# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 6088 | 0 | 1.0000 | Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection. Achromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa. Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been documented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the complete genome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucumber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq and contained 6,930,067 nucleotides with 67.55% G + C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, including those associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity. Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plant growth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpea is discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizosphere in sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security. | 2024 | 39278894 |
| 8448 | 1 | 0.9986 | Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean. | 2023 | 37372451 |
| 6094 | 2 | 0.9986 | Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems. | 2021 | 33911103 |
| 6095 | 3 | 0.9985 | Isolation and characterization of plant growth promoting endophytic diazotrophic bacteria from Korean rice cultivars. We have isolated 576 endophytic bacteria from the leaves, stems, and roots of 10 rice cultivars and identified 12 of them as diazotrophic bacteria using a specific primer set of nif gene. Through 16S rDNA sequence analysis, nifH genes were confirmed in the two species of Penibacillus, three species of Microbacterium, three Bacillus species, and four species of Klebsiella. Rice seeds treated with these plant growth-promoting bacteria (PGPB) showed improved plant growth, increased height and dry weight and antagonistic effects against fungal pathogens. In addition, auxin and siderophore producing ability, and phosphate solubilizing activity were studied for the possible mechanisms of plant growth promotion. Among 12 isolates tested, 10 strains have shown higher auxin producing activity, 6 isolates were confirmed as strains with high siderophore producing activity while 4 isolates turned out to have high phosphate-solubilizing activity. These results strongly suggest that the endophytic diazotrophic bacteria characterized in this study could be successfully used to promote plant growth and inducing fungal resistance in plants. | 2014 | 23871145 |
| 6138 | 4 | 0.9985 | Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments. | 2020 | 32405446 |
| 5151 | 5 | 0.9984 | Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes. Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches. | 2021 | 34659348 |
| 5190 | 6 | 0.9984 | Genomic Analysis of Cronobacter condimenti s37: Identification of Resistance and Virulence Genes and Comparison with Other Cronobacter and Closely Related Species. Cronobacter condimenti are environmental commensals that have not been associated with any clinical infections. To date, they are the least understood and described Cronobacter species within the genus. The objective of this study was to use a draft genome sequence (DGS) of the Cronobacter condimenti strain s37 to screen for genes encoding for antibiotic resistance, virulence, response to environmental stress, and biofilm formation. The strain was isolated in Poland from commercial small radish sprouts. This is the second genome of this species available in the GenBank database. The comparative genome analysis (cgMLST) of C. condimenti s37 with other Cronobacter spp. including the pathogenic species C. sakazakii and the plant-associated closely related genera Franconibacter and Siccibacter was also performed. The assembled and annotated genome of the C. condimenti s37 genome was 4,590,991 bp in length, with a total gene number of 4384, and a GC content of 55.7%. The s 37 genome encoded for genes associated with resistance to stressful environmental conditions (metal resistance genes: zinc, copper, osmotic regulation, and desiccation stress), 17 antimicrobial resistance genes encoding resistance to various classes of antibiotics and 50 genes encoding for the virulence factors. The latter were mainly genes associated with adhesion, chemotaxis, hemolysis, and biofilm formation. Cg-MLST analysis (3991 genes) revealed a greater similarity of C. condimenti s37 to S. turicensis, F. pulveris, and C. dublinensis than to other species of the genus Cronobacter. Studies on the diversity, pathogenicity, and virulence of Cronobacter species isolated from different sources are still insufficient and should certainly be continued. Especially the analysis of rare strains such as s37 is very important because it provides new information on the evolution of these bacteria. Comparative cgMLST analysis of s37 with other Cronobacter species, as well as closely related genera Franconibacter and Siccibacter, complements the knowledge on their adaptability to specific environments such as desiccation. | 2024 | 39201307 |
