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The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant. [ABSTRACT FROM AUTHOR]

This study focused on the discovery of the antimicrobial peptide (AMP) derived from mangrove bacteria. The most promising isolate, NNS5-6, showed the closest taxonomic relation to Paenibacillus thiaminolyticus, with the highest similarity of 74.9%. The AMP produced by Paenibacillus thiaminolyticus NNS5-6 exhibited antibacterial activity against various Gram-negative pathogens, especially Pseudomonas aeruginosa and Klebsiella pneumoniae. The peptide sequence consisted of 13 amino acids and was elucidated as Val-Lys-Gly-Asp-Gly-Gly-Pro-Gly-Thr-Val-Tyr-Thr-Met. The AMP mainly exhibited random coil and antiparallel beta-sheet structures. The stability study indicated that this AMP was tolerant of various conditions, including proteolytic enzymes, pH (1.2–14), surfactants, and temperatures up to 40 °C for 12 h. The AMP demonstrated 4 µg/mL of MIC and 4–8 µg/mL of MBC against both pathogens. Time-kill kinetics showed that the AMP acted in a time- and concentration-dependent manner. A cell permeability assay and scanning electron microscopy revealed that the AMP exerted the mode of action by disrupting bacterial membranes. Additionally, nineteen biosynthetic gene clusters of secondary metabolites were identified in the genome. NNS5-6 was susceptible to various commonly used antibiotics supporting the primary safety requirement. The findings of this research could pave the way for new therapeutic approaches in combating antibiotic-resistant pathogens. [ABSTRACT FROM AUTHOR]

Aims: To unfold the full potential of plant growth-promoting rhizobacteria in crop production it is desirable to explore the mechanisms through which they promote growth. We investigated the potential mechanisms of plant growth promotion by Streptomyces rochei S32 in two crops. Methods: The effects of S. rochei S32 on plant growth and its antagonistic activity against soil-borne pathogenic fungi were tested. The underlying molecular mechanisms were identified based on whole-genome sequencing and bioinformatics analysis. The results of genomic analysis were verified by widely targeted metabolomics and mechanism studies of plant growth promotion. Results: S. rochei S32 significantly improved the growth of wheat and tomato. The shoot length (24.7%) and root length (25.3%) of wheat (400-fold dilution of cell-free fermentation filtrate) were increased, and the root length of tomato (200-fold dilution) was prolonged (40.9%), and the field yield was also increased. S. rochei S32 showed antagonistic activity against multiple pathogenic fungi, especially Macropoma kawatsukai. The bacterial genome contains an 8,041,158-bp chromosome and two plasmids. A total of 7486 annotated genes were classified into 31 Gene Ontology functional categories. Genomic analysis revealed the potential for the production of indole-3-acetic acid, fungal cell wall hydrolases, antibiotics (e.g., candicidin, streptothricin, borrellin, albaflavenone), and siderophores. Thirty-nine phytohormones and 2205 secondary metabolites were detected, including indole-3-acetic acid, phytosphingosine, acivicin, and corynebactin. Normal bacterial growth occurred on a nitrogen-free medium. Conclusion: S. rochei S32 can promote plant growth directly or indirectly through nitrogen fixation and production of phytohormones, extracellular hydrolases, antibiotics, and siderophores. [ABSTRACT FROM AUTHOR]

