferable antibiotic resistance were detected, thereby confirming the probiotic properties of B. velezensis K12. B. velezensis K12 exhibits broad-spectrum bacteriostatic activity and in vitro safety, positioning it as a potential candidate strain for developing probiotic Bacillus preparations.

Tabrizicola caldifontis sp. nov., Isolated from Hot Spring Sediment Sample

A Gram-stain-negative, ovoid to rod-shaped, aerobic, non-motile bacterial strain, designated YIM 73028T, was isolated from a sediment sample collected from a hot spring in Tibet, China. Phylogenetic analysis (based on the 16S rRNA gene sequences) indicated that strain YIM 73028T belongs to the genus Tabrizicola and showed the highest sequence similarity to the type strain of Tabrizicola aquatica (97.0%). Growth occurred at 30-50 °C (optimum, 37-45 °C) and pH 6.5-8.5 (optimum, pH 7.0-7.5). The respiratory isoprenoid quinone was ubiquinone Q-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, unidentified amino lipid and unidentified lipid. The major cellular fatty acids (> 10%) were C18:1 ω7c, C18:1 ω7c 11-methyl, C16:0 and C18:0. The genomic DNA G + C content was 65.7%. The average nucleotide identity value between strain YIM 73028T and type species of Tabrizicola aquatica was lower than 95-96% threshold recommended for distinguishing novel prokaryotic species. Based on the phenotypic, physiological, chemotaxonomic, genotypic, and phylogenetic data, strain YIM 73028T represents a novel species of the genus Tabrizicola, for which the name Tabrizicola caldifontis sp. nov. is proposed. The type strain is YIM 73028T (= KCTC 52713T = CGMCC 1.16151T).

Characterization and anti-biofilm potentiality of an isolated novel Aeromonas hydrophila-infecting bacteriophage AHPMCC11, belonging to the genus Ahphunavirus

Aeromonas hydrophila is a major aquatic habitat pathogen responsible for huge economic losses in the aquaculture and food industries. In this study, a lytic bacteriophage AHPMCC11 was isolated by using A. hydrophila MTCC 1739. AHPMCC11 showed a short latent period of 10 min and the burst size was 215 PFU/cell. AHPMCC11 had potent bacteriolytic activity within 2 h in liquid culture inhibition assay and exhibited biofilm scavenging activity against A. hydrophila MTCC 1739. AHPMCC11 was found stable at a wide range of pH levels (3-12), temperature ranges (4-37 °C), and salinity conditions (0-40 ppt). The AHPMCC11 genome was determined to be 42,439 bp in length with 58.9 % G + C content, 51 CDS, and no tRNA. Comparative genome study suggested that AHPMCC11 may represent a novel species within the Autographiviridae family, belonging to the Ahphunavirus genus. In conclusion, AHPMCC11 might be used as a biocontrol agent in aquaculture and the food industry.

Quasi-species prevalence and clinical impact of evolving SARS-CoV-2 lineages in European COVID-19 cohorts, January 2020 to February 2022

BackgroundEvolution of SARS-CoV-2 is continuous.AimBetween 01/2020 and 02/2022, we studied SARS-CoV-2 variant epidemiology, evolution and association with COVID-19 severity.MethodsIn nasopharyngeal swabs of COVID-19 patients (n = 1,762) from France, Italy, Spain, and the Netherlands, SARS-CoV-2 was investigated by reverse transcription-quantitative PCR and whole-genome sequencing, and the virus variant/lineage (NextStrain/Pangolin) was determined. Patients' demographic and clinical details were recorded. Associations between mild/moderate or severe COVID-19 and SARS-CoV-2 variants and patient characteristics were assessed by logistic regression. Rates and genomic locations of mutations, as well as quasi-species distribution (≥ 2 heterogeneous positions, ≥ 50× coverage) were estimated based on 1,332 high-quality sequences.ResultsOverall, 11 SARS-CoV-2 clades infected 1,762 study patients of median age 59 years (interquartile range (IQR): 45-73), with 52.5% (n = 925) being male. In total, 101 non-synonymous substitutions/insertions correlated with disease prognosis (severe, n = 27; mild-to-moderate, n = 74). Several hotspots (mutation rates ≥ 85%) occurred in Alpha, Delta, and Omicron variants of concern (VOCs) but none in pre-Alpha strains. Four hotspots were retained across all study variants, including spike:D614G. Average number of mutations per open-reading-frame (ORF) increased in the spike gene (average < 5 per genome in January 2020 to > 15 in 2022), but remained stable in ORF1ab, membrane, and nucleocapsid genes. Quasi-species were most prevalent in 20A/EU2 (48.9%), 20E/EU1 (48.6%), 20A (38.8%), and 21K/Omicron (36.1%) infections. Immunocompromised status and age (≥ 60 years), while associated with severe COVID-19 or death irrespective of variant (odds ratio (OR): 1.60-2.25; p ≤ 0.014), did not affect quasi-species' prevalence (p > 0.05).ConclusionSpecific mutations correlate with COVID-19 severity. Quasi-species potentially shaping VOCs' emergence are relevant to consider.