| 6035 | 7 | 0.9981 | Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09. Probiotics are widely used to improve pet health and welfare due to their significant biological activity and health benefits. Lactobacillus acidophilus GLA09 was derived from the intestinal tract of healthy beagles. The safety and suitability evaluation of GLA09 was completed through a combination of whole genome sequence and phenotypic analyses, including tests for the inhibition of harmful bacteria, acid resistance, bile salt tolerance, adhesion, and amine-producing substance content. The findings revealed that GLA09 has good gastrointestinal tolerance, inhibits the growth of pathogenic bacteria, and does not produce toxic biogenic amines. The genome of GLA09 comprises one chromosome and one plasmid, with a genome size of 2.10 M and a Guanine + Cytosine content of 38.71%. It encodes a total of 2208 genes, including 10 prophages, and 1 CRISPR sequence. Moreover, 56 carbohydrate-encoding genes were identified in the CAZy database, along with 11 genes for cold and heat stress tolerance, 5 genes for bile salt tolerance, 12 genes for acid tolerance, and 14 predicted antioxidant genes. Furthermore, GLA09 has one lincosamide resistance gene, but there is no risk of transfer. GLA09 harbors a cluster of Helveticin J and Enterolysin A genes linked to antimicrobial activity. Genomic analysis validated the probiotic attributes of GLA09, indicating its potential utility as a significant probiotic in the pet food industry. In summary, L. acidophilus GLA09 has the potential to be used as a probiotic in pet food and can effectively combat intestinal health in pets. | 2025 | 40005717 |
| 4360 | 8 | 0.9981 | Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes. Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes. | 2023 | 37761923 |
| 6115 | 9 | 0.9981 | Role of Plasmid in Pesticide Degradation and Metal Tolerance in Two Plant Growth-Promoting Rhizobacteria Bacillus cereus (NCIM 5557) and Bacillus safensis (NCIM 5558). Disha A (Bacillus cereus) and Disha B (Bacillus safensis) were isolated from pesticide-infested agricultural field and showed tolerance against pesticides, heavy metals, and antibiotics. The isolates exhibited PGPR activities in vitro as well as in field conditions in lentil (Lens culinaris) and cow pea (Vigna unguiculata). Both the Bacillus species could not be grown in mineral salt medium but efficiently grown in the media supplemented with pesticide (imidacloprid/carbendazim) demonstrating the utilization of pesticide as carbon/nitrogen source. The HPLC studies exhibited the pesticide (imidacloprid/carbendazim) degradation by both the bacteria. B. safensis showed better degradation of carbendazim (88.93%) and imidacloprid (82.48%) than that of B. cereus 78.07% and 49.12%, respectively. The bacterial isolates showed high concentration of heavy metal tolerance viz. lead, molybdenum, cadmium, copper, cobalt, and zinc, except mercury. Both the bacteria possessed single plasmid. The plasmid-cured isolates of B. cereus did not tolerate any pesticide, whereas that of B. safensis tolerated all the pesticides, like wild strains. The plasmid curing experiments did not affect the heavy metal tolerance ability of both the bacteria indicating the genomic nature of heavy metal tolerance genes, whereas pesticide resistance genes are plasmid-dependent in B. cereus but genomic in B. safensis. | 2022 | 35157142 |
| 5150 | 10 | 0.9981 | Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients. The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia-Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria. | 2021 | 34790179 |
| 4448 | 11 | 0.9981 | The screening of antimicrobial bacteria with diverse novel nonribosomal peptide synthetase (NRPS) genes from South China sea sponges. Nonribosomal peptide synthetase (NRPS) adenylation (A) domain genes were investigated by polymerase chain reaction for 109 bacteria isolated from four South China Sea sponges, Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis. Meanwhile, the antimicrobial bioassay of bacteria with NRPS genes were carried out to confirm the screening of NRPS genes. Fifteen bacteria were found to contain NRPS genes and grouped into two phyla Firmicutes (13 of 15) and Proteobacteria (two of 15) according to 16S rDNA sequences. Based on the phylogenetic analysis of the conserved A domain amino acid sequences, most of the NRPS fragments (11 of 15) showed below 70% similarity to their closest relatives suggesting the novelty of these NRPS genes. All of the 15 bacteria with NRPS genes have antimicrobial activities, with most of them exhibiting activity against multiple indicators including fungi and gram-positive and gram-negative bacteria. The different antimicrobial spectra indicate the chemical diversity of biologically active metabolites of sponge-associated bacteria and the possible role of bacterial symbionts in the host's antimicrobial chemical defense. Phylogenetic analysis based on the representative NRPS genes shows high diversity of marine NRPS genes. The combined molecular technique and bioassay strategy will be useful to obtain sponge-associated bacteria with the potential to synthesize bioactive compounds. | 2009 | 18853226 |
