Search Results (281)

Background/Objectives: The bacterium Brochothrix campestris is closely related to Brochothrix thermosphacta, a known food spoilage agent, and Listeria monocytogenes, the causative agent of listeriosis. B. campestris garnered attention several years ago because it produces brochocin-C, a bacteriocin capable of inhibiting the growth of certain pathogens. It has been recently suggested that phages play a significant role in the evolution of B. thermosphacta, similar to the role they play for L. monocytogenes. However, understanding the role of phages in the evolution of B. campestris has been challenging because only a draft of genome sequences of a single B. campestris strain was previously available. Methods: In this study, DNA from the B. campestris type strain DSM 4712 was sequenced using Oxford Nanopore and Illumina technologies to obtain complete, high-quality genome sequences. Results: The assembly revealed the presence of a plasmid and a phage-plasmid. Additionally, chromosomal analysis identified several genomic islands, including one harboring the brochocin genes, suggesting that these genes may have undergone horizontal transfer. Conclusions: This study underscores the potential importance of phages in the evolution of B. campestris, and also highlights the need for further research into the interactions between Brochothrix species and their associated phages to better understand these complex biological relationships. Full article

Background/Objectives: Sepiella japonica is a highly adaptable cephalopod with an advanced nervous system and complex reproductive behavior, capable of reproducing two to three generations annually depending on water temperature. However, the absence of a complete genome assembly has limited molecular investigations of its unique biological characteristics. This study aimed to perform a genome survey of female and male S. japonica, systematically characterize and compare key genomic characteristics. Methods: Quality-filtered short reads enabled K-mer-based estimation of genome size, heterozygosity, repeat content, and GC content; generation of draft genome assemblies, SSR identification from the draft assemblies, complete mitogenome assemblies and annotations with ML phylogeny based on 13 concatenated PCGs, and PSMC-based demographic inference. Results: The estimated genome sizes were 4317 Mb (female) and 4222 Mb (male), with revised estimates of 4310 Mb and 4215 Mb, respectively. K-mer analysis revealed heterozygosity rates of 0.85% (female) and 0.77% (male) and repeat content of 76.05% (female) and 75.91% (male). The assembled genome sizes were 4197 Mb for females (N50: 508 bp) and 4206 Mb for males (N50: 511 bp); the GC content was 34.15% for both genomes. Deduplicated data showed GC content of 35.16% (female) and 35.27% (male). Microsatellite analysis revealed that mononucleotide repeats were the most abundant simple sequence repeat motif. The mitochondrial genome sequences measured 16,729 bp for the female genome and 16,725 bp for the male genome. Conclusions: This study provides fundamental data for subsequent high-quality whole-genome assembly and comparative analysis of female and male genomes. Full article

Background/Objectives: Actinobacillus pleuropneumoniae is an important respiratory tract pathogen of swine worldwide. Insertion sequences (ISs) play a major role in the transfer of antimicrobial resistance (AMR) among various porcine respiratory tract pathogens. In this study, three A. pleuropneumoniae genomes were investigated for the presence of a novel IS. Methods: Analysis of the draft genomes of three A. pleuropneumoniae serovar 8 isolates (AP_1, AP_120, AP_123) suggested the presence of a novel IS. A closed whole-genome sequence was generated for strain AP_123 by hybrid assembly of Oxford Nanopore MinION long-reads and Illumina MiSeq short-reads, followed by sequence analysis using standard online tools. Transfer was tested by natural transformation. Antimicrobial susceptibility testing was conducted by broth microdilution following Clinical and Laboratory Standards Institute standards. Results: A novel IS, designated ISApl4, was detected in all three genomes. ISApl4 is 712 bp in size and has a transposase gene (tnp) of 654 bp. Moreover, it has perfect terminal 14-bp inverted repeats and produces 8-bp direct repeats at its integration site. This IS was found in 39 copies in the AP_123 genome, two of which formed the 5,765-bp pseudo-compound transposon Tn7560. This transposon carries four AMR genes: sul2 (sulfonamide resistance), strA-strB (streptomycin resistance), and tet(Y) (tetracycline resistance). RT-PCR confirmed tnp gene expression and horizontal transfer of Tn7560 into A. pleuropneumoniae MIDG2331. Conclusions: This study identified the novel ISApl4 in porcine A. pleuropneumoniae and its association with the novel pseudo-compound transposon Tn7560, which proved to be an active element capable of disseminating multidrug resistance amongst A. pleuropneumoniae. Full article

