Here, we present the complete genome sequence of Rothia aeria type strain JCM 11412, isolated from air in the Russian space laboratory Mir. Recently, there has been an increasing number of reports on infections caused by R. aeria The genomic information will enable researchers to identify the pathogenicity of this organism. Copyright © 2016 Nambu et al.
Streptococcus sp. strain NPS 308, isolated from an 8-year-old girl diagnosed with infective endocarditis, likely presents a novel species of Streptococcus Here, we present a complete genome sequence of this species, which will contribute to better understanding of the pathogenesis of infective endocarditis. Copyright © 2016 Kondo et al.
Here, we present the complete genome sequence of Actinomyces naeslundii strain ATCC 27039, isolated from an abdominal wound abscess. This strain is genetically transformable and will thus provide valuable information related to its crucial role in oral multispecies biofilm development. Copyright © 2016 Mashimo et al.
Escherichia coli serotype O25b:H4 is involved in human urinary tract infections.In this study, we sequenced and analyzed E. coli O25b:H4 isolated from a patient sufferingfrom recurring UTI infections in an intensive care unit at Hera General Hospital inMakkah, Saudi Arabia. We aimed to determine the virulence genes for pathogenesis anddrug resistance of this isolate compared to other E. coli strains. We sequenced and analyzedthe E. coli O25b:H4 Saudi strain clinical isolate using next generation sequencing. Usingthe ERGO genome analysis platform, we performed annotations and identified virulenceand antibiotic resistance determinants of this clinical isolate. The E. coli O25b:H4 genomewas assembled into four contigs representing a total chromosome size of 5.28 Mb, andthree contigs were identified, including a 130.9 kb (virulence plasmid) contig bearing thebla-CTX gene and 32 kb and 29 kb contigs. In comparing this genome to otheruropathogenic E. coli genomes, we identified unique drug resistance and pathogenicityfactors. In this work, whole-genome sequencing and targeted comparative analysis of aclinical isolate of uropathogenic Escherichia coli O25b:H4 was performed. This strainencodes virulence genes linked with extraintestinal pathogenic E. coli (ExPEC) that areexpressed constitutively in E. coli ST131. We identified the genes responsible forpathogenesis and drug resistance and performed comparative analyses of the virulenceand antibiotic resistance determinants with those of other E. coli UPEC isolates. This isthe first report of genome sequencing and analysis of a UPEC strain from Saudi Arabia.
Streptomyces laurentii ATCC 31255 produces thiostrepton, a thiopeptide class antibiotic. Here, we report the complete genome sequence for this strain, which contains a total of 8,032,664 bp, 7,452 predicted coding sequences, and a G+C content of 72.3%. Copyright © 2016 Doi et al.
Although ubiquitous and abundant in soils, acidobacteria have mostly escaped isolation and remain poorly investigated. Only a few cultured representatives and just eight genomes of subdivisions 1, 3, and 4 are available to date. Here, we determined the complete genome sequence of strain HEG_-6_39, the first genome of Acidobacterium subdivision 6. Copyright © 2016 Huang et al.
In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence?Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50.Available at github.com/samhykim/nsgcourtade@eecs.berkeley.edu or dntse@stanford.eduSupplementary data are available at Bioinformatics online.© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormapehaghshe@sfu.ca or cedric.chauve@sfu.caSupplementary data are available at Bioinformatics online.© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM(12)), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM(12). By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.