| 5148 | 12 | 0.9981 | Unveiling the whole genomic features and potential probiotic characteristics of novel Lactiplantibacillus plantarum HMX2. This study investigates the genomic features and probiotic potential of Lactiplantibacillus plantarum HMX2, isolated from Chinese Sauerkraut, using whole-genome sequencing (WGS) and bioinformatics for the first time. This study also aims to find genetic diversity, antibiotic resistance genes, and functional capabilities to help us better understand its food safety applications and potential as a probiotic. L. plantarum HMX2 was cultured, and DNA was extracted for WGS. Genomic analysis comprised average nucleotide identity (ANI) prediction, genome annotation, pangenome, and synteny analysis. Bioinformatics techniques were used to identify CoDing Sequences (CDSs), transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, and antibiotic resistance genes, as well as to conduct phylogenetic analysis to establish genetic diversity and evolution. The study found a significant genetic similarity (99.17% ANI) between L. plantarum HMX2 and the reference strain. Genome annotation revealed 3,242 coding sequences, 65 tRNA genes, and 16 rRNA genes. Significant genetic variety was found, including 25 antibiotic resistance genes. A phylogenetic study placed L. plantarum HMX2 among closely related bacteria, emphasizing its potential for probiotic and food safety applications. The genomic investigation of L. plantarum showed essential genes, including plnJK and plnEF, which contribute to antibacterial action against foodborne pathogens. Furthermore, genes such as MurA, Alr, and MprF improve food safety and probiotic potential by promoting bacterial survival under stress conditions in food and the gastrointestinal tract. This study introduces the new genomic features of L. plantarum HMX2 about specific genetics and its possibility of relevant uses in food security and technologies. These findings of specific genes involved in antimicrobial activity provide fresh possibilities for exploiting this strain in forming probiotic preparations and food preservation methods. The future research should focus on the experimental validation of antibiotic resistance genes, comparative genomics to investigate functional diversity, and the development of novel antimicrobial therapies that take advantage of L. plantarum's capabilities. | 2024 | 39611087 |
| 8458 | 13 | 0.9981 | A PCR-based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Plant genes for pathogen resistance can be used to engineer disease resistant crops. Oligonucleotides were designed from sequence motifs conserved between resistance genes of tobacco and Arabidopsis thaliana and used as PCR primers in potato DNA. Amplification products were obtained that were homologous to known resistance genes and linked without recombination with the nematode resistance locus Gro1 and the Phytophthora infestans resistance locus R7 of potato. Map positions of PCR-derived potato gene fragments were also correlated with resistance loci of the related tomato and tobacco genomes. Our results indicate that plant resistance genes that are effective against nematodes, fungi, viruses and bacteria may be isolated based on common sequence motifs and PCR methodology. | 1996 | 8944022 |
| 4358 | 14 | 0.9981 | Genomic profiling of pediococcus acidilactici BCB1H and identification of its key features for Biotechnological innovation, food technology and medicine. Lactic acid bacteria has been extensively used in food industry because of widespread properties and Pediococcus is among one of them. This study aims to conduct a comprehensive genomic analysis of Pediococcus acidilactici strain BCB1H to elucidate its genetic composition, functional elements, and potential biotechnological applications. The objectives include identifying key genomic features such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, which will highlight the adaptability and potential of P. acidilactici strain BCB1H for use in a variety of industrial and therapeutic applications. P. acidilactici strain BCB1H was analyzed using whole-genome sequencing, which used advanced sequencing technologies to obtain comprehensive genomic data. Key genomic features, such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, were identified through bioinformatics analyses. The genomic analysis of P. acidilactici