scholarly journals Aeromonas veronii and Plesiomonas shigelloides (Gammaproteobacteria) isolated from Glossogobius aureus (Gobiidae) in Lake Sampaloc, Laguna, Philippines

2020 ◽  
Vol 14 (1) ◽  
Keyword(s):  
Bacterial Infections ◽  
Management Practices ◽  
16S Rrna Gene Sequencing ◽  
Gut Bacteria ◽  
Inland Waters ◽  
Rrna Gene ◽  
Farmed Fish ◽  
Biochemical Tests ◽  
Plesiomonas Shigelloides ◽  
Aeromonas Veronii

Bacterial infections are high-risk factors in fisheries, with reports of high mortality among diseased fish stocks posing a threat to both capture and aquaculture fisheries in inland waters. Diseases-causing bacteria in fishes may lead to decreased yield and economic loss to fishers, whose livelihood primarily depends on landed catch. Lake fisheries are most affected by such disruptive changes because of limitations in water turnover aggravated by wastewater inputs. In this study, we isolated and characterized gut bacteria from landed catch of the gobiid Glossogobius aureus from Lake Sampaloc, a small but commercially important aquaculture area in Luzon. Isolated axenic gut bacteria were identified through Gram stain reaction, microscopy, API biochemical tests, and 16s rRNA gene sequencing. From these, we identified two species with known fish pathogenicity, namely Aeromonas veronii and Plesiomonas shigelloides which are known to thrive in disrupted and nutrient-rich habitats and cause visible damage to fish health. Interestingly, our samples have shown no such visible signs of the disease. It is therefore important for future researches to determine what conservation and management practices in small inland waters like lakes will limit potential environmental stressors that may trigger susceptibility of both capture and farmed fish species to infection. Ultimately, rehabilitation of inland water aquaculture areas such as Lake Sampaloc is essential not only to fish conservation but also to public health and local food security.

Streptococcus orisasini sp. nov. and Streptococcus dentasini sp. nov., isolated from the oral cavity of donkeys

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2782-2786 ◽  
Author(s):  
Kazuko Takada ◽  
Masanori Saito ◽  
Osamu Tsudukibashi ◽  
Takachika Hiroi ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies

Four Gram-positive, catalase-negative, coccoid isolates that were obtained from donkey oral cavities formed two distinct clonal groups when characterized by phenotypic and phylogenetic studies. From the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus . Two of the isolates were related most closely to Streptococcus ursoris with 95.6 % similarity based on the 16S rRNA gene and to Streptococcus ratti with 92.0 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates, however, were related to Streptococcus criceti with 95.