The global rise of antimicrobial resistance (AMR) presents a critical challenge necessitating the discovery of novel antimicrobial agents. Mangrove microbes are valuable sources of new antimicrobial compounds. This study reports the discovery of a potent antimicrobial peptide (AMP) from Bacillus paralicheniformis NNS4-3, isolated from mangrove sediment, exhibiting significant activity against methicillin-resistant Staphylococcus aureus (MRSA). The AMP demonstrated a minimum inhibitory concentration ranging from 1 to 16 µg/mL in the tested bacteria and exhibited bactericidal effects at higher concentrations. Structural analysis revealed a bacitracin-like configuration and the peptide acted by disrupting bacterial membranes in a time- and concentration-dependent manner. The AMP maintained stability under heat, proteolytic enzymes, surfactants, and varying pH treatments. The ten biosynthetic gene clusters (BGCs) of secondary metabolites were found in the genome. Detailed sequence comparison of the predicted bacitracin BGC indicated distinct DNA sequences compared to previously reported strains. Although the antibiotic resistance genes were found, this strain was susceptible to antibiotics. Our findings demonstrated the potential of Bacillus paralicheniformis NNS4-3 and its AMP as a promising agent in combating AMR. The genetic information could be pivotal for future applications in the healthcare industry, emphasizing the need for continued exploration of marine microbial diversity in drug discovery. [ABSTRACT FROM AUTHOR]

Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature. Using machine learning (ML) based approaches, we have analysed Relative Synonymous Codon Usage (RSCU) values between essential and non-essential genes in Escherichia coli and thirty-four other bacterial genomes whose gene essentiality features were available in public databases. We observed significant differences in codon usage patterns between essential and non-essential genes for majority of the bacterial genomes and accordingly, ML based classifiers achieved high area under curve (AUC) scores, with a minimum score of 70.0 across twenty-eight organisms. Further, importance of the codons towards classifying genes found to differ among the codons in each genome. Arg codon CGT and Gly codon GGT were observed to be the most preferred codons among essential genes in Escherichia coli. Interestingly, some of the codons like CGT, ATA, GGT and GGG observed to be contributing consistently towards classifying essential genes across thirty-five bacteria genomes studied. In other hand, codons TGY and CAY encoding amino acids Cys and His respectively were among the least contributing codons towards classification among all these bacteria. This study demonstrates the gene essentiality based differences in synonymous codon usage in bacteria genomes and presents a common codon usage pattern across bacteria. [ABSTRACT FROM AUTHOR]

The article discusses the complete genome of Cedecea neteri A2, a bacterial pathogen responsible for causing yellow rot disease in Pleurotus pulmonarius, an edible fungus in Guangxi, China. The disease leads to the formation of purulent tissues and deformed fruiting bodies, reducing the economic value of the fungus. The C. neteri A2 strain is gram-negative, motile, and lacks capsules or endospores. The genome sequencing of C. neteri A2 was conducted using two different platforms, and the resulting genome sequence will aid in understanding the pathogenicity mechanisms and developing control approaches for yellow rot disease. [Extracted from the article]

Background: Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. Methods: The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. Results: The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. Conclusions: The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.

This study focused on the discovery of the antimicrobial peptide (AMP) derived from mangrove bacteria. The most promising isolate, NNS5-6, showed the closest taxonomic relation to Paenibacillus thiaminolyticus, with the highest similarity of 74.9%. The AMP produced by Paenibacillus thiaminolyticus NNS5-6 exhibited antibacterial activity against various Gram-negative pathogens, especially Pseudomonas aeruginosa and Klebsiella pneumoniae. The peptide sequence consisted of 13 amino acids and was elucidated as Val-Lys-Gly-Asp-Gly-Gly-Pro-Gly-Thr-Val-Tyr-Thr-Met. The AMP mainly exhibited random coil and antiparallel beta-sheet structures. The stability study indicated that this AMP was tolerant of various conditions, including proteolytic enzymes, pH (1.2–14), surfactants, and temperatures up to 40 °C for 12 h. The AMP demonstrated 4 µg/mL of MIC and 4–8 µg/mL of MBC against both pathogens. Time-kill kinetics showed that the AMP acted in a time- and concentration-dependent manner. A cell permeability assay and scanning electron microscopy revealed that the AMP exerted the mode of action by disrupting bacterial membranes. Additionally, nineteen biosynthetic gene clusters of secondary metabolites were identified in the genome. NNS5-6 was susceptible to various commonly used antibiotics supporting the primary safety requirement. The findings of this research could pave the way for new therapeutic approaches in combating antibiotic-resistant pathogens.