Bacillus cereus AS_3 and Bacillus cereus AS_5 are bacterial endophytes isolated from sterilized leaves of the medical plant Alectra sessiliflora, which were previously identified using 16S rRNA sequencing. Here, we present the whole-genome sequencing and annotation of strains AS_3 and AS_5, the first genome report of Bacillus cereus strains from A. sessiliflora. The genome of strain AS_3 has 59 contigs, 5 503 542 bp draft circular chromosome, an N₅₀ of 211,274 bp, and an average G+C content of 35.2%; whereas strain AS_5 has 38 contigs, 5,510,121 bp draft circular chromosome, an N₅₀ of 536,033 bp, and an average G+C content of 35.2%. A total of 5679 protein-coding genes, 62 genes coding for RNAs, and 122 pseudogenes in the strain AS_3 genome were identified by the National Center for Biotechnology Information Prokaryotic Annotation pipeline, whereas a total of 5688 gene protein-coding genes were identified in AS_5, with 60 genes coding for RNAs and 120 pseudogenes. Phenotypic analysis and whole-genome sequencing analysis showed that AS_3 and AS_5 share similar characteristics, including Gram-positive, motile, rod-shaped, and endospore-forming have shown a high sequence similarity with Bacillus cereus, type strain ATCC 14579^T. Strains AS_3 and AS_5 had genomic digital DNA–DNA hybridization (dDDH) with the type strain Bacillus cereus ATCC 14579^T of 85.8% and 86%, respectively, and average nucleotide identities (ANIs) of 98% and 98.01%, respectively. Phylogenomic analysis confirmed that strains AS_3 and AS_5 share very similar genomic and phenotypic characteristics, and are closely related to the type strain Bacillus cereus type strain ATCC 14579^T, supporting their classification within the Bacillus cereus species. A total of 10 secondary metabolite gene clusters, including siderophore type petrobactin, terpene type molybdenum cofactor, non-ribosomal peptide synthetase (NRPS) type bacillibactin, and β-lactone type fengycin, were predicted using AntiSMASH software (version 5.0). Putative genes potentially involved in bioremediation and endophytic lifestyle were identified in the genome analysis. Genome sequencing of Bacillus cereus AS_3 and Bacillus cereus AS_5 has provided genomic information and demonstrated potential biotechnological applications. Full article

Excessive alcohol consumption is associated with systemic health risks due to the production of acetaldehyde, a primary carcinogen that not only pollutes the environment but also endangers human health. In this study, a promising bacterial strain for biodegrading both ethanol and acetaldehyde was successfully isolated from the traditional fermented food Jiaosu and identified as Acetobacter ghanensis JN01 based on average nucleotide identity (ANI) analysis. Initial ethanol of 1 g/L was completely biodegraded within 4 h, while initial acetaldehyde of 1 g/L was also rapidly removed at 2 or 1 h by whole cells or cell-free extracts (CEs) of JN01, respectively, which indicated that JN01 indeed has a strong ability in the biodegradation of both ethanol and acetaldehyde. Whole-genome sequencing revealed a 2.85 Mb draft genome of JN01 with 57.0% guanine–cytosine (GC) content and the key metabolic genes (adh1, adh2, and aldh) encoding involving alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), co-located with NADH dehydrogenase genes and ethanol-responsive regulatory motifs, supporting the metabolic pathway of transforming ethanol to acetaldehyde, and, subsequently, converting acetaldehyde to acetic acid. Furthermore, selected in vitro safety-related traits of JN01 were also assessed, which is very important in the development of microbial catalysts against both ethanol and acetaldehyde. Full article

Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation—differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966^T) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings. Full article

The date palm (Phoenix dactylifera L.) is a key crop in the arid regions of North Africa and the Middle East, with substantial socioeconomic value. Although multiple genome assemblies have been generated using next-generation sequencing (NGS) technologies, they primarily focus on Middle Eastern cultivars, leaving North African varieties unrepresented. This study aims to address this gap by sequencing and assembling the first genome of a North African date palm using Illumina sequencing technology. We present a draft genome assembly of the elite Tunisian variety Deglet Nour. By comparing it with the Barhee BC4 reference genome, we identify key genetic variants, including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), potentially associated with ripening processes and fruit quality. This work expands the genomic resources for date palm research, particularly for North African cultivars, and provides new insights into the nucleotide-level variability of the genes linked to key agronomic traits. Full article