[Pasteurella] pneumotropica is a ubiquitous bacterium frequently isolated from laboratory rodents. Although this bacterium causes various diseases in immunosuppressed animals, little is known about major virulence factors and their roles in pathogenicity. To identify virulence factors, we sequenced the genome of [P.] pneumotropica biotype Heyl strain ATCC 12555, and compared the resulting non-contiguous draft genome sequence with the genome of biotype Jawetz strain ATCC 35149. Among a large number of genes encoding virulence-associated factors in both strains, four genes encoding for YadA-like proteins, which are known virulence factors that function in host cell adherence and invasion in many pathogens. In this study, we assessed YadA distribution and biological activity as an example of one of virulence-associated factor shared, with biotype Jawetz and Heyl. More than half of mouse isolates were found to have at least one of these genes; whereas, the majority of rat isolates did not. Autoagglutination activity, and ability to bind to mouse collagen type IV and mouse fibroblast cells, was significantly higher in YadA-positive than YadA-negative strains. To conclude, we identified a large number of candidate genes predicted to influence [P.] pneumotropica pathogenesis.© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Fmb60 is a wild-type Bacillus subtilis isolated from compost with significant broad-spectrum antimicrobial activities. Two novel PKS clusters were recognized in the genome sequence of fmb60, and then three polyene antibiotics, aurantinins B, C, and D, 1-3, were obtained by bioactivity-guided isolation from the fermentation of fmb60. The structures of aurantinins B-D were elucidated by LC-HRMS and NMR data analysis. Aurantinins C and D were identified as new antimicrobial compounds. The three aurantinins showed significant activity against multidrug-resistant Staphylococcus aureus and Clostridium sporogenes. However, aurantinins B-D did not exhibit any cytotoxicity (IC50 > 100 µg/mL) against LO2 and Caco2 cell lines by MTT assay. Furthermore, using S. aureus as a model bacterium to explore the antibacterial mechanism of aurantinins B-D, it was revealed that the bactericidal activity of aurantinins B-D was related to their ability to disrupt the cell membrane.
A major roadblock to understanding how microbes in the gastrointestinal tract colonize and influence the physiology of their hosts is our inability to genetically manipulate new bacterial species and experimentally assess the function of their genes. We describe the application of population-based genomic sequencing after chemical mutagenesis to map bacterial genes responsible for motility in Exiguobacterium acetylicum, a representative intestinal Firmicutes bacterium that is intractable to molecular genetic manipulation. We derived strong associations between mutations in 57 E. acetylicum genes and impaired motility. Surprisingly, less than half of these genes were annotated as motility-related based on sequence homologies. We confirmed the genetic link between individual mutations and loss of motility for several of these genes by performing a large-scale analysis of spontaneous suppressor mutations. In the process, we reannotated genes belonging to a broad family of diguanylate cyclases and phosphodiesterases to highlight their specific role in motility and assigned functions to uncharacterized genes. Furthermore, we generated isogenic strains that allowed us to establish that Exiguobacterium motility is important for the colonization of its vertebrate host. These results indicate that genetic dissection of a complex trait, functional annotation of new genes, and the generation of mutant strains to define the role of genes in complex environments can be accomplished in bacteria without the development of species-specific molecular genetic tools.
The genus Serinibacter belongs, based on the phylogenetic analysis of the nearly full-length 16S rRNA gene, to the Beutenbergiaceae together with the genera Beutenbergia, Salana, and Miniimonas. The two species of the genus Serinibacter shared 99.6% 16S rRNA gene sequence similarity but low DNA DNA relatedness. Cells are irregular rods, Gram-stain positive, not acid-fast. Endospores are not formed. Nonmotile. Aerobic to anaerobic. Oxidase-negative, catalase-positive. The peptidoglycan type is A4a with an l-Ser residue at position 1 of the peptide subunit. The acyl type is acetyl. The major cell-wall sugar is galactose. The predominant menaquinone is MK-8(H4). The major polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and unidentified phospholipids. Phosphatidylethanolamine is absent. The cellular fatty acid profile is dominated by the occurrence of iso- and anteiso-branched-chain acids. Mycolic acids are absent. The genomic G+C content is 70.7 to 72.8 mol%.
Pedobacter steynii DX4, isolated from Qinghai-Tibet plateau, exhibited capability to effectively degrade crude oil at low temperature. In order to illustrate its biodegradation mechanism, whole genome and transcriptome sequencing were performed. It is the first genome of crude oil degrading strain in Pedobacter genus. The P. steynii DX4 genome consists of a single circular chromosome of 6,581,659 bp with an average G+C content of 41.31% and encodes 5464 genes in all. GIs were predicted and comparison analysis was performed between relative species. Genome annotation predicted several hydrocarbon oxygenases, chemotaxis proteins and biosurfactant synthetases. The transcriptional sequences profiled a lot of differently expressed genes when cells respectively grown on crude oil and pyruvate mediums. Crude oil significantly stimulated the expression of the genes related to the hydrocarbon oxidation and resparitory chain. Genomic and transcriptomic analysis of P. steynii DX4 have revealed the machenism of the crude oil degradation in Pedobacter steynii DX4 and provided us with valuable knowledge base to make effective strategy to mitigate the ecological damage caused by crude oil pollution.
Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elements Vibrio seventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.
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