Morganella morganii WA01/MUTU is a heavy metal tolerant strain capable of producing silver nanoparticles (AgNPs) from AgNO3. Here we present the draft genome sequence of M. morganii WA01/MUTU isolated from a water sample collected in Nakhon Pathom province, Thailand. The draft genome was sequenced on the Illumina NextSeq 550 sequencer. The genome consisted of 34 contigs with a total size of 3,991,804 bp, an N50 value of 364,423 bp and a GC content of 50.93%. The digital DNA-DNA hybridisation (dDDH) between WA01/MUTU and Morganella morganii (NBRC 3848) was 83.9%, identifying the strain as Morganella morganii. The data presented here can be used in comparative genomics to identify gene clusters involved in AgNP biosynthesis and secondary metabolite production. The draft genome sequence data was deposited at NCBI under Bioproject accession number PRJNA493966.

The global rise of antimicrobial resistance (AMR) presents a critical challenge necessitating the discovery of novel antimicrobial agents. Mangrove microbes are valuable sources of new antimicrobial compounds. This study reports the discovery of a potent antimicrobial peptide (AMP) from Bacillus paralicheniformis NNS4-3, isolated from mangrove sediment, exhibiting significant activity against methicillin-resistant Staphylococcus aureus (MRSA). The AMP demonstrated a minimum inhibitory concentration ranging from 1 to 16 µg/mL in the tested bacteria and exhibited bactericidal effects at higher concentrations. Structural analysis revealed a bacitracin-like configuration and the peptide acted by disrupting bacterial membranes in a time- and concentration-dependent manner. The AMP maintained stability under heat, proteolytic enzymes, surfactants, and varying pH treatments. The ten biosynthetic gene clusters (BGCs) of secondary metabolites were found in the genome. Detailed sequence comparison of the predicted bacitracin BGC indicated distinct DNA sequences compared to previously reported strains. Although the antibiotic resistance genes were found, this strain was susceptible to antibiotics. Our findings demonstrated the potential of Bacillus paralicheniformis NNS4-3 and its AMP as a promising agent in combating AMR. The genetic information could be pivotal for future applications in the healthcare industry, emphasizing the need for continued exploration of marine microbial diversity in drug discovery.

Management of shoulder periprosthetic joint infection remains a clinical challenge with patients failing both medical and operative treatment despite adherence to best practice guidelines. An important question is whether these failures reflect reinfection of the causative organism or the persistence of infection due to inadequate treatment at the index surgery. Utilizing next-generation sequencing (NGS) and longitudinal clinical follow-up, this study hypothesized that some of these failures were the result of an organism that was present at the time of initial surgery but not isolated by traditional culture. In this prospective study, samples were collected from 41 patients undergoing revision shoulder surgeries between June 2016 and May 2017. Synovial fluid and deep tissue samples (anterior capsule, inferior capsule, glenoid, humeral canal, and underneath prosthetic humeral head) were obtained intraoperatively in a standardized fashion and analyzed by NGS (MicroGenDx, TX). Concordant samples from these sites were also sent for institutional culture and held for 13 days. Demographics, comorbidities, and inflammatory markers were collected per standard-of-care. Patients were classified per the 2018 International Consensus Meeting Consensus definition of shoulder periprosthetic joint infection. Treatment failure was defined as any unplanned procedure for infection that yielded positive cultures, during the 3-year follow-up. Concordance of the infecting pathogen cultured at failure with the NGS analysis at the index revision procedure was determined. There were 19 NGS-positive and 32 NGS-negative cases. During the study follow-up period, 6 unexpected reoperations (failures) occurred that yielded positive cultures, as well as 3 unexpected procedures for instability (n = 2) or cuff insufficiency (n = 1). NGS-positive results at index revision were significantly associated with subsequent failure by infection (P =.022), whereas positive cultures at index revision were not (P =.671). Furthermore, the organism cultured at subsequent failure was present on NGS testing at the index revision procedure in the majority of cases (4 of 6 patients; 66.7%). Five of the 6 cases (83.3%) that underwent unexpected reoperation did not receive prolonged antibiotics beyond standard perioperative prophylaxis due to negative cultures at the time of revision. Our findings suggest that most of the unexpected failures (66.7%) by infection could be attributed to an organism previously detected by NGS and not identified by culture. Further multicenter work with larger numbers and longer-term follow-up is needed to corroborate any association between NGS analysis and subsequent treatment failure. [ABSTRACT FROM AUTHOR]