Strain 53B2 was isolated from a commercial maize (Zea mays L.) field located in the Yaqui Valley, Mexico. Its draft genome comprises 5,844,085 bp, with a G + C content of 37.5%, an N50 of 602,122 bp, an L50 of 4, and a total of 129 contigs. Genome-based taxonomic affiliation showed this strain belonged to Priestia megaterium. Genome annotation revealed 6394 coding DNA sequences (CDSs), organized into 332 subsystems. Among these, several CDSs were associated with traits relevant to plant growth promotion, including categories such as iron acquisition and metabolism (40 CDSs) and secondary metabolism (6 CDSs), among others. In vitro metabolic assays supported genomic predictions, confirming the strain’s ability to produce IAA, solubilize phosphate, and tolerate abiotic stress. Additionally, greenhouse trials demonstrated that inoculation with Priestia megaterium 53B2 significantly enhanced plant growth parameters (p ≤ 0.05) versus uninoculated control: stem height increased by 22.8%, root length by 35.7%, stem and root fresh weights by 39.6% and 66.1%, and stem and root dry weights by 33.7% and 44.7%, respectively. This first report on the beneficial potential of Priestia megaterium 53B2 highlights its potential as a sustainable bioinoculant for maize cultivation. Full article

Sparganosis is a neglected food- and water-borne zoonotic disease caused by members of the tapeworm genus Spirometra. More than 1600 human cases have been reported in the literature, primarily in Korea and China; however, the clinical significance of sparganosis is likely underestimated. The control of this disease is challenging in endemic regions because of the complexity of its lifecycle and the involvement of many animal host species, and treatment of clinical disease in humans and animals with selected drugs (e.g., mebendazole and/or praziquantel), even at elevated doses, is often ineffective, such that novel interventions are needed. It is anticipated that the use of molecular technologies should allow the identification of new intervention targets in crucial biological processes and/or pathways of Spirometra spp. While some draft genomes of Spirometra have been produced, their assemblies are incomplete. Here, we employed an advanced DNA sequencing–informatic approach to assemble and annotate the first high-quality genome of an isolate of Spirometra from Australia, with chromosome-level contiguity and a curated gene set. This improved genome provides a useful resource to support fundamental and applied molecular investigations of Spirometra species and should assist in the design of new tools for the intervention against sparganosis of companion animals (including dogs and cats) and humans. Full article

The whole-genome sequencing of lactic acid bacteria provides a valuable resource for identifying the genetic determinants underlying molecular mechanisms related to their probiotic properties. Analysis of draft genome sequences relies on bioinformatics tools for genetic data processing and in silico analytical methods to pinpoint the genetic determinants encoding biologically active compounds. The aim of this study was to perform the phenotypic determination of the antibiotic sensitivity and bioinformatics analyses on whole-genome assemblies from LAB from the human oral microbiome, and determine the presence of acquired antibiotic resistance genes, peptidases, adhesion proteins, and bacteriocins. Bioinformatics processing was performed in order to establish the molecular mechanisms responsible for the previously observed probiotic properties. The tested LAB strains exhibited a broad spectrum of antibiotic multiresistance, but did not possess acquired antibiotic resistance genes. The detected genes for peptidase activity were from the Pep family of hydrolase enzymes. Genetic determinants for adhesion proteins contained LPxTG, YSIRK, KxYKxGKxW, and SEC 10/PgrA domains, as well as MucBP domains. Lectins were found for five of the strains with the presence of WxL domains from the CscC protein family and L-type lectin domains. The in silico analyses show that some of the tested strains possessed mechanisms for bacteriocin production. Full article

Hyperuricemia arises from urate overproduction and/or underexcretion. Probiotics offer the potential for alleviating hyperuricemia by degrading urate precursors. This study characterized Enterococcus faecium YC07 isolated from the traditional Chinese fermented food Jiangshui, which demonstrated efficient biodegradation of nucleosides (urate precursors), converting 2.0 g/L to nucleobases within 48 h. Whole genome sequencing revealed a 2.53 Mb draft genome (59 contigs, 38.21% GC content) containing 2387 protein-coding genes. Genomic and phenotypic analysis confirmed its probiotic potential, including high tolerance of simulated gastric fluid (98.89% survival) and intestinal fluid (44.51% survival), and strong adhesion capacity (24.16% auto-aggregation, 35.48% hydrophobicity), pathogen inhibition, and antioxidant activity. The identified antibiotic resistance genes and virulence factors were assessed alongside acute oral toxicology, cytotoxicity, antibiotics susceptibility, hemolysis, and enzymatic activity assays, confirming safety. Furthermore, successful pilot-scale fermentation in a 100 L fermenter demonstrated industrial feasibility. These findings established E. faecium YC07 as a safe and effective probiotic candidate for functional foods targeting hyperuricemia management. Full article

