Comprehensive whole-genome analysis of Streptococcus infantarius strains from Moroccan farmhouse dairy products: Genomic insights into dairy adaptation, safety, and biotechnological potential.

Cereibacter sphaeroides strains S3W10 and SS15, isolated from shrimp ponds, exhibit potential probiotic benefits for aquaculture. In this study, the genomic features of S3W10 and SS15 were thoroughly characterized to evaluate their probiotic properties and safety for aquaculture use. The genomes of S3W10 and SS15 consist of 130 and 74 contigs, with sizes of 4.6 Mb and 4.4 Mb and GC contents of 69.2%. Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomic analyses confirmed that these strains belong to C. sphaeroides. Genome annotation predicted 4260 coding sequences (CDS) in S3W10 and 4086 CDS in SS15, including genes associated with stress tolerance, nutrient absorption, and antioxidant activity. Notably, genes related to vitamin B12 synthesis, digestive enzyme production, and carotenoid biosynthesis, which support shrimp health, were identified in both genomes. CAZyme analysis identified 116 and 115 carbohydrate-active enzymes in S3W10 and SS15, respectively, supporting adaptation to gastrointestinal environments and the host immune response. Pan-genome analysis across C. sphaeroides strains revealed 7918 gene clusters, highlighting the open pan-genome structure of this species and its high genetic diversity. Further bioinformatic analyses assessing mobile genetic elements, antibiotic-resistance genes, and virulence factors demonstrated the safety of both strains for aquaculture, as no plasmids or virulence genes were identified. The genomic insights in this study provide a deeper understanding of the strains' adaptability and functional potential, aligning with previous in vitro and in vivo studies and highlighting their potential for use in shrimp cultivation.

Lactiplantibacillus species have been historically used for food applications. Although several species are regarded as safe according to their regulatory status, the safety issues and functional roles of these lactic acid bacteria have been given attention. A selected Lactiplantibacillus strain TBRC 20328, with probiotic properties isolated from fermented Isan-style pork sausage (Mam), was evaluated for its safety through whole-genome sequencing and analysis using integrative bioinformatics tools. The metabolic genes were assessed through comparative genome analysis among Lactiplantibacillus species. The genome of the strain TBRC 20328 consisted of one circular chromosome (3.49 Mb) and five plasmids (totaling 0.25 Mb), encoding 3056 and 284 protein-coding genes, respectively. It exhibited an average nucleotide identity (ANI) with other Lactiplantibacillus pentosus strains of over 95%. Whole-genome analysis confirmed the absence of virulence and antimicrobial resistance genes, supporting its safety for food applications. Functional annotation revealed clusters for bacteriocins (plantaricin EF and pediocin) and polyketides, indicating potential roles in biopreservation and host interactions. Genes involved in the biosynthesis of some short-chain fatty acids and exopolysaccharides were also identified. Comparative genomic analysis across 33 other Lactiplantibacillus strains identified 2380 orthogroups, with 94 unique to the Lp. pentosus group. These included gene clusters involved in malonate decarboxylation, leucine biosynthesis, and 5-oxoprolinase activity. Such distinct genomic features emphasize the sustainable biotechnological potential and safety of Lp. pentosus TBRC 23028. Together, the findings highlight its promise as a safe and functional probiotic candidate with broad applications in functional food development and precision fermentation technologies.

The growing threat of antimicrobial resistance underscores the urgent need to identify new bioactive compounds. In this study, a Streptomyces strain, ACT158, was isolated from a Ramsar wetland ecosystem and found to exhibit broad-spectrum effects against Gram-positive and Gram-negative bacteria, as well as fungal pathogens. The active strain was characterized as S. cavourensis according to its morphology, phylogenetic analysis, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH). Whole-genome sequencing (WGS) and annotation revealed a genome size of 6.86 Mb with 5122 coding sequences linked to carbohydrate metabolism, secondary metabolite biosynthesis, and stress responses. Genome mining through antiSMASH revealed 32 biosynthetic gene clusters (BGCs), including those encoding polyketides, nonribosomal peptides, and terpenes, many of which showed low similarity to known clusters. Comparative genomic analysis, showing high genomic synteny with closely related strains. Unique genomic features of ACT158 included additional BGCs and distinct genes associated with biosynthesis pathways and stress adaptation. These findings highlight the strain's potential as a rich source of bioactive compounds and provide insights into its genomic basis for antimicrobial production and its ecological and biotechnological significance.