Identifiable endophytic bacteria with plant growth-promoting traits promise to ensure sustainable agriculture. However, information on the versatility and exploration of sunflower-associated bacteria as bioinoculants is less studied. Here, we present the whole-genome sequence and annotation of Stenotrophomonas maltophilia JVB5 isolated from the sunflower root endosphere from the North West province, South Africa. The whole-genome analysis revealed a genome size of 4 771 305 bp, a sequence read count of 8 764 890, a 66% guanine-cytosine content, 57 tRNAs, 268 contigs, and 4 160 protein-coding genes with functions in various metabolic pathways. Pathways involved in the indole acetic acid production were found in the S. maltophilia JVB5 genome. The whole-genome annotation predicted notable genes involved in bacterial colonisation, antibiosis, and plant growth promotion. The predicted genes are involved in the sulfur metabolism, and the oxidative stress may enhance the plant growth promotion and boost plant the resistance to stress. Upon inoculation, S. maltophilia JVB5 efficiently colonised the sunflower root under greenhouse conditions with a significant improvement on the wet plant weight of 437.20 g compared to the uninoculated control with a 331.04 g wet weight. The genomic analysis revealing specific functional genes in the bacteria genome suggests their bioprospecting in agriculture. Hence, understanding the mechanisms employed by S. maltophilia JVB5 based on the predicted multifunctional genes will help harness their bioresource in sustainable plant health.

Bacterial sphingomyelinases (SMases) hydrolyze sphingomyelin and play an important role in membrane dynamics and the host immune system. While the number of sequenced genomes and metagenomes is increasing, a limited number of experimentally validated SMases have been reported, and the genomic diversity of SMases needs to be elucidated extensively. This study investigated the sequence and structural characteristics of SMases in bacterial genomes and metagenomes. Using previously identified SMases, such as the β-toxin of Staphylococcus aureus, we identified 276 putative SMases and 15 metagenomic SMases by a sequence homology search. Among the predicted metagenomic SMases, six non-redundant metagenomic SMases (M-SMase1−6) were selected for further analysis. The predicted SMases were confirmed to contain highly conserved residues in the central metal-binding site; however, the edge metal-binding site showed high diversity according to the taxon. In addition, protein structure modeling of metagenomic SMases confirmed structural conservation of the central metal-binding site and variance of the edge metal-binding site. From the activity assay on M-SMase2 and M-SMase5, we found that they displayed sphingomyelinase activity compared to Bacillus cereus SMase. This study elucidates a comprehensive genomic characterization of SMases and provides insight into the sequence-structure-activity relationship. [ABSTRACT FROM AUTHOR]

The Oxford Nanopore (ONT) MinION enables sequencing of longer DNA/RNA fragments compared to other sequencers, such as Illumina, etc. This nanopore method provides distinct advantages for generating complete genome assemblies from microorganisms. Specifically, the R9.4 flow cells used for MinION sequencing have much lower error rates compared with earlier versions of the ONT platform. Coupled with base calling using Dorado software, higher-quality long reads can now be generated for complete bacterial genome assembly. In this chapter, we describe a detailed MinION method to assemble a complete genome from a microorganism, polish the final assembly, and evaluate the genome quality using various software tools. Because of the low cost for MinION sequencing, this platform could be an asset for virtually any laboratory interested in generating complete genomes from microorganisms., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

