Gordonibacter urolithinfaciens DSM 27213T was isolated from human feces and is able to metabolize ellagic acid (a dietary phenolic compound present in various fruits) to urolithins. Here, we report the finished and annotated genome sequence of this organism.
In this work, we report the draft genome sequence ofLactobacillus salivariusSGL 03, a novel potential probiotic strain isolated from healthy infant stools. Antibiotic resistance analysis revealed the presence of a tetracycline resistance gene without elements potentially responsible for interspecific horizontal gene transfer. Copyright © 2017 Federici et al.
Bacillus altitudinis P-10 was isolated from the rhizosphere of rice grown in an organic rice field and provides strong antagonism against the bacterial blight caused by Xanthomonas oryzae pv. oryzae in rice. Herein, we provide the complete genome sequence and a possible explanation of the antibiotic function of the P-10 strain.
Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 µmol m-2 s-1 suppressed the effects of illumination.
Pectobacterium carotovorum subsp. actinidiae KKH3 is an Enterobacteriaceae bacterial pathogen that infects kiwi plants, causing canker-like symptoms that pose a threat to the kiwifruit industry. Because the strain was originally isolated from woody plants and possesses numerous plant cell wall-degrading enzymes, this draft genome report provides insight into possible bioconversion applications, as well as a better understanding of this important plant pathogen.
Photosynthetic euglenids are major components of aquatic ecosystems and relatives of trypanosomes. Euglena gracilis has considerable biotechnological potential and great adaptability, but exploitation remains hampered by the absence of a comprehensive gene catalogue. We address this by genome, RNA and protein sequencing: the E. gracilis genome is >2Gb, with 36,526 predicted proteins. Large lineage-specific paralog families are present, with evidence for flexibility in environmental monitoring, divergent mechanisms for metabolic control, and novel solutions for adaptation to extreme environments. Contributions from photosynthetic eukaryotes to the nuclear genome, consistent with the shopping bag model are found, together with transitions between kinetoplastid and canonical systems. Control of protein expression is almost exclusively post-transcriptional. These data are a major advance in understanding the nuclear genomes of euglenids and provide a platform for investigating the contributions of E. gracilis and its relatives to the biosphere.
This is a de novo assembly and annotation of a complete mitochondrial genome from Pyrus pyrifolia in the family Rosaceae. The complete mitochondrial genome of P. pyrifolia was assembled from PacBio RSII P6-C4 sequencing reads. The circular genome was 458,873?bp in length, containing 39 protein-coding genes, 23 tRNA genes and three rRNA genes. The nucleotide composition was A (27.5%), T (27.3%), G (22.6%) and C (22.6%) with GC content of 45.2%. Most of protein-coding genes use the canonical start codon ATG, whereas nad1, cox1, matR and rps4 use ACG, mttB uses ATT, rpl16 and rps19 uses GTG. The stop codon is also common in all mitochondrial genes. The phylogenetic analysis showed that P. pyrifolia was clustered with the Malus of Rosaceae family. Maximum-likelihood analysis suggests a clear relationship of Rosids and Asterids, which support the traditional classification.
Dust particles from the deserts and semiarid lands in northern China cause pollution that increase the burden of allergic disease particularly in the urban population of East Asia. Dust particles that carried with windstorm are associated with microbial populations, which include virus, bacteria, and fungi. Spirosoma pulveris JSH 5-14T isolated from the gamma ray-irradiated dust sample collected at Nonsan, Chungnam province, South Korea and showed resistance against gamma and UV radiation. We carried out the whole genome sequencing to understand insight of radiation resistance and their mechanisms of survival. The whole genome of strain JSH 5-14T is comprised of 7,188,680 bp (G+C content of 50.50%) including 5,896 protein-coding genes and 52 RNA genes. The genome analysis of strain JSH 5-14T showed the presence of several genes involved in DNA repair pathways and defense mechanism against irradiation. In this study, we discuss the implication of such findings concerning other radiation resistant bacteria.