Revealing the hidden diversity of Chlorella heliozoae-infecting giant viruses

A new level of viral complexity has emerged from the isolation of green algae-infecting chloroviruses from diverse aquatic environments around the world over the past few decades. This study focuses on describing and comparing the genomic features of gammachloroviruses, previously referred to as SAG-viruses. We present 24 novel isolates capable of forming plaques on lawns of Chlorella heliozoae SAG 3.83, including the first giant virus isolated from Greenland. Together with 13 previous isolates, these new viruses form a robust dataset that we used to investigate the genomic landscape and to test whether environmental conditions influence the species diversity of gammachloroviruses. Genome sizes range from 283 kbp to 385 kbp, with one new isolate having the smallest genome found in the genus Chlorovirus. Based on phylogenomics and global genome identity analysis, we defined 10 species of "Gammachlorovirus", half of which are represented by a single isolate. We observed a high level of genome synteny, and the tRNA islets maintain a distinct interspecific pattern, although some notable variations are evident. Our analysis reveals an open pan-genome composed of 681 COGs, more than 30% of which consist of uncharacterized genes, highlighting significant innovative genetic potential for these viruses. Our results suggest that the subgenus "Gammachlorovirus" exhibits the greatest genetic diversity among chloroviruses, with variability that is independent of geographic location. Overall, these findings underscore the considerable diversity within these ten newly defined species and the importance of isolating and characterizing chloroviruses from new locations worldwide to enhance our understanding of the ecology and evolution of this group of giant algal viruses.

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.

The Complete Genome Sequences of Bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo isolated using Microbacterium foliorum

We report the discovery and characterization of bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo, isolated from grass samples collected in Quincy, Massachusetts, using Microbacterium foliorum B-24224 as the isolation host. Based on gene content similarity, these phages are assigned to actinobacteriophage clusters ED2, ED1, EG, and EK2 respectively.

Complete genome sequence of Pseudoxanthomonas koreensis strain TDY-1, an odor-reducing bacterium isolated from livestock wastewater

We report the complete genome sequence of Pseudoxanthomonas koreensis TDY-1, an odor-reducing strain isolated from livestock wastewater on a pig farm. Its genome consists of a 2.97-Mb chromosome.

Complete genome sequence of Pseudomonas brenneri strain JD2-26, a potential pollutant-reducing bacterium isolated from a municipal solid waste landfill facility

We report here the complete genome sequence of Pseudomonas brenneri strain JD2-26 isolated from a municipal solid waste landfill facility. The genome consists of a 6.32-Mbp chromosome and a plasmid having a total of 6,100 genes, including 5,914 coding sequences.

Characterization and genomic analysis of Cronobacter sakazakii phage JC03, a new member of the genus Pseudotevenvirus

The Cronobacter sakazakii-infecting phage JC03 was isolated and characterized. Its genome is composed of 177,089 bp of double-stranded DNA, contains 268 predicted open reading frames (ORFs) and two tRNA genes, and it has a G + C content of 44.67%. The predicted ORFs were classified into functional groups, including DNA replication/modification, assembly/packaging, phage structure, host lysis, and hypothetical proteins, and no genes associated with antibiotic resistance or virulence were found. Based on the results of gene annotation, genome features, and comparative genomics, we propose that JC03 is a new member of the genus Pseudotevenvirus.