This paper presents the genome sequence of a Shigella sonnei mutant strain (S. sonnei 4351) and the effect of mutation in lipopolysaccharide biosynthesis on bacterial fitness. Lipopolysaccharides are the major component of the outer leaflet of the Gram-negative outer membrane. We report here a frameshift mutation of the gene gmhD in the genome of S. sonnei 4351. The mutation results in a lack of epimerization of the core heptose while we also found increased thermosensitivity, abnormal cell division, and increased susceptibility to erythromycin and cefalexin compared to the S. sonnei 4303. Comparative genomic analysis supplemented with structural data helps us to understand the effect of specific mutations on the virulence of the bacteria and may provide an opportunity to study the effect of short lipopolysaccharides. [ABSTRACT FROM AUTHOR]

Recombinant DNA and genetic engineering technologies have made it possible to manipulate and carry out important advances in biology. However designing reliable, safe and accurate system for genome editing in prokaryotes and eukaryotes has been an issue for a long time. Enzymes (such as polymerases, ligases, and restriction endonucleases) and the polymerase chain reaction (PCR) provided ways to isolate genes and gene fragments, as well as to introduce mutations into gens in vitro, in cells and in a model organism. Today, the field of biology is undergoing a transformative phase with the advent of easy genome engineering using RNA-programmable CRISPR-Cas9. The CRISPR-Cas9 system is an immune system present in prokaryotes that allows the identification of exogenous DNA or RNA molecules. The Cas9 endonuclease is associated with a guide RNA molecule (RNAg) that allows it to form base pairs with target DNA or RNA sequencing, allowing Cas9 to introduce a site-specific double-strand break. Thanks to this breakthrough in genetic engineering Doudna Jennifer and Charpentier Emmanuelle were awarded the Nobel Prize in Chemistry in 2020 (Doudna and Charpentier., 2014). In what follows I will talk about the applicability of this system to edit bacterial genomes by punctiform, genetic and metabolic modifications.

Polyporus umbellatus is a well-known edible and medicinal mushroom, and some bacteria isolated from mushroom sclerotia may have beneficial effects on their host. These mushroom growth-promoting bacteria (MGPBs) are of great significance in the mushroom production. In this work, we aimed to isolate and identify MGPBs from P. umbellatus sclerotia. Using the agar plate dilution method, strain CACMS001 was isolated from P. umbellatus sclerotia. The genome of CACMS001 was sequenced using PacBio platform, and the phylogenomic analysis indicated that CACMS001 could not be assigned to known Rhizobium species. In co-culture experiments, CACMS001 increased the mycelial growth of P. umbellatus and Armillaria gallica and increased xylanase activity in A. gallica. Comparative genomic analysis showed that CACMS001 lost almost all nitrogen fixation genes but specially acquired one redox cofactor cluster with pqqE, pqqD, pqqC, and pqqB involved in the synthesis of pyrroloquinoline quinone, a peptide-derived redox participating in phosphate solubilization activity. Strain CACMS001 has the capacity to solubilize phosphate using Pikovskaya medium, and phnA and phoU involved in this process in CACMS001 were revealed by quantitative real-time PCR. CACMS001 is a new potential Rhizobium species and is the first identified MGPB belonging to Rhizobium. This novel bacterium would play a vital part in P. umbellatus, A. gallica, and other mushroom cultivation. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen capable of causing illness in humans. In a previous study, our group showed that a STEC isolate belonging to O22:H8 serotype (strain 154) can interfere with STEC O157:H7 colonization both in vitro and in vivo. Using whole-genome sequencing and genomic comparative, we predicted a subset of genes acquired by O22:H8 strain 154 through horizontal gene transfer that might be responsible for the phenotype previously described by our group. Among them were identified genes related to the pathogenesis of non-LEE (locus of enterocyte effacement) STEC, specific metabolic processes, antibiotic resistance and genes encoding for the T6SS-1 that is related to inter-bacterial competition. In addition, we showed that this strain carries stx1c and stx2dact, a mucus-inducible variant. The results obtained in this study provide insights into STEC genomic plasticity and the importance of genomic islands in the adaptation and pathogenesis of this pathogen. [ABSTRACT FROM AUTHOR]

