scholarly journals Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Andrej Benjak ◽  
Charlotte Avanzi ◽  
Yvonne Benito ◽  
Franck Breysse ◽  
Christophe Chartier ◽  
...  
Keyword(s):  
Causative Agent ◽  
Clinical Manifestations ◽  
Distinct Species ◽  
Close Relative ◽  
Protein Coding ◽  
Content Type ◽  
Mycobacterial Genome ◽  
Mycobacterium Lepromatosis ◽  
Dairy Animals ◽  
Phylogenomic Analyses

ABSTRACT Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis. In this study, the genome of this pathogen was sequenced and analyzed. Phylogenomic analyses confirmed that the pathogen present in nodular thelitis and tuberculoid scrotitis is a distinct species related to the leprosy bacilli and Mycobacterium haemophilum. Because the pathogen was originally isolated from a bovine udder, it was named “Mycobacterium uberis.” The genome of “M. uberis” is only 3.12 Mb in length, which represents the smallest mycobacterial genome identified so far but which is close to that of leprosy bacilli in size. The genome contains 1,759 protein-coding genes and 1,081 pseudogenes, indicative of extensive reductive evolution and likely the reason that M. uberis cannot be grown axenically. The pseudogenization and genome reduction in M. uberis seem to have been to some extent independent from the results determined for the genomes of the leprosy bacilli. IMPORTANCE M. uberis is an emerging skin pathogen in dairy animals. Its genome underwent massive reduction and gene decay, leading to a minimal set of genes required for an obligatory intracellular lifestyle, which highly resembles the evolution of the leprosy agents M. leprae and M. lepromatosis. The genomic similarity between M. uberis and the leprosy bacilli can help in identifying key virulence factors of these closely related species or in identifying genes responsible for the distinct differences between thelitis or scrotitis and leprosy with respect to clinical manifestations. Specific DNA markers can now be developed for quick detection of this pathogen.

scholarly journals Sequence-Defined Transposon Mutant Library of Burkholderia thailandensis

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Larry A. Gallagher ◽  
Elizabeth Ramage ◽  
Rapatbhorn Patrapuvich ◽  
Eli Weiss ◽  
Mitch Brittnacher ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Burkholderia Pseudomallei ◽  
Large Scale ◽  
Close Relative ◽  
Mutant Library ◽  
Safety Level ◽  
Protein Coding ◽  
Burkholderia Thailandensis ◽  
Content Type ◽  
Level 3

ABSTRACTWe constructed a near-saturation transposon mutant library forBurkholderia thailandensis, a low-virulence surrogate for the causative agent of melioidosis (Burkholderia pseudomallei). A primary set of nearly 42,000 unique mutants (~7.5 mutants/gene) was generated using transposon Tn5derivatives. The strains carry insertions in 87% of the predicted protein-coding genes of the organism, corresponding to nearly all of those nonessential for growth on nutrient agar. To achieve high genome coverage, we developed procedures for efficient sequence identification of insertions in extremely GC-rich regions of DNA. To facilitate strain distribution, we created a secondary library with two mutants per gene for which most transposon locations had been confirmed by resequencing. A map of mutations in the two-allele library and procedures for obtaining strains can be found athttp://tools.nwrce.org/tn_mutants/andhttp://www.gs.washington.edu/labs/manoil/. The library should facilitate comprehensive mutant screens and serve as a source of strains to test predicted genotype-phenotype associations.IMPORTANCEThe Gram-negative bacteriumBurkholderia pseudomalleiis a biothreat agent due to its potential for aerosol delivery and intrinsic antibiotic resistance and because exposure produces pernicious infections. Large-scale studies ofB. pseudomalleiare limited by the fact that the organism must be manipulated under biological safety level 3 conditions. A close relative ofB. pseudomalleicalledBurkholderia thailandensis, which can be studied under less restrictive conditions, has been validated as a low-virulence surrogate in studies of virulence, antibiotic resistance and other traits. To facilitate large-scale studies ofB. thailandensis, we created a near-saturation, sequence-defined transposon mutant library of the organism. The library facilitates genetic studies that identify genotype-phenotype associations conserved inB. pseudomallei.

Chryseobacterium angstadtii sp. nov., isolated from a newt tank

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4777-4783 ◽  
Author(s):  
Karen E. Kirk ◽  
Jessica A. Hoffman ◽  
Katherine A. Smith ◽  
Brittane L. Strahan ◽  
Kevin C. Failor ◽  
...  
Keyword(s):  
Type Species ◽  
Distinct Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Yellow Orange ◽  
Polyphasic Characterization

As part of an undergraduate microbiology course, a yellow–orange-pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain was isolated from a glass tank housing several red-spotted newts (Notophthalmus viridescens). The sequence of the 16S rRNA gene of this strain, designated KMT, was 97.4–98.0 % similar to those of the type strains of Chryseobacterium luteum , C. shigense and C. vrystaatense , while the similarity levels for protein-coding genes were less than 94.7 % for rpoB, less than 92.1 % for groEL and less than 87.1 % for gyrB. These values are lower than for many other established distinct species. Polyphasic characterization and comparison to these relatives revealed that strain KMT was similar to other Chryseobacterium strains in that it contained MK-6 as its major respiratory quinone and phosphatidylethanolamine as the most abundant polar lipid, produced flexirubin-type pigments, oxidase and catalase and primarily contained the fatty acids iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). Based on the results of this study, strain KMT represents a novel species, for which the name Chryseobacterium angstadtii sp. nov. is proposed. The type strain is KMT ( = ATCC BAA-2160T = NRRL B-59516T = KCTC 23297T).

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew C. Canver ◽  
Tsigereda Tekle ◽  
Samantha T. Compton ◽  
Katrina Callan ◽  
Eileen M. Burd ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Species Level ◽  
Accurate Identification ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Staphylococcus Intermedius ◽  
Animal Pathogens ◽  
Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

scholarly journals Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic

2011 ◽  
Vol 78 (2) ◽  
pp. 549-559 ◽  
Author(s):  
Thibault Varin ◽  
Connie Lovejoy ◽  
Anne D. Jungblut ◽  
Warwick F. Vincent ◽  
Jacques Corbeil
Keyword(s):  
High Arctic ◽  
Environmental Stresses ◽  
The Arctic ◽  
Functional Responses ◽  
Protein Coding ◽  
Content Type ◽  
Stress Genes ◽  
Cyanobacterial Genes ◽  
Shock Proteins ◽  
The Antarctic

ABSTRACTPolar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived fromProteobacteriaandCyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation ofActinobacteriaandAlphaproteobacteriain the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

Photobacterium arenosum sp. nov., isolated from marine sediment sand

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Veeraya Weerawongwiwat ◽  
Seokmin Yoon ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung Sook Lee ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
The Republic ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).

scholarly journals Draft Genome Sequences of 10 Clinical K2-Type Klebsiella pneumoniae Strains Isolated in Russia

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Angelina A. Kislichkina ◽  
Anastasia I. Lev ◽  
Ekaterina V. Solovieva ◽  
Vera P. Myakinina ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Klebsiella Pneumoniae ◽  
Draft Genome ◽  
Capsular Type ◽  
Genome Sequences ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Neurosurgical Intensive Care ◽  
Neurosurgical Intensive Care Unit

We report here the genome sequences of 10 Klebsiella pneumoniae strains of capsular type K2 isolated in Russia from patients in an infectious clinical hospital and neurosurgical intensive care unit. The draft genome sizes range from 5.34 to 5.87 Mb and include 5,448 to 6,137 protein-coding sequences.

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