Fusarium oxysporum f. sp. cubense (Foc) causes Fusarium wilt, a devastating epidemic disease that has caused widespread damage to banana crops worldwide. We report the draft genomes of Foc race 1 (16117) and Foc tropical race 4 (Fusarium odoratissimum) (CNSD1) isolates from China, assembled using PacBio HiFi sequencing reads, with functional annotation performed. The strains group in distinct lineages within the Fusarium oxysporum species complex. This genetic resource will contribute towards understanding the pathogenicity and evolutionary dynamics of Foc populations in banana-growing regions around the world. Full article

Three isolates of a novel, rapidly growing, non-pigmented Mycobacterium species were recovered from the water and runoff of a public fountain in a rural village in central Portugal, formerly used by the local population as a source of drinking water and not accessible to animals. High-quality draft genome sequencing, in silico DNA–DNA hybridization, and phylogenetic analyses confirmed that isolates 21AC1^T, 21AC14, and 21AC21 represent a previously undescribed species within the genus Mycobacterium, forming a distinct phylogenetic lineage closely related to Mycobacterium wolinskyi, Mycobacterium goodii and Mycobacterium smegmatis. MALDI-TOF MS analysis of the type strain 21AC1^T revealed a unique spectral profile. A comprehensive polyphasic characterization was performed, including chemotaxonomic analyses of fatty acid and mycolic acid composition, as well as an extensive biochemical characterization. Their susceptibility to 12 antimicrobials was also assessed. The identification and characterization of novel nontuberculous mycobacteria species are of increasing environmental and clinical relevance, as infections by these opportunistic pathogens are on the rise globally. Based on our findings, we propose that isolates 21AC1^T, 21AC14, and 21AC21 represent a novel species, for which we propose the name Mycobacterium appelbergii sp. nov., with the type strain designated as 21AC1^T (=BCCM/ITM 501212 = DSM 113570) and the additional two strains as 21AC14 (=BCCM/ITM 501447 = DSM 118402) and 21AC21 (=BCCM/ITM 501448 = DSM 118403). Full article

Understanding the mechanisms of sexual development would pave the way for producing mono-sex populations to aid the aquaculture industry. This study investigates the functions of the Y-linked iDmrt1 paralogue (Po-iDMY) and insulin-like androgenic gland hormone (Po-IAG) in the process of sexual development in the tropical rock lobster, Panulirus ornatus (TRL). Previously, we identified that Po-iDMY, a male-specific heterogametic (Y-linked) paralogue of the autosomal Po-iDmrt1 found in TRL, is a second sex-linked iDmrt gene identified in invertebrates. Using 5′ and 3′ rapid amplification of cDNA ends and data from a draft male genome (with an assembly genome size of approximately 2.446 Gbp and 87% BUSCO completeness), we obtained the full-length Po-iDMY gene (encoding a protein of 312 amino acids). A 411 bp male-specific sequence located at the 3′ untranslated region of Po-iDMY mRNA was used as a sex marker, which was reported for the first time in our draft genome. However, Po-iDMY is not a master sex-determining factor since it was not expressed across developmental stages of embryos, juveniles and adults. Instead, we silenced Po-IAG at an early juvenile stage, generating two potential neo-females, implying that sexual manipulation could be a promising technique in TRL. Full article

The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. A Gram-positive, pink-pigmented Streptomyces strain designated HC307^T was isolated from a soil sample collected in Xizang (Tibet), China. The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. In this study, the 16S rRNA sequence of strain HC307^T exhibited the highest similarity with Streptomyces prasinosporus NRRL B-12431^T (97.5%) and Streptomyces chromofuscus DSM 40273^T (97.3%), which were below 98.7%. The draft genome of the bacteria was 10.0 Mb, with a G+C content of 70.0 mol%. The average nucleotide identity (ANI) values of strain HC307^T and similar type strains ranged from 78.3% to 87.5% (<95%). The digital DNA-DNA hybridization (dDDH) values ranged from 22.6% to 33.9% (<70%), which was consistent with the results obtained from phylogenetic tree analysis. Phenotypically, this bacterium grew within the temperature range of 25–40 °C, at a pH range of 5 to 9, and in NaCl concentrations from 0% to 6% (w/v). The polar lipid profile of strain HC307^T was diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The analysis of 32 biosynthetic gene clusters (BGCs) indicated the strain’s capacity to synthesize diverse compounds. Phylogenetic and phenotypic analyses demonstrated that strain HC307^T represented a novel species within the genus Streptomyces, and proposed the name Streptomyces flavusporus sp. nov., with strain HC307^T (=DSM 35222^T=CGMCC 32047^T). The strain was deposited in Deutsche Sammlung von Mikroorganismen und Zellkulturen and the China General Microbiological Culture Collection Center for patent procedures under the Budapest Treaty. Full article