Identifiable endophytic bacteria with plant growth-promoting traits promise to ensure sustainable agriculture. However, information on the versatility and exploration of sunflower-associated bacteria as bioinoculants is less studied. Here, we present the whole-genome sequence and annotation of Stenotrophomonas maltophilia JVB5 isolated from the sunflower root endosphere from the North West province, South Africa. The whole-genome analysis revealed a genome size of 4 771 305 bp, a sequence read count of 8 764 890, a 66% guanine-cytosine content, 57 tRNAs, 268 contigs, and 4 160 protein-coding genes with functions in various metabolic pathways. Pathways involved in the indole acetic acid production were found in the S. maltophilia JVB5 genome. The whole-genome annotation predicted notable genes involved in bacterial colonisation, antibiosis, and plant growth promotion. The predicted genes are involved in the sulfur metabolism, and the oxidative stress may enhance the plant growth promotion and boost plant the resistance to stress. Upon inoculation, S. maltophilia JVB5 efficiently colonised the sunflower root under greenhouse conditions with a significant improvement on the wet plant weight of 437.20 g compared to the uninoculated control with a 331.04 g wet weight. The genomic analysis revealing specific functional genes in the bacteria genome suggests their bioprospecting in agriculture. Hence, understanding the mechanisms employed by S. maltophilia JVB5 based on the predicted multifunctional genes will help harness their bioresource in sustainable plant health. [ABSTRACT FROM AUTHOR]

We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes. [ABSTRACT FROM AUTHOR]

Bacteria belonging to the genus Kocuria were identified as bacteria peculiar to a sake brewery in Toyama, Japan. Comparison of the 16S rRNA gene sequences revealed two groups of Kocuria isolates. Among known species, one group was similar to K. koreensis (Kk type), and the other, K. uropygioeca (Ku type). We determined complete genomic DNA sequences from two isolates, TGY1120_3 and TGY1127_2, which belong to types Kk and Ku, respectively. Comparison of these genomic information showed that these isolates differ at the species level with different genomic characters. Isolate TGY1120_3 comprised one chromosome and three plasmids, and the same transposon coding region was located on two loci on the chromosome and one locus on one plasmid, suggesting that the genetic element may be transferred between the chromosome and plasmid. Isolate TGY1127_2 comprised one chromosome and one plasmid. This plasmid encoded an identical transposase coding region, strongly suggesting that the genetic element may be transferred between these different isolates through plasmids. These four plasmids carried a highly similar region, indicating that they share a common ancestor. Thus, these two isolates may form a community and exchange their genetic information during sake brewing.

We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes.

Featured Application: The findings from this study might help researchers in setting up the assembly process of ONT long-read sequencing. Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo assemblers, Canu is highly flexible, with its dozens of adjustable parameters. Different Canu parameters were compared for assembling reads of Salmonellaenterica ser. Bovismorbificans (genome size of 4.8 Mbp) from three runs on MinION (N50 651, 805, and 5573). Two of them, with low quality and highly fragmented DNA, were not usable alone for assembly, while they were successfully assembled when combining the reads from all experiments. The best results were obtained by modifying Canu parameters related to the error correction, such as corErrorRate (exclusion of overlaps above a set error rate, set up at 0.40), corMhapSensitivity (the coarse sensitivity level, set to "high"), corMinCoverage (set to 0 to correct all reads, regardless the overlaps length), and corOutCoverage (corrects the longest reads up to the imposed coverage, set to 100). This setting produced two contigs corresponding to the complete sequences of the chromosome and a plasmid. The overall results highlight the importance of a tailored bioinformatic analysis. [ABSTRACT FROM AUTHOR]

Abstract Background Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms. Results In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance. Conclusions Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex.