BackgroundRare actinomycetes, particularly Gordoni spp., are emerging as critical sources of bioactive metabolites and opportunistic pathogens.ResultsIn this study, we isolated three novel Gordonia strains from soil samples and characterized their taxonomic status using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA genes and whole-genome comparisons indicated that strains CPCC 205333 T, CPCC 205515 T, and CPCC 206044 T represent three distinct novel species. The overall genome relatedness indices of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between these studied strains and their related type strains of the genus Gordonia were all below the established thresholds for species delineation, confirming the classification of these three as novel species, for which we propose the names Gordonia altitudinis sp. nov., Gordonia ligustrum sp. nov., and Gordonia pistacia sp. nov., respectively. Functional annotation revealed their ecological versatility, with Gordonia spp. contributing significantly to soil microbiome functionality through plant growth-promoting traits (e.g., nitrogen fixation, siderophore production) and biosynthetic gene clusters (BGCs), while also harboring virulence factors. Pan-genomic analysis of 225 Gordonia strains delineated an open gene pool (α = 0.82; 22% fluidity), reflecting adaptive plasticity. Core genomes were enriched in conserved metabolic pathways, whereas accessory and strain-specific genes showed niche-driven functional diversification, suggesting ecological specialization.ConclusionThese findings expand the genomic and functional understanding of Gordonia, highlighting its dual role in environmental resilience and pathogenicity, with potential applications in biotechnology and microbiome engineering.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04362-0.

Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya.

Improved understanding of the genetic basis of Campylobacter spp. colonization of poultry at specific growth stage is the key to developing a farm-based strategy to prevent flock colonization. In this study, 39 Campylobacter spp. strains (chicken isolates, n = 29; environmental isolates, n = 10) were collected from six marked chickens at the growth stage from week 7 to week 13. Then, we use comparative genomics techniques to analyze the temporal genomic characteristics of Campylobacter spp. in individual chickens across a production cycle. Genotype, average nucleotide identity (ANI), and phylogenetic trees all indicated the evolutionary relationships between the strains from different sampling weeks. The clustering of isolates was not dependent on sampling time and sample source, indicating that strains could persist over several weeks in a flock. Notably, 10 antimicrobial resistance (AMR) genes were identified in the genome of Campylobacter coli isolates, and the genomes of isolates sampled at week 11 harbored fewer AMR genes and insertion sequences (IS) than the isolates from other weeks. Consistent with this, pangenome-wide association analysis demonstrated that gene acquisition and loss could happen at week 11 and week 13. These genes were mainly associated with cell membrane biogenesis, ion metabolism, and DNA replication, suggesting that genomic change may be related to Campylobacter adaptive response. This is a novel study focused on the genetic changes occurring in Campylobacter spp. isolates in a particular space and time; it highlights that accessory genes and AMR genes were overall stable at chicken farm, which will help us understand the survival and the transmission route of Campylobacter spp. better, and have the potential to inform the strategy on the safety control of market-ready chickens.

The mechanisms underlying the survival of bacteria in low temperature and high radiation are not yet fully understood. Nakamurella sp. PAMC28650 was isolated from a glacier of Rwenzori Mountain, Uganda, which species belonged to Nakamurella genus based on 16S rRNA phylogeny, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis among Frankineae suborder. We conducted the whole genome sequencing and comparative genomics of Nakamurella sp. PAMC28650, to understand the genomic features pertaining to survival in cold environment, along with high UV (ultraviolet) radiation. This study highlights the role of polysaccharide in cold adaptation, mining of the UV protection-related secondary metabolites and other related to cold adaptation mechanism through different bioinformatics tools, and providing a brief overview of the genes present in DNA repair systems. Nakamurella sp. PAMC28650 contained glycogen and cellulose metabolism pathways, mycosporine-like amino acids and isorenieratene-synthesizing gene cluster, and a number of DNA repair systems. Also, the genome analysis showed osmoregulation-related genes and cold shock proteins. We infer these genomic features are linked to bacterial survival in cold and UV radiation.

Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study its genomic characteristics and metabolic potential, linked to environmental adaptation and the production of secondary metabolites with possible biotechnological applications. Whole-genome sequencing, assembly, phylogenetic analysis, functional annotation, and genomic islands prediction were performed to determine the taxonomic affiliation and differential characteristics of the strain So.54. Additionally, Biosynthetic Gene Clusters (BGCs) responsible for secondary metabolites production were identified. The assembled genome of strain So.54 has 3,871,805 bp with 66.0% G + C content. Phylogenetic analysis confirmed that strain So.54 belongs to the Pseudarthrobacter genus; nevertheless, its nucleotide and amino acid identity values were below the species threshold. The main metabolic pathways and 64 genomic islands associated with stress defense and environmental adaptation, such as heavy metal resistance genes, were identified. AntiSMASH analysis predicted six BGCs with low or no similarity to known clusters, suggesting potential as novel natural products. These findings indicate that strain So.54 could be a novel Pseudarthrobacter species with significant environmental adaptation and biotechnological potential.

Lactiplantibacillus pentosus 9D3, a prominent gamma-aminobutyric acid (GABA)-producing bacteria isolated from Thai pickled weed was characterized for its safety and probiotic properties via whole-genome analysis and in vitro testing. The whole-genome sequence of L. pentosus 9D3 was determined using a hybrid-sequencing approach, combining PacBio and Illumina technologies. A 3.81-Mbp genome of L. pentosus 9D3 consisting of one 3.65-Mbp chromosome and six plasmids (1.9–71.9 Kbp) was identified with an estimated GC content of 46.09% and 3,456 predicted genes. The strain was confirmed to be Lactiplantibacillus pentosus according to the high average nucleotide identity value of >95% and digital DNA–DNA hybridization scores of >70% to the L. pentosus type strain. Comparative genome analysis with other L. pentosus strains showed that the GABA-producing capability was specific to the strain 9D3. Genes related to GABA biosynthesis and transport were identified on a plasmid, pLPE-70K, indicating the acquired nature of this property. The safety of L. pentosus 9D3 was demonstrated through the lack of genes related to the production of toxins, biogenic amines, and antimicrobial drugs. Although the strain exhibited resistance to ampicillin and chloramphenicol, none of the antimicrobial resistance (AMR) genes were associated with mobile elements, i.e., plasmids and prophages. Therefore, the strain is considered to have low risk of transferring the AMR genes to other, potentially pathogenic bacteria. In addition, L. pentosus 9D3 showed good survivability in the gastrointestinal tract environment and was able to adhere to the intestinal cell in vitro. Therefore, L. pentosus 9D3 is concluded to be safe, with the potential to be used as a probiotic, exerting its health benefit through GABA production in the food system. The GABA-producing capability of the strain in vivo is the subject of further investigation.

Motility is achieved in most bacterial species by the flagellar apparatus. It consists of dozens of different proteins with thousands of individual subunits. The published literature about bacterial chemotaxis and flagella documented 51 protein–protein interactions (PPIs) so far. We have screened whole genome two-hybrid arrays of Treponema pallidum and Campylobacter jejuni for PPIs involving known flagellar proteins and recovered 176 and 140 high-confidence interactions involving 110 and 133 proteins, respectively. To explore the biological relevance of these interactions, we tested an Escherichia coli gene deletion array for motility defects (using swarming assays) and found 159 gene deletion strains to have reduced or no motility. Comparing our interaction data with motility phenotypes from E. coli, Bacillus subtilis, and Helicobacter pylori, we found 23 hitherto uncharacterized proteins involved in motility. Integration of phylogenetic information with our interaction and phenotyping data reveals a conserved core of motility proteins, which appear to have recruited many additional species-specific components over time. Our interaction data also predict 18 110 interactions for 64 flagellated bacteria.