Potato (Solanum tuberosum L.) is one of the world’s most economically important food crops and holds major significance for future food security. Despite its importance, the study of potato genetics and breeding has lagged behind mainly due to its polyploid genome and high levels of heterozygosity. Conventional marker and genotyping approaches have been helpful in progressing potato genetic research but have also had limitations in exploiting the outcome from these studies for gene discovery and applied research applications. The sequencing of the potato genome, followed by advancements in marker and genotyping technologies, has brought a step change in the way potato genetic studies are conducted. Potato is now amenable to modern sequence-based marker and genotyping methods with their increased ability to put thousands of markers on any population of interest without a priori knowledge. This has increased the precision and resolution of genetic studies previously not feasible in potato. A diverse range of fixed and flexible genotyping platforms, for a wide variety of research and breeding applications, are now available. Concerted research efforts are now needed to screen the available genetic diversity for this important crop to identify novel and beneficial trait alleles in order to enable efficient and precise introgression breeding permitting breeding of climate smart, and resilient, potato cultivars. This chapter provides an overview of sequence-based marker development and genotyping methods along with their implications for potato research and breeding in the post-genomics era.
The genus Pectobacterium, which belongs to the bacterial family Enterobacteriaceae, contains numerous species that cause soft rot diseases in a wide range of plants. The species Pectobacterium carotovorum is highly heterogeneous, indicating a need for re-evaluation and a better classification of the species. PacBio was used for sequencing of two soft-rot-causing bacterial strains (NIBIO1006T and NIBIO1392), initially identified as P. carotovorumstrains by fatty acid analysis and sequencing of three housekeeping genes (dnaX, icdA and mdh). Their taxonomic relationship to other Pectobacterium species was determined and the distance from any described species within the genus Pectobacterium was less than 94?% average nucleotide identity (ANI). Based on ANI, phylogenetic data and genome-to-genome distance, strains NIBIO1006T, NIBIO1392 and NCPPB3395 are suggested to represent a novel species of the genus Pectobacterium, for which the name Pectobacterium polaris sp. nov. is proposed. The type strain is NIBIO1006T (=DSM 105255T=NCPPB 4611T).
Lactobacillus plantarum is widely found in fermented foods and has various phenotypic and genetic characteristics to adapt to the environment. Here we report the complete annotated genome sequence of the L. plantarum strain JBE245 (= KCCM43243) isolated for malolactic fermentation of apple juice. The genome comprises a single circular 3,262,611 bp chromosome with 2907 coding regions, 45 pseudogenes, and 91 RNA genes. The genome contains 4 malate dehydrogenase genes, 3 malate permease genes and various types of plantaricin-synthesizing genes. These genetic traits meet the selection criteria of the strains that should prevent the spoilage of apple juice during fermentation and efficiently convert malate to lactic acid.
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.© 2017 Prasad et al.; Published by Cold Spring Harbor Laboratory Press.
We examined extended-spectrum ß-lactamase-producing isolates from livestock, humans, companion animals, food, and the environment during 2009-2016 in Germany for the presence of CTX-M-27 allele within Escherichia coli sequence type (ST) 131. E. coli ST131 C1-M27 was exclusively present in humans; its incidence increased from 0% in 2009 to 45% in 2016.
A Gram-negative, yellow-pigmented, long-rod shaped bacterium Spirosoma montaniterrae DY10T was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk Province, Republic of Korea. Cells showed extreme gamma radiation resistance with the D10 value of 12 KGy. The complete genome sequence of strain DY10T is consist of a circular chromosome (5,797,678 bp) encoding 5,116 genes, 9 rRNA genes and 39 tRNA genes. The genomic features contain the key enzymes for gamma and UVC radiation.
Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India.Using next-generation sequencing, we sequenced the complete genome of 100 Salmonella Bareilly isolates obtained from patients who consumed contaminated product, from natural sources, and from unrelated historically and geographically disparate foods. Pathogen genomes were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission network.Phylogenetic analysis of WGS data revealed a common origin for outbreak strains, indicating that patients in Maryland and New York were infected from sources originating at a facility in India.These data represent the first report fully integrating WGS analysis with geographic mapping and a novel use of transmission networks. Results showed that WGS vastly improves our ability to delimit the scope and source of bacterial food-borne contamination events. Furthermore, these findings reinforce the extraordinary utility that WGS brings to global outbreak investigation as a greatly enhanced approach to protecting the human food supply chain as well as public health in general. Published by Oxford University Press for the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.
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