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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]

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]

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]

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]

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]

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]

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]

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]

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]

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. 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]

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Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts. [ABSTRACT FROM AUTHOR]

Background: The human gut microbiome contains millions of genes and many undetected bacteria species. Recovering bacterial genomes from large complex metagenomes remains highly challenging, and current binning methods show insufficient recall rates. Objective: This study was performed to put forward a new metagenome binning method with promising recall rate and accuracy. Methods: We found that more than 85% of the genes could be aligned to only one bacteria species by using strict BLAST parameters (identity > 90% and aligning length > 100 bp). This phenomenon was called "the gene uniqueness", which indicated that the most bacterial genes could be exclusive to the species' taxonomy. In our new metagenome binning method, we could cluster contigs based on gene similarity via a graph model. Any contig shared with same gene under Strict Blast parameters would be clustered into one bin. Results: we obtained 1,131 bins and reconstructed the genomes of 12 unknown species for MetaHIT data Our method exhibited a more promising recall rate, faster running speed and lower time complexity than the current methods. Conclusions: The present new metagenome binning method based on gene uniqueness had high recall rate and low error, which could be applied to assemble the bacterial genomes efficiently in complex metagenome. [ABSTRACT FROM AUTHOR]

De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria. [ABSTRACT FROM AUTHOR]

Aims: Plants host communities of fungal and bacterial endophytes, establishing a complex network of multipartite interactions, but the mechanisms whereby they interact are poorly understood. Some fungi, such as the beneficial mycorrhiza-like fungus Serendipita (=Piriformospora) indica, can be helped by bacteria for establishment, survival and colonization. Although this fungus harbors a Rhizobium as an endofungal bacterium, we hypothesized that other bacteria might also establish associations with the fungus and combining S. indica with bacteria might enhance plant growth and health. Methods: The interactions among S. indica and four endophytic Proteobacteria belonging to Methylobacterium, Tardiphaga, Rhodanobacter and Trinickia spp. were characterized in vitro and for their effect on tomato growth and biocontrol of Fusarium oxysporum and Rhizoctonia solani. Possible mechanisms behind these interactions were described based on genome and microscopic analyses, using fungal and bacterial strains tagged with fluorescent markers. Results: All bacteria stimulated S. indica growth in vitro. Moreover, several of the bacteria stimulated growth of tomato plants, but co-inoculations with S. indica and bacteria did not perform better than single inoculations. Contrarily, combinations of S. indica and bacteria significantly reduced disease progression of fungal pathogens. These microbes seem to cooperate in the process of root colonization for instance by increasing fungal sporulation and hyphae expansion, showing multipartite interaction between microbes and plants. Interestingly, the strain of Trinickia internally colonizes spores of S. indica as an endofungal bacterium during in vitro-co-culturing, suggesting further that the fungus might acquire formerly unrecognized genera of bacteria and genome analysis of the bacteria revealed many genes potentially involved in fungal and plant growth stimulation, biocontrol and root colonization, highlighting putative mechanisms of plant-fungal-bacterial interaction. Conclusions: Our study represents an important step towards unraveling the complex interactions among plants, S. indica, endophytic bacteria and fungal pathogens, and indicates that adding bacteria to fungal inoculum could have a remarkable impact on the plant-S. indica symbiosis. [ABSTRACT FROM AUTHOR]

Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods: We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result: The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search. Conclusion: The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further. [ABSTRACT FROM AUTHOR]

This study characterized the biosynthetic potential of the bacterium Achromobacter xylosoxidans strain ISP2-142-O-2-A associated with the sponge Haliclona sp. nov. Chemistry- and bioactivityguided purification of extracts from A. xylosoxidans afforded three compounds (1-3). The nucleoside 5'-deoxyadenosine (Compound 1) showed significant HIV cytoprotection activity with no cytotoxic activity to normal mammalian cells. The alkylquinolines 2-heptylquinolin-4-ol (Compound 2) and 2-nonylquinolin-4-ol (Compound 3) showed antimicrobial activity against Staphylococcus aureus and cytotoxicity to normal mammalian cells. This is the first report of Compounds 1-3 in A. xylosoxidans, and it is proposed that they have distinct roles for the bacterium to persist as a sponge-associated microorganism. Genomic analysis revealed the presence of 10 biosynthetic gene clusters (BGCs), indicating the potential of A. xylosoxidans strain ISP2-142-O-2-A as a source organism for other classes of bioactive natural products. [ABSTRACT FROM AUTHOR]

Many models of genome rearrangement involve operations that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the elements of a group, and consequently, between evolutionary paths and walks on the Cayley graph. Many common methods for phylogenetic reconstruction rely on calculating the minimal distance between two genomes; this omits much of the other information available from the Cayley graph. In this paper, we begin an exploration of some of this additional information, in particular describing the phylogeny as a Steiner tree within the Cayley graph, and exploring the "interval" between two genomes. While motivated by problems in systematic biology, many of these ideas are of independent group-theoretic interest. [ABSTRACT FROM AUTHOR]

The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable de novo bacterial genome assembly. Although many algorithms and tools have been developed for base calling, read mapping, de novo assembly, and polishing, an automated pipeline is not available for one-stop analysis for circular bacterial genome reconstruction. In this paper, we present the pipeline CCBGpipe for completing circular bacterial genomes. Raw current signals are demultiplexed and base called to generate sequencing data. Sequencing reads are de novo assembled several times by using a sampling strategy to produce circular contigs that have a sequence in common between their start and end. The circular contigs are polished by using raw signals and sequencing reads; then, duplicated sequences are removed to form a linear representation of circular sequences. The circularized contigs are finally rearranged to start at the start position of dnaA / repA or a replication origin based on the GC skew. CCBGpipe implemented in Python is available at https://github.com/jade-nhri/CCBGpipe. Using sequencing data produced from a single MinION run, we obtained 48 circular sequences, comprising 12 chromosomes and 36 plasmids of 12 bacteria, including Acinetobacter nosocomialis , Acinetobacter pittii , and Staphylococcus aureus. With adequate quantities of sequencing reads (80×), CCBGpipe can provide a complete and automated assembly of circular bacterial genomes. [ABSTRACT FROM AUTHOR]

PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool – Enhanced Release) have become two of the most widely used web servers for identifying putative prophages in bacterial genomes. Here we review the main capabilities of these web resources, provide some practical guidance regarding their use and discuss possible future improvements. PHAST, which was first described in 2011, made its debut just as whole bacterial genome sequencing and was becoming inexpensive and relatively routine. PHAST quickly gained popularity among bacterial genome researchers because of its web accessibility, its ease of use along with its enhanced accuracy and rapid processing times. PHASTER, which appeared in 2016, provided a number of much-needed enhancements to the PHAST server, including greater processing speed (to cope with very large submission volumes), increased database sizes, a more modern user interface, improved graphical displays and support for metagenomic submissions. Continuing developments in the field, along with increased interest in automated phage and prophage finding, have already led to several improvements to the PHASTER server and will soon lead to the development of a successor to PHASTER (to be called PHASTEST). [ABSTRACT FROM AUTHOR]