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July 7, 2019  |  

Closed genome sequences and antibiograms of 16 Pasteurella multocida isolates from bovine respiratory disease complex cases and apparently healthy controls.

Pasteurella multocida is an animal-associated Gram-negative member of the Pasteurellaceae family. It is an opportunistic pathogen and is one of the principal bacterial species contributing to bovine respiratory disease complex (BRDC) in feedlot cattle. We present 16 closed genome sequences and antibiograms of isolates cultured from calves exhibiting clinical signs of BRDC and from control calves not showing signs of BRDC.


July 7, 2019  |  

Complete genome sequence of Marinobacterium aestuarii ST58-10T, a benzene-degrading bacterium isolated from estuarine sediment.

Marinobacterium aestuarii ST58-10Twas identified as a benzene-degrading aerobic bacterium isolated from estuarine sediment in the Republic of Korea. The ge- nome of strain ST58-10Twas found to be composed of a single circular chromosome (5,191,608bp) with a G+C content of 58.78% and harboring 4,473 protein-coding genes. The assembled sequence data will help elucidate potential metabolic pathways and mechanisms responsible for the hydrocarbon-degrading ability of M. aestuarii ST58-10T.


July 7, 2019  |  

Complete genome sequence of herpes simplex virus 2 strain 333.

Herpes simplex virus 2, or human herpesvirus 2, is a ubiquitous human pathogen that causes genital ulcerations and establishes latency in sacral root ganglia. We fully sequenced and manually curated the viral genome sequence of herpes simplex virus 2, strain 333 using Pacific Biosciences and Illumina sequencing technologies.


July 7, 2019  |  

Complete genome sequences of historic Clostridioides difficile food-dwelling ribotype 078 strains in Canada identical to that of the historic human clinical strain M120 in the United Kingdom.

Clostridioides (Clostridium) difficile is a spore-forming anaerobic bacte- rium that causes severe intestinal diseases in humans. Here, we report the complete genome sequence of the first C. difficile foodborne type strain (PCR ribotype 078) isolated from food animals in Canada in 2004, which has 100% similarity to the ge- nome sequence of the historic human clinical strain M120.


July 7, 2019  |  

Complete genome sequence of Bacillus megaterium strain TG1-E1, a plant drought tolerance-enhancing bacterium.

Based on a combination of next-generation sequencing and single-molecule sequencing, we obtained the whole-genome sequence of Bacillus megaterium strain TG1-E1, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress. The complete genome is estimated to be approximately 5.48 Mb containing a total of 5,858 predicted protein-coding DNA sequences.


July 7, 2019  |  

Complete genome sequence of a wild-type isolate of Caulobacter vibrioides strain CB1.

The complete genome sequence of Caulobacter vibrioides strain CB1 consists of a chromosome of 4,137,285 bp, with a GC content of 67.2% and 3,990 coding DNA sequences. This strain contains the typical genome rearrangement that is characteristic of the Caulobacter strains that are currently sequenced. However, this strain is so closely related to sequenced strain NA1000 that rearrangements were minimal. This will allow further clarification of the causes of rearrangements in the species.


July 7, 2019  |  

Complete genome sequences of two Rhodobacter strains.

We report the complete genome sequences of two strains of the Alphaproteobacteria genus Rhodobacter, Rhodobacter blasticus 28/5, the source of the commercially available enzyme RsaI, and a new isolate of Rhodobacter sphaeroides 2.4.1. Both strains contain multiple restriction-modification systems, and their DNA methylation motifs are included in this report.


July 7, 2019  |  

Myxobacteria: Unraveling the potential of a unique microbiome niche

Natural products obtained from microorganisms have been playing an imperative role in drug discovery for decades. Hence, rightfully, microorganisms are considered as the richest source of biochemical remedies. In this review, we represent an unexplored family of bacteria considered to be prolific producers of diverse metabolites. Myxobacteria are gram-negative bacteria which have been reported to produce large families of secondary metabolites with prominent antimicrobial, antifungal, and antitumor activities. Klaus Gerth, Norbert Bedorf, Herbert Irschik, and Hans Reichenbach observed the antifungal activity of Sorangium cellulosum against Mucor hiemalis. In 2006, Hans Reichenbach and his team obtained a novel macrolide cruentaren A from Byssovorax cruenta (myxobacteria). Cruentaren A showed inhibitory activity against yeast and filamentous fungi. It also showed selective inhibitory activity against mitochondrial F-type ATPase. Cruentaren A has been found to be cytotoxic against various human cancer cell lines. In 2007, Reichenbach and his colleagues named an antibiotic produced by Sorangium cellulosum strain Soce895 as thuggacin. This antibiotic acts on the respiration of some bacteria. Other antibiotics from myxobacteria, myxovirescin, and megovalicin show broad-spectrum bactericidal activity. The College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China, evaluated the antitumor property of epothilone, which has shown promise for breast cancer treatment. The study determined high potential and versatile antimicrobial and antitumor secondary metabolites of myxobacteria. In yet another study, Ratjadone A, that exhibited strong antiviral activity against HIV, was obtained from Sorangium cellulosum strain. This compound shows antiviral activity in vitro but has low selectivity. Further search on the derivatives of this compound might help in the future. This is rationale enough to pre-empt that every strain of myxobacteria might be endowed to produce secondary metabolites with novel mechanisms of action which are rarely produced by other microbes. The available data establishes the impact of myxobacterial studies in search for novel metabolites as a front runner in microbiological research and worthy enough to be a thrust area of research in pharmacology.