Recombinant DNA and genetic engineering technologies have made it possible to manipulate and carry out important advances in biology. However, designing reliable, safe and accurate system for genome editing in prokaryotes and eukaryotes has been an issue for a long time. Enzymes (such as polymerases, ligases, and restriction endonucleases) and the polymerase chain reaction (PCR) provided ways to isolate genes and gene fragments, as well as to introduce mutations into genes in vitro, in cells and in a model organism. Today, the field of biology is undergoing a transformative phase with the advent of easy genome engineering using RNA-programmable CRISPR-Cas9. The CRISPR-Cas9 system is an immune system present in prokaryotes that allows the identification of exogenous DNA or RNA molecules. The Cas9 endonuclease is associated with a guide RNA molecule (gRNA) that allows it to form base pairs with target DNA or RNA sequencing, allowing Cas9 to introduce a sitespecific double-strand break. Thanks to this breakthrough in genetic engineering Doudna Jennifer and Charpentier Emmanuelle were awarded the Nobel Prize in Chemistry in 2020 (Doudna and Charpentier., 2014). In what follows I will talk about the applicability of this system to edit bacterial genomes by punctiform, genetic and metabolic modifications. [ABSTRACT FROM AUTHOR]

To study the contamination of microorganisms in the food industry, pharmaceutical industry, clinical diagnosis, or bacterial taxonomy, accurate identification of species is a key starting point of further investigation. The conventional method of identification by the 16S rDNA gene or other marker gene comparison is not accurate, because it uses a tiny part of the genomic information. The average nucleotide identity calculated between two whole bacterial genomes was proven to be consistent with DNA–DNA hybridization and adopted as the gold standard of bacterial species delineation. Furthermore, there are more bacterial genomes available in public databases recently. All of those contribute to a genome era of bacterial species identification. However, wrongly labeled and low-quality bacterial genome assemblies, especially from type strains, greatly affect accurate identification. In this study, we employed a multi-step strategy to create a type-strain genome database, by removing the wrongly labeled and low-quality genome assemblies. Based on the curated database, a fast bacterial genome identification platform (fIDBAC) was developed (http://fbac.dmicrobe.cn/). The fIDBAC is aimed to provide a single, coherent, and automated workflow for species identification, strain typing, and downstream analysis, such as CDS prediction, drug resistance genes, virulence gene annotation, and phylogenetic analysis.

To study the contamination of microorganisms in the food industry, pharmaceutical industry, clinical diagnosis, or bacterial taxonomy, accurate identification of species is a key starting point of further investigation. The conventional method of identification by the 16S rDNA gene or other marker gene comparison is not accurate, because it uses a tiny part of the genomic information. The average nucleotide identity calculated between two whole bacterial genomes was proven to be consistent with DNA–DNA hybridization and adopted as the gold standard of bacterial species delineation. Furthermore, there are more bacterial genomes available in public databases recently. All of those contribute to a genome era of bacterial species identification. However, wrongly labeled and low-quality bacterial genome assemblies, especially from type strains, greatly affect accurate identification. In this study, we employed a multi-step strategy to create a type-strain genome database, by removing the wrongly labeled and low-quality genome assemblies. Based on the curated database, a fast bacterial genome identification platform (fIDBAC) was developed (http://fbac.dmicrobe.cn/). The fIDBAC is aimed to provide a single, coherent, and automated workflow for species identification, strain typing, and downstream analysis, such as CDS prediction, drug resistance genes, virulence gene annotation, and phylogenetic analysis. The framework of fIDBAC. fIDBAC platform contains a bacterial type-strain genome database, genome analysis pipeline, and separated analysis tools. Genome assemblies from the public database were quality checked and filtered. And the identification strategy was evaluated by three high-quality datasets—GEBA, FDA-ARGROS, and NCTC-3000 datasets. [ABSTRACT FROM AUTHOR]