A novel roseosiphovirus infecting dinoroseobacter shibae DFL12T represents a new genus

Bacteria belonging to the Roseobacter clade are key players in marine ecosystems, contributing significantly to carbon and sulfur cycles. Marine viruses, particularly those targeting Roseobacter, play crucial roles in regulating microbial communities and biogeochemical processes. Despite their importance, phages infecting organisms of the Roseobacter clade remain poorly understood. In this study, a novel roseophage, vB_DshS-R26L (R26L), infecting Dinoroseobacter shibae DFL12T, was isolated and characterized in terms of physiological and genomic properties. R26L has siphovirus morphology with an elongated head and a long, non-flexible tail. The phage has a narrow host range and demonstrates a long infection cycle with a latent period of 3.5 h and a burst size of 22 plaque-forming units (PFU cell- 1). R26L possesses a circular, double-stranded DNA genome of 79,534 bp with a G + C content of 62.6%, encoding a total of 116 open reading frames. Notably, seven auxiliary metabolic genes (AMGs), including those related to phosphate metabolism and queuosine biosynthesis, were identified. Phylogenetic and taxonomic analyses revealed that R26L represents a new genus, with its highest intergenomic similarities being 54.7% to another roseophage (R5C). By elucidating the unique characteristics of R26L, this study highlights the complexity of phage infections and the genomic diversity of roseophages, offering valuable insights into the ecological significance of Roseobacter-phage interactions in marine environments.

Biological characterization of novel Escherichia coli O157:H7 phages and their bacteriostatic effects in milk and pork

Foodborne bacteria, particularly Escherichia coli (E. coli) O157:H7, are significant contributors to foodborne illnesses, with antibiotic overuse exacerbating the issue through the emergence of multidrug-resistant strains. This study investigated the potential of E. coli phages in food safety, examining their biological traits and bacteriostatic properties. Two phages (vB_EcoP_SD2, vB_EcoP_SD6) of E. coli O157:H7 were isolated from slaughterhouse sewage and characterized for morphology, genomic composition, phage phylogenetic tree, optimal multiplicity of infection (MOI), one-step growth curve, thermal and pH stability and antibacterial efficacy. The optimal MOIs of vB_EcoP_SD2 and vB_EcoP_SD6 was 0.1 and 0.01, and temperature range for maintaining activity was 4°C to 55°C. The host range of vB_EcoP_SD2 and vB_EcoP_SD6 was 65% (13/20) and 55% (11/20), which was partially complementary to each other (75%, 15/20). Notably, vB_EcoP_SD2 displayed a latent period of 10 min, a burst period of 80 min, and a burst volume of 80 PFU per cell, while vB_EcoP_SD6 had a burst volume of 10 PFU per cell. Comprehensive whole-genome analysis confirmed two phages has no presence of pathogenic factors or resistance genes. Genomic comparisons suggest vB_EcoP_SD2 and vB_EcoP_SD6, respectively, constituted a novel member of a new genus, Justusliebigvirus genus and Kayfunavirus genus which genome, respectively, was found to be 1,49,066 bp, 40,202 bp long with an average GC content of 37.5 and 49.8%. The phages effectively inhibited host bacteria in LB broth for at least 6 h and showed promise in inhibiting bacteria in milk and pork, which indicated that the two phages exhibited a favorable bacteriostatic effect on milk and pork within the first 6 h under the optimal MOI. In the milk bacteriostasis experiment, vB_EcoP_SD2 could reduce bacteria by 3.16 × 104 CFU/mL, and vB_EcoP_SD6 could reduce bacteria by 1.05 × 104 CFU/mL. Phage vB_EcoP_SD2 decreased bacteria by 1.14 × 104 CFU/mL, and vB_EcoP_SD6 decreased bacteria by 2.04 × 103 CFU/mL in the pork. There was no disparity in bacteriostatic effect of different MOI within the first 6 h, but bacteriostatic effect of all groups still remained different from that of the control group. This study indicates the two phages possess excellent biological characteristics, thereby providing a theoretical foundation for the subsequent development of natural fungicides.

Probiotic Characteristics and Whole Genome Analysis of Lactiplantibacillus plantarum PM8 from Giant Panda (Ailuropoda melanoleuca) Milk

Milk is a rich source of probiotics, particularly lactic acid bacteria (LAB), which have been shown to promote gut health, support the immune system, enhance digestion, and prevent pathogen colonization. This study aimed to isolate and identify LAB strains from giant panda (Ailuropoda melanoleuca) milk, evaluate their probiotic properties, and analyze the genomic characteristics of a promising strain. Thirteen LAB strains were isolated from 12 samples of giant panda milk. Among all LAB strains, Lactiplantibacillus plantarum PM8 (PM8) demonstrated probiotic properties and safety features. It exhibited strong growth performance, high antipathogenic activity against four pathogens, and strong survival rates under simulated gastrointestinal conditions. PM8 also showed excellent adhesion capabilities to Caco-2 cells. Additionally, safety assessment revealed no hemolysin production and minimal antibiotic resistance, making it a promising candidate for probiotic applications. The genome of PM8 consists of 3,227,035 bp with a GC content of 44.60% and contains 3171 coding sequences, including 113 carbohydrate-active enzyme genes and genes related to exopolysaccharides synthesis, vitamin B biosynthesis, adhesion, antioxidant activity, and bile salt hydrolysis. Notably, it contains genes involved in nonribosomally synthesized secondary metabolite and bacteriocin production. The genomic safety analysis confirmed that PM8 lacks the capacity to transmit bacterial antimicrobial resistance and is non-pathogenic to both humans and animals. These findings suggest that PM8 holds considerable potential for enhancing gut health and supporting the development of safe probiotic products.