Bacillus sp. THPS1 is a novel strain isolated from a high-temperature hot spring in Thailand, exhibiting distinctive genomic features that enable adaptation to an extreme environment. This study aimed to characterize the genomic and functional attributes of Bacillus sp. THPS1 to understand its adaptation strategies and evaluate its potential for biotechnological applications. The draft genome is 5.38 Mbp with a GC content of 35.67%, encoding 5606 genes, including those linked to stress response and sporulation, which are essential for survival in high-temperature conditions. Phylogenetic analysis and average nucleotide identity (ANI) values confirmed its classification as a distinct species within the Bacillus genus. Pangenome analysis involving 19 others closely related thermophilic Bacillus species identified 1888 singleton genes associated with heat resistance, sporulation, and specialized metabolism, suggesting adaptation to nutrient-deficient, high-temperature environments. Genomic analysis revealed 12 biosynthetic gene clusters (BGCs), including those for polyketides and non-ribosomal peptides, highlighting its potential for synthesizing secondary metabolites that may facilitate its adaptation. Additionally, the presence of three Siphoviridae phage regions and 96 mobile genetic elements (MGEs) suggests significant genomic plasticity, whereas the existence of five CRISPR arrays implies an advanced defense mechanism against phage infections, contributing to genomic stability. The distinctive genomic features and functional capacities of Bacillus sp. THPS1 make it a promising candidate for biotechnological applications, particularly in the production of heat-stable enzymes and the development of resilient bioformulations.

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4T (KCTC 43402T = GDMCC 1.3498T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4T. 16S rRNA sequence analysis showed that strain SS4T most closely resembled Paenibacillus marchantiophytorum DSM 29850T (98.22%), Paenibacillus nebraskensis JJ-59T (98.19%), and Paenibacillus aceris KCTC 13870T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

Isolation of manumycin-type derivatives and genome characterization of a marine Streptomyces sp. C1-2

A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya, with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae. The orthologous average nucleotide identity (ANI) and digital DNA-DNAhybridization (dDDH) values among these six strains ranged from 96.8-99.9% and 73.7-99.8%, which supported that they were belonged to the same species. However, strain ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya. Based on the results of the polyphasic approaches, we propose that strain ZYY5T represents a novel species in the genus Dickeya, for which the name Dickeya oryzae sp. nov. (=JCM 33020 T=ACCC 61554 T) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5T.

Mangrove ecosystems are critical for coastal protection and biodiversity but are increasingly threatened by plastic pollution, particularly polyethylene terephthalate (PET). In this study, a novel marine bacterium, strain SCSIO 80796T, was isolated from PET debris collected from the mangrove in QiAo Island, Zhuhai, China. Using a polyphasic taxonomic approach, including 16S rRNA gene sequencing, genome-based comparisons (average nucleotide identity [ANI] 72.2%, digital DNA-DNA hybridization [dDDH] 19.0%, average amino acid identity [AAI] 70.6%), and phenotypic and chemotaxonomic analyses, the strain was classified as a novel species within the genus Neptunicella. It is proposed as Neptunicella plasticusilytica sp. nov. (type strain SCSIO 80796ᵀ = MCCC 1K08369T = KCTC 92826T). Genomic analysis revealed that strain SCSIO 80796ᵀ encodes a novel PET-degrading enzyme, NmCut, which degrades PET and yields 105-120 µM of degradation products [terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), bis(2-hydroxyethyl) terephthalate (BHET)] within 48 h at 60°C. NmCut exhibits both structural and evolutionary novelty, featuring a unique PET-binding module (PBM) absent in known PETases. PBM is characterized by a long, positively charged α-helix enriched in aromatic residues, forming a distinct substrate-interacting surface with potential as a transferable domain to enhance the efficiency of other plastic-degrading enzymes. This study not only expands the known diversity within Neptunicella but also highlights the potential of marine-derived microbes in addressing plastic pollution through biotechnological applications.IMPORTANCEThe discovery of Neptunicella plasticusilytica sp. nov. advances marine microbial ecology by revealing a novel species in the scarcely studied genus Neptunicella, which previously contained only one cultured representative. Isolated from plastic-polluted mangroves, this bacterium exemplifies microbial adaptation to anthropogenic habitats. Its functional uniqueness is underscored by a phylogenetically distinct polyethylene terephthalate (PET)-degrading enzyme (NmCut), forming an evolutionary clade separate from all known plastic-degrading enzymes. By integrating taxonomic discovery with functional genomics, this study bridges the gap between microbial diversity and biotechnological potential. The dual novelty of N. plasticusilytica-as a taxonomic addition and a source of evolutionarily unique enzymes-highlights the importance of exploring understudied environments to address global challenges like plastic pollution.