We now live in a generation, where we can make our own medicine based on our genes, which was the idea of our previous generation. It is all because of a method called sequencing, which has made it far beyond the latest in science. In the early days of succession this method was very expensive and time consuming to complete but now with all this modern technology, it is less expensive and is made in every corner and side of the country. This project is about part of the analysis of the complete genome sequence. Genome sequencing analyzes all cell sequence DNA simultaneously, providing the most complete genetic expression [IASLC Thoracic Oncology (Second Edition), 2018]. This paper describes which bioinformatics tools are used for genome analysis by analyzing 2 different types of Lactobacillus rhamnosus in comparison with the reference genome. This bacterium is widely used as a probiotic and can cure many intestinal-related diseases. In this paper, we compared two different types of Lactobacillus rhamnosus with the complete Lactobacillus rhamnosus GG commonly used as probiotics. Although creatures are similar the challenges are different from each other. We have therefore attempted to distinguish this analysis method. With the differences, we have identified, we plan to genetically modify the body to test its ability to function as a bacterium as a probiotic and an inhibitor in several other diseases. This paper used different types of bioinformatics tools for analysis like that FastQC, MultiQC, Unicycler, CONTIGuator, BLAST, CGView, etc. described below and these tools provide a perfect result and result has shown the pale orange color in the middle of the circle is the reference genome while the brown colour ring is the sample BIOML_A6 and the outer ring of red colour is the sample DSM_20021. This comparison reveals the presence and absence of certain coding and non-coding region which explains the difference among the 3 sequences. The picture also shows both the samples are more or less similar. The black color ring is GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). The purple color ring is GC skew is when the nucleotides guanine and cytosine are over-or under-abundant in a particular region of DNA or RNA. [ABSTRACT FROM AUTHOR]

Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (IS Enfa4 and IS Efa5) mobile genetic elements for the first time in the E. avium genome. The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium , which leads to hospital-acquired infections. [ABSTRACT FROM AUTHOR]

Toxic effectors secreted by the type VI secretion system (T6SS) facilitate interbacterial warfare, as well as pathogenesis toward humans, animals and plants. However, systematically predicting T6SS effectors remains challenging due to their sequence and functional diversity. In this study, we systematically identified putative T6SS toxic effectors in prokaryotic genomes on the basis of the observation that genes encoding adaptor proteins and genes encoding cognate effector proteins are generally adjacent in the genome. Adaptor proteins are mediators that help to load their cognate effectors onto the T6SS spike complex. The contextual genes of the known adaptor proteins (DUF1795, DUF2169 or DUF4123) all exhibited a high proportion of encoding T6SS spike complex protein (VgrG or PAAR) and effector proteins. On the basis of the genomic context, we found that PRK06147 might be a novel adaptor protein. These four adaptors are widely distributed among the bacterial genomes. From neighbors of 5297 adaptor genes, we identified 1356 putative effector genes from 92 different families, and two-thirds were currently annotated as hypothetical proteins or as having unknown functions. Our results indicate that each class of adaptors can be used as an effective marker to identify T6SS toxic effectors, moreover, this approach can promote the discovery of new effectors.

Abstract Background Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2’s inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not. Results Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 T ) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 T ). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains. Conclusions Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability.

Sequence filtering is an essential step regardless of the type of technology applied for sequencing a genome, in which low-quality readings or a portion are eliminated. In an assembly, the construction of a genome is carried out from the union of short reads in contigs. Some assemblers measure the relationship between sequences of a fixed length (k-mer) that can be affected by the presence of low-quality sequences. A common approach to evaluating assemblies is based on the analysis of the number of contigs, the length of the longest contig, and the value of N50 defined as the length of the contig representing 50 % of the length of the assembly. In this context, the objective of this study was to evaluate the effect of the use of crude and filtered reads on the values of the quality parameters obtained from the genome assembly of Bacillus altituidinis 19RS3 isolated from Ilex paraguariensis. The quality analysis of both starting files was performed with the FastqC software and the readings were filtered with the Trimmomatic software. The SPAdes software was used for the assembly and the QUAST tool for its evaluation. The best assembly for B. altitudinis 19RS3 was obtained from the filtered readings with the value of k-mer 79, which generated 16 contigs greater than 500 bp with a N50 of 931 914 bp and the longest contig of 966 271 bp. [ABSTRACT FROM AUTHOR]