A comprehensive safety assessment of a novel starter Weissella confusa M1 combining with whole-genome sequencing

At present, the range of starter cultures utilized in soybean fermented products is rather limited. In our prior research, it was discovered that Weissella confusa holds potential as a starter for soybean fermentation products. This study further probed into its entire genome and safety. Firstly, based on the safety assessment of the genome, we can gain a more profound understanding of gene functions, encompassing potential virulence factors, pathogenic traits, and glycosidase functions. The findings demonstrated that its gene function mainly concentrated on carbohydrate metabolism and amino acid metabolism, which further elaborated its capacity to ferment soybean products. Next, we verified that it did not possess genotoxicity through bacterial reversion mutation and in vitro mammalian cell micronucleus assays. Subsequently, the sensitivity of the antibiotic resistance gene to drugs was tested, and the results indicated that it was only resistant to vancomycin. Additionally, the determination results of extracellular enzymes were all negative, and the yield of biogenic amines was extremely low, with only weak α-hemolysis. Finally, in the acute toxicity test and subchronic toxicity test of mice, no adverse reactions associated with the tested substances were observed. In conclusion, it is demonstrated that Weissella confusa M1 is safe and can be utilized as a potential strain for food culture in the fermentation process.

The characterization of outer membrane vesicles (OMVs) and their role in mediating antibiotic-resistance gene transfer through natural transformation in Riemerella anatipestifer

Riemerella anatipestifer (R. anatipestifer, RA) is the etiological agent of duck serositis, an acute multisystemic disease in ducks that is globally distributed and causes serious economic losses in the duck industry. Despite exhibiting multidrug resistance, the transmission mechanism of its antibiotic resistance genes (ARGs) remains incompletely identified. To contribute to addressing this gap, in this study, outer membrane vesicles (OMVs) from the RA strain CH-1 were isolated and characterized to investigate their involvement in ARG transfer in RA. Sequencing and data analysis revealed that RA CH-1 OMVs had ∼2.04 Mb genomic size, representing 88.3 % of the RA CH-1 genomic length. Proteomic analysis showed that OMVs contained 577 proteins, representing 27.2 % of the bacterial proteins. Subsequent investigations demonstrated that OMVs from antibiotic-resistant strains transferred ARG fragments and plasmids to the sensitive strain RA ATCC11845, relying on the natural transformation system, and the transformants exhibited corresponding resistance. Overall, OMV-mediated horizontal transfer of ARGs serving as a significant mechanism for acquiring multiple resistance genes in R. anatipestifer.

The Genome Sequences of Baculoviruses from the Tufted Apple Bud Moth, Platynota idaeusalis, Reveal Recombination Between an Alphabaculovirus and a Betabaculovirus from the Same Host

The USDA-ARS collection of insect viruses at Beltsville, MD, USA, contains samples of an alphabaculovirus from larvae of the tufted apple bud moth, Platynota idaeusalis Walker, as well as a presumptive betabaculovirus from the same host species. The viruses in these samples-Platynota idaeusalis nucleopolyhedrovirus isolate 2680 (PlidNPV-2680) and Platynota idaeusalis granulovirus isolate 2683 (PlidGV-2683)-were characterized by electron microscopy of their occlusion bodies (OBs) and determination and analysis of their genome sequences. Scanning and transmission electron microscopy of the OBs revealed morphologies typical for alphabaculoviruses and betabaculoviruses. Sequencing viral DNA resulted in circular genomes of 121,881 bp and 106,633 bp for PlidNPV-2680 and PlidGV-2683, respectively. Similar numbers of ORFs (128 for PlidNPV-2680, 125 for PlidGV-2683) were annotated, along with ten homologous regions (hrs) in the PlidNPV-2680 genome and five intergenic regions of tandem direct repeats (drs) in the PlidGV genome. Phylogenetic inference from core gene alignments suggested that PlidMNPV-2680 represents a unique lineage within the genus Alphabaculovirus, while PlidGV-2683 was grouped with clade b betabaculoviruses. A comparison of the PlidNPV-2680 and PlidGV-2683 genomes revealed a 1516 bp region in PlidNPV-2680 that exhibited 97.5% sequence identity to a region of the PlidGV-2683 genome, suggesting that recombination had occurred recently between viruses from these lineages.