July 7, 2019  |  

The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group during para-hydroxybenzoate catabolism.

The NIH shift is a chemical rearrangement in which a substituent on an aromatic ring undergoes an intramolecular migration, primarily during an enzymatic hydroxylation reaction. The molecular mechanism for the NIH shift of a carboxyl group has remained a mystery for 40 years. Here, we elucidate the molecular mechanism of the reaction in the conversion of para-hydroxybenzoate (PHB) to gentisate (GA, 2, 5-dihydroxybenzoate). Three genes (phgABC) from the PHB utilizer Brevibacillus laterosporus PHB-7a encode enzymes (p-hydroxybenzoyl-CoA ligase, p-hydroxybenzoyl-CoA hydroxylase and gentisyl-CoA thioesterase, respectively) catalyzing the conversion of PHB to GA via a route involving CoA thioester formation, hydroxylation concomitant with a 1, 2-shift of the acetyl CoA moiety and thioester hydrolysis. The shift of the carboxyl group was established rigorously by stable isotopic experiments with heterologously expressed phgABC, converting 2, 3, 5, 6-tetradeutero-PHB and [carboxyl-13 C]-PHB to 3, 4, 6-trideutero-GA and [carboxyl-13 C]-GA respectively. This is distinct from the NIH shifts of hydrogen and aceto substituents, where a single oxygenase catalyzes the reaction without the involvement of a thioester. The discovery of this three-step strategy for carboxyl group migration reveals a novel role of the CoA thioester in biochemistry and also illustrates the diversity and complexity of microbial catabolism in the carbon cycle.© 2018 John Wiley & Sons Ltd.


July 7, 2019  |  

Genomic features of the Helicobacter pylori strain PMSS1 and its virulence attributes as deduced from its in vivo colonisation patterns.

The human gastric pathogen Helicobacter pylori occurs in two basic variants, either exhibiting a functional cagPAI-encoded type-4-secretion-system (T4SS) or not. Only a few cagPAI-positive strains have been successfully adapted for long-term infection of mice, including the pre-mouse Sydney strain 1 (PMSS1). Here we confirm that PMSS1 induces gastric inflammation and neutrophil infiltration in mice, progressing to intestinal metaplasia. Complete genome analysis of PMSS1 revealed 1,423 coding sequences, encompassing the cagPAI gene cluster and, unusually, the location of the cytotoxin-associated gene A (cagA) approximately 15 kb downstream of the island. PMSS1 harbours three genetically exchangeable loci that are occupied by the hopQ coding sequences. HopQ represents a critical co-factor required for the translocation of CagA into the host cell and activation of NF-?B via the T4SS. Long-term colonisation of mice led to an impairment of cagPAI functionality. One of the bacterial clones re-isolated at four months post-infection revealed a mutation in the cagPAI gene cagW, resulting in a frame shift mutation, which prevented CagA translocation, possibly due to an impairment of T4SS function. Rescue of the mutant cagW re-established CagA translocation. Our data reveal intriguing insights into the adaptive abilities of PMSS1, suggesting functional modulation of the H. pylori cagPAI virulence attribute.© 2018 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.


July 7, 2019  |  

Emergence of gyrovirus 3 in commercial broiler chickens with transmissible viral proventriculitis.

Gyrovirus 3 (GyV3) has been identified in faeces from children with acute gastroenteritis. However, whether GyV3 is prevalent in poultry has not been determined to date. To the best of our knowledge, this study is the first to isolate GyV3 from commercial broiler chickens with transmissible viral proventriculitis (TVP) in China. The complete genome of the virus shares 98.4% sequence identity with the FecGy strain that causes acute gastroenteritis in children. Epidemiological investigation from 2013 to 2017 revealed that the infection rate of GyV3 reached 12.5% (42/336) in commercial broiler chickens with TVP, indicating that the infection of GyV3 was ubiquitous in chickens. The emergence of GyV3 in commercial broiler chickens should be highly concerning for public health.© 2018 Blackwell Verlag GmbH.


July 7, 2019  |  

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.


July 7, 2019  |  

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.

Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both on strains and on food matrix. Several B. thermosphacta genome sequences have been reported, all issued from meat isolates. Here, we report four genome sequences, one complete and three as drafts. The four B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated from different ecological niches (seafood or meat products either spoiled or not and bovine slaughterhouse). These strains known as phenotypically and genetically different were selected to represent intraspecies diversity. CD 337 genome is 2,594,337 bp long, complete and circular, containing 2593 protein coding sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding sequences, respectively. These genomes were compared with two other B. thermosphacta complete genome sequences. The main genome content differences between strains are phages, plasmids, restriction/modification systems, and cell surface functions, suggesting a similar metabolic potential but a different niche adaptation capacity.


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