strain BCB1H revealed a genome size of approximately 1.92 million base pairs with a GC content of 42.4%. The annotation identified 1,895 genes across 192 subsystems, highlighting the metabolic pathways and functional categories. Notably, specialty genes associated with carbohydrate metabolism, stress response, pathogenicity, and amino acid synthesis were identified, underscoring the versatility and potential applications in food technology and medicine. These findings shed light on the genetic makeup and functional potential of P. acidilactici strain BCB1H, highlighting its flexibility and industrial importance. The genetic traits discovered suggest its prospective use in probiotics, food preservation, and biotechnological advancements. | 2025 | 39971970 |
| 5145 | 15 | 0.9980 | Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BACKGROUND: Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity. RESULTS: We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99% sequence identity in rDNA sequence and orthology across 85.6% of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8%) were present in Serratia while 33 (84.6%) and 35 (89%) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively. CONCLUSION: The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result - killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes. | 2015 | 26187596 |
| 6037 | 16 | 0.9980 | The Complete Genome of Probiotic Lactobacillus sakei Derived from Plateau Yak Feces. Probiotic bacteria are receiving increased attention due to the potential benefits to their hosts. Plateau yaks have resistance against diseases and stress, which is potentially related to their inner probiotics. To uncover the potential functional genes of yak probiotics, we sequenced the whole genome of Lactobacillus sakei (L. sakei). The results showed that the genome length of L. sakei was 1.99 Mbp, with 1943 protein coding genes (21 rRNA, 65 tRNA, and 1 tmRNA). There were three plasmids found in this bacteria, with 88 protein coding genes. EggNOG annotation uncovered that the L. sakei genes were found to belong to J (translation, ribosomal structure, and biogenesis), L (replication, recombination, and repair), G (carbohydrate transport and metabolism), and K (transcription). GO annotation showed that most of the L. sakei genes were related to cellular processes, metabolic processes, biological regulation, localization, response to stimulus, and organization or biogenesis of cellular components. CAZy annotation found that there were 123 CAZys in the L. sakei genome, with glycosyl transferases and glycoside hydrolases. Our results revealed the genome characteristics of L. sakei, which may give insight into the future employment of this probiotic bacterium for its functional benefits. | 2020 | 33371298 |
| 6036 | 17 | 0.9980 | 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. | 2025 | 40150327 |
| 8459 | 18 | 0.9980 | A physical map of traits of agronomic importance based on potato and tomato genome sequences. Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes. | 2023 | 37564870 |
| 6091 | 19 | 0.9980 | Isolation of Heavy Metal-Tolerant and Anti-Phytopathogenic Plant Growth-Promoting Bacteria from Soils. In this study, multifunctional soil bacteria, which can promote plant development, resist heavy metals, exhibit anti-phytopathogenic action against plant diseaes, and produce extracellular enzymes, were isolated to improve the effectiveness of phytoremediation techniques. In order to isolate multifunctional soil bacteria, a variety of soil samples with diverse characteristics were used as sources for isolation. To look into the diversity and structural traits of the bacterial communities, we conducted amplicon sequencing of the 16S rRNA gene on five types of soils and predicted functional genes using Tax4Fun2. The isolated bacteria were evaluated for their multifunctional capabilities, including heavy metal tolerance, plant growth promotion, anti-phytopathogenic activity, and extracellular enzyme activity. The genes related to plant growth promotion and anti-phytopathogenic activity were most abundant in forest and paddy soils. Burkholderia sp. FZ3 and FZ5 demonstrated excellent heavy metal resistance (≤ 1 mM Cd and ≤ 10 mM Zn), Pantoea sp. FC24 exhibited the highest protease activity (24.90 μmol tyrosine·g-DCW(-1)·h(-1)), and Enterobacter sp. PC20 showed superior plant growth promotion, especially in siderophore production. The multifunctional bacteria isolated using traditional methods included three strains (FC24, FZ3, and FZ5) from the forest and one strain (PC20) from paddy field soil. These results indicate that, for the isolation of beneficial soil microorganisms, utilizing target gene information obtained from isolation sources and subsequently exploring target microorganisms is a valuable strategy. | 2024 | 39468992 |