Exploring Viral Interactions in Clavibacter Species: In Silico Analysis of Prophage Prevalence and Antiviral Defenses

Clavibacter is a phytopathogenic genus that causes severe diseases in economically important crops, yet the role of prophages in its evolution, pathogenicity, and adaptation remains poorly understood. In this study, we used PHASTER, Prophage Hunter, and VirSorter2 to identify prophage-like sequences in publicly available Clavibacter genomes. Prophage predictions were checked by hand to make them more accurate. We identified 353 prophages, predominantly in chromosomes, with some detected phage-plasmids. Most prophages exhibited traits of advanced domestication, such as an unimodal genome length distribution, reduced numbers of integrases, and minimal transposable elements, suggesting long-term interactions with their bacterial hosts. Comparative genomic analyses uncovered high genetic diversity, with distinct prophage clusters showing species-specific and interspecies conservation patterns. Functional annotation revealed prophage-encoded genes were involved in sugar metabolism, heavy metal resistance, virulence factors, and antibiotic resistance, highlighting their contribution to host fitness and environmental adaptation. Defense system analyses revealed that, despite lacking CRISPR-Cas, Clavibacter genomes harbor diverse antiviral systems, including PD-Lambda-1, AbiE, and MMB_gp29_gp30, some encoded within prophages. These findings underscore the pervasive presence of prophages in Clavibacter and their role in shaping bacterial adaptability and evolution.

Chromosome-level genome assembly of Cyperus iria, an aggressive weed of rice

Cyperus iria is an aggressive weed of rice throughout the world. Until now, the reference genome of C. iria has not been published. Here, we completed the chromosome-level genome assembly of C. iria based on Illumina, PacBio and Hi-C reads. The assembled genome size of C. iria was 479.08 Mb with a contig N50 of 7.02 Mb. 68 pseudochromosomes were produced using Hi-C scaffolding, accounting for 99.65% of the assembled genome. The number of predicted protein-coding genes is 47,395, of which 93.26% were annotated, and 37.69% repetitive sequences were identified. Our study provided a valuable genomic resource for the molecular biology research and the management of C. iria.

Polysaccharide lyase PL3.3 possibly potentiating Clostridioides difficile clinical symptoms based on complete genome analysis of RT046/ST35 and RT012/ST54

Clostridioides difficile has rapidly become a major cause of nosocomial infectious diarrhea worldwide due to the misuse of antibiotics. Our previous study confirmed that RT046/ST35 strain is associated with more severe clinical symptoms compared to RT012/ST54 strain. We conducted genome comparison of the RT046/ST35 and RT012/ST54 strains using whole-genome sequencing technology. The RT046/ST35 strain had a genome length of 7,869,254 bp with a GC content of 29.49%. The original length of the RT012/ST54 strain was 7,499,568 bp with a GC content of 29.64%. Additionally, we detected plasmid1 in the RT046/ST54 strain. We found that the RT046/ST35 strain had more genomic islands compared to the RT012/ST54 strain, and we identified polysaccharide lyase (PL) in the region around 2.2 M. Furthermore, we discovered that the increased severity of clinical symptoms in the RT046/ST35 strain compared to the RT012/ST54 strain was unrelated to virulence factors and emphasized the potential crucial role of PL in RT046/ST35. There were almost no differences in eggNOG annotation and KEGG annotation between RT046/ST35 and RT012/ST54. RT046/ST35 had more mRNA processes in GO annotation. In conclusion, our study suggests that the core factor contributing to the more serious clinical symptoms of the RT046/ST35 strain compared to the RT012/ST54 strain is possibly PL.

Effector proteins of Funneliformis mosseae BR221: unravelling plant-fungal interactions through reference-based transcriptome analysis, in vitro validation, and protein‒protein docking studies

BACKGROUND

Arbuscular mycorrhizal (AM) fungi form a highly adaptable and versatile group of fungi found in natural and man-managed ecosystems. Effector secreted by AM fungi influence symbiotic relationship by modifying host cells, suppressing host defense and promoting infection to derive nutrients from the host. Here, we conducted a reference-based transcriptome sequencing of Funneliformis mosseae BR221 to enhance understanding on the molecular machinery involved in the establishment of interaction between host and AM fungi.

RESULTS

A total of 163 effector proteins were identified in F. mosseae isolate BR221, of these, 79.14% are extracellular effectors and 5.5% are predicted cytoplasmic effectors. In silico prediction using a pathogen-host interaction database suggested four of the 163 effectors could be crucial in establishing AM fungi-host interactions. Protein-protein docking analysis revealed interactions between these potential effectors and plant proteins known to be differentially expressed during mycorrhizal association, such as defensins, aquaporins, and PTO proteins. These interactions are multifaceted in modulating host physiological and defense mechanisms, including immune suppression, hydration, nutrient uptake, and oxidative stress modulation.

CONCLUSIONS

These findings of the current study provide a foundational understanding of fungal-host molecular interactions and open avenues for exploring pathways influenced by these effectors. By deepening our knowledge of these mechanisms, the use of AM fungi in biofertilizer formulations can be refined by selecting strains with specific effectors that enhance nutrient uptake, improve drought and disease resistance, and tailor the fungi's symbiotic efficiency to different crops or environmental conditions, thus contributing to more targeted and sustainable agricultural practices.

Genome sequences of two Klebsiella phages isolated from wastewater treatment samples that infect a clinical Klebsiella isolate

We announce the complete genomes of Klebsiella phages ValerieMcCarty03 and ValerieMcCarty04 isolated from wastewater treatment plant samples that infect a multidrug-resistant Klebsiella oxytoca clinical isolate. These phages belong to the T4-like cluster and fall within the Jiaodavirus genus.

Klebsiella pneumoniae Phage M198 and Its Therapeutic Potential

The rapid worldwide spread of antibiotic resistance is quickly becoming an increasingly concerning problem for human healthcare. Non-antibiotic antibacterial agents are in high demand for many Gram-negative bacterial pathogens, including Klebsiella pneumoniae. Klebsiella-targeting phages are among the most promising alternative therapy options. They have already been successfully applied in a number of cases, and it is expected that the need for anti-Klebsiella phages will only increase in the future. This prospect highlights the need for well-characterized therapeutic phages. In this work, we describe a K. pneumoniae phage, which also infects strains of Klebsiella oxytoca. Here, we characterize phage M198 in terms of its biological and genetic properties. Since in some phage therapy cases, phages are administered in combination with antibiotics, here, we also screen for possible synergistic effects of combining phage M198 with six different antibiotics. We found that phage M198 has good lytic activity against clinical isolates; it does not have any indications of a temperate lifestyle, and it has synergistic potential when combined with some therapeutically relevant antibiotics.

Vic9 mycobacteriophage: the first subcluster B2 phage isolated in Russia

Mycobacteriophages are viruses that specifically infect bacteria of the Mycobacterium genus. A substantial collection of mycobacteriophages has been isolated and characterized, offering valuable insights into their diversity and evolution. This collection also holds significant potential for therapeutic applications, particularly as an alternative to antibiotics in combating drug-resistant bacterial strains. In this study, we report the isolation and characterization of a new mycobacteriophage, Vic9, using Mycobacterium smegmatis mc (2)155 as the host strain. Vic9 has been classified within the B2 subcluster of the B cluster. Morphological analysis revealed that Vic9 has a structure typical of siphophages from this subcluster and forms characteristic plaques. The phage adsorbs onto host strain cells within 30 min, and according to one-step growth experiments, its latent period lasts about 90 min, followed by a growth period of 150 min, with an average yield of approximately 68 phage particles per infected cell. In host range experiments, Vic9 efficiently lysed the host strain and also exhibited the ability to lyse M. tuberculosis H37Rv, albeit with a low efficiency of plating (EOP ≈ 2 × 10-5), a typical feature of B2 phages. No lysis was observed in other tested mycobacterial species. The genome of Vic9 comprises 67,543 bp of double-stranded DNA and encodes 89 open reading frames. Our analysis revealed unique features in Vic9, despite its close relationship to other B2 subcluster phages, highlighting its distinct characteristics even among closely related phages. Particularly noteworthy was the discovery of a distinct 435 bp sequence within the gene cluster responsible for queuosine biosynthesis, as well as a recombination event within the structural cassette region (Vic_0033-Vic_0035) among members of the B1, B2, and B3 subclusters. These genetic features are of interest for further research, as they may reveal new mechanisms of phage-bacteria interactions and their potential for developing novel phage therapy methods.