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July 7, 2019

Evidence for an opportunistic and endophytic lifestyle of the Bursaphelenchus xylophilus-associated bacteria Serratia marcescens PWN146 isolated from wilting Pinus pinaster.

Pine wilt disease (PWD) results from the interaction of three elements: the pathogenic nematode, Bursaphelenchus xylophilus; the insect-vector, Monochamus sp.; and the host tree, mostly Pinus species. Bacteria isolated from B. xylophilus may be a fourth element in this complex disease. However, the precise role of bacteria in this interaction is unclear as both plant-beneficial and as plant-pathogenic bacteria may be associated with PWD. Using whole genome sequencing and phenotypic characterization, we were able to investigate in more detail the genetic repertoire of Serratia marcescens PWN146, a bacterium associated with B. xylophilus. We show clear evidence that S. marcescens PWN146 is able to withstand and colonize the plant environment, without having any deleterious effects towards a susceptible host (Pinus thunbergii), B. xylophilus nor to the nematode model C. elegans. This bacterium is able to tolerate growth in presence of xenobiotic/organic compounds, and use phenylacetic acid as carbon source. Furthermore, we present a detailed list of S. marcescens PWN146 potentials to interfere with plant metabolism via hormonal pathways and/or nutritional acquisition, and to be competitive against other bacteria and/or fungi in terms of resource acquisition or production of antimicrobial compounds. Further investigation is required to understand the role of bacteria in PWD. We have now reinforced the theory that B. xylophilus-associated bacteria may have a plant origin.


July 7, 2019

Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio Single-Molecule Real-Time Technology

Mycobacterium avium is an important pathogenic bacterium in birds and has never, to our knowledge, reported to be isolated from domestic ducks. We present here the complete genome sequence of a virulent strain of Mycobacterium avium, isolated from domestic Pekin ducks for the first time, which was determined by PacBio single-molecule real-time technology. Copyright © 2016 Song et al.


July 7, 2019

Complete Genome Sequences of Four Enterohemolysin-Positive (ehxA) Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains

Shiga toxin-producing Escherichia coli (STEC) strains are important foodborne pathogens associated with human disease. Most disease-associated STEC strains carry the locus of enterocyte effacement (LEE); however, regularly LEE-negative STEC strains are recovered from ill patients. Few reference sequences are available for these isolate types. Here, we report here the complete genome sequences for four LEE-negative STEC strains. Copyright © 2016 Lorenz et al.


July 7, 2019

First complete genome sequence of the skin-improving Lactobacillus curvatus strain FBA2, isolated from fermented vegetables, determined by PacBio single-molecule real-time technology.

The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II. The single circular chromosome (1,848,756 bp, G+C content of 42.1%) of L. curvatus FBA2, isolated from fermented vegetables, contained low G+C regions (26.9% minimum) and 43 sets of >1,000-bp identical sequence pairs. No plasmids were detected. Copyright © 2016 Nakano et al.


July 7, 2019

Complete genome of the starch-degrading myxobacteria Sandaracinus amylolyticus DSM 53668T.

Myxobacteria are members of d-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 a-amylases and two ?-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other d-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative ß-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


July 7, 2019

Improved complete genome sequence of the extremely radioresistant bacterium Deinococcus radiodurans R1 obtained using PacBio single-molecule sequencing.

The genome sequence of Deinococcus radiodurans R1 was published in 1999. We resequenced D. radiodurans R1 using PacBio and compared the sequence with the published one. Large insertions and single nucleotide polymorphisms (SNPs) were observed among the genome sequences. A more accurate genome sequence will be helpful to studies of D. radiodurans. Copyright © 2016 Hua and Hua.


July 7, 2019

High-quality genome assembly and annotation for Plasmodium coatneyi, generated using single-molecule real-time PacBio technology.

Plasmodium coatneyi is a protozoan parasite species that causes simian malaria and is an excellent model for studying disease caused by the human malaria parasite, P. falciparum Here we report the complete (nontelomeric) genome sequence of P. coatneyi Hackeri generated by the application of only Pacific Biosciences RS II (PacBio RS II) single-molecule real-time (SMRT) high-resolution sequence technology and assembly using the Hierarchical Genome Assembly Process (HGAP). This is the first Plasmodium genome sequence reported to use only PacBio technology. This approach has proven to be superior to short-read only approaches for this species. Copyright © 2016 Chien et al.


July 7, 2019

The Lysobacter capsici AZ78 genome has a gene pool enabling it to interact successfully with phytopathogenic microorganisms and environmental factors.

Lysobacter capsici AZ78 has considerable potential for biocontrol of phytopathogenic microorganisms. However, lack of information about genetic cues regarding its biological characteristics may slow down its exploitation as a biofungicide. In order to obtain a comprehensive overview of genetic features, the L. capsici AZ78 genome was sequenced, annotated and compared with the phylogenetically related pathogens Stenotrophomonas malthophilia K729a and Xanthomonas campestris pv. campestris ATCC 33913. Whole genome comparison, supported by functional analysis, indicated that L. capsici AZ78 has a larger number of genes responsible for interaction with phytopathogens and environmental stress than S. malthophilia K729a and X. c. pv. campestris ATCC 33913. Genes involved in the production of antibiotics, lytic enzymes and siderophores were specific for L. capsici AZ78, as well as genes involved in resistance to antibiotics, environmental stressors, fungicides and heavy metals. The L. capsici AZ78 genome did not encompass genes involved in infection of humans and plants included in the S. malthophilia K729a and X. c. pv. campestris ATCC 33913 genomes, respectively. The L. capsici AZ78 genome provides a genetic framework for detailed analysis of other L. capsici members and the development of novel biofungicides based on this bacterial strain.


July 7, 2019

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe.

We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were reported. Therefore, to characterize its biological and medical significance, we sought to determine and analyze the complete genome sequence of Bacillus sp. NRRL B-14911.Based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) genes, sequence analysis of the 16S-23S rDNA intergenic transcribed spacers, phenotypic microarray, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we propose that this organism belongs to the species Bacillus infantis, previously shown to be associated with sepsis in a newborn child. Analysis of the complete genome of Bacillus sp. NRRL B-14911 revealed several virulence factors including adhesins, invasins, colonization factors, siderophores and transporters. Likewise, the bacterial genome encodes a wide range of methyl transferases, transporters, enzymatic and biochemical pathways, and insertion sequence elements that are distinct from other closely related bacilli.The complete genome sequence of Bacillus sp. NRRL B-14911 provided in this study may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence. Additionally, this bacterium may serve as a useful tool to establish a disease model that permits systematic analysis of autoimmune events in various susceptible rodent strains.


July 7, 2019

Complete genome sequence of the D-amino acid catabolism bacterium Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea

Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. Copyright © 2016 Fu et al.


July 7, 2019

Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function.

Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny. Copyright © 2016 Elsevier GmbH. All rights reserved.


July 7, 2019

Development of Streptomyces sp. FR-008 as an emerging chassis

Microbial-derived natural products are important in both the pharmaceutical industry and academic research. As the metabolic potential of original producer especially Streptomyces is often limited by slow growth rate, complicated cultivation profile, and unfeasible genetic manipulation, so exploring a Streptomyces as a super industrial chassis is valuable and urgent. Streptomyces sp. FR-008 is a fast-growing microorganism and can also produce a considerable amount of macrolide candicidin via modular polyketide synthase. In this study, we evaluated Streptomyces sp. FR-008 as a potential industrial-production chassis. First, PacBio sequencing and transcriptome analyses indicated that the Streptomyces sp. FR-008 genome size is 7.26 Mb, which represents one of the smallest of currently sequenced Streptomyces genomes. In addition, we simplified the conjugation procedure without heat-shock and pre-germination treatments but with high conjugation efficiency, suggesting it is inherently capable of accepting heterologous DNA. In addition, a series of promoters selected from literatures was assessed based on GusA activity in Streptomyces sp. FR-008. Compared with the common used promoter ermE*-p, the strength of these promoters comprise a library with a constitutive range of 60–860%, thus providing the useful regulatory elements for future genetic engineering purpose. In order to minimum the genome, we also target deleted three endogenous polyketide synthase (PKS) gene clusters to generate a mutant LQ3. LQ3 is thus an “updated” version of Streptomyces sp. FR-008, producing fewer secondary metabolites profiles than Streptomyces sp. FR-008. We believe this work could facilitate further development of Streptomyces sp. FR-008 for use in biotechnological applications.


July 7, 2019

Complete genome sequence of Lactobacillus plantarum LZ227, a potential probiotic strain producing B-group vitamins.

B-group vitamins play an important role in human metabolism, whose deficiencies are associated with a variety of disorders and diseases. Certain microorganisms such as Lactic acid bacteria (LAB) have been shown to have capacities for B-group vitamin production and thus could potentially replace chemically synthesized vitamins for food fortification. A potential probiotic strain named Lactobacillus plantarum LZ227, which was isolated from raw cow milk in this study, exhibits the ability to produce B-group vitamins. Complete genome sequencing of LZ227 was performed to gain insights into the genetic elements involved in B-group vitamin production. The genome of LZ227 contains a circular 3,131,750-bp chromosome, three circular plasmids and two predicted linear plasmids. LZ227 also contains gene clusters for biosynthesis of both riboflavin and folate. This genome sequence provides a basis for further elucidation of its molecular genetics and probiotic functions, and will facilitate its applications as starter cultures in food industry. Copyright © 2016 Elsevier B.V. All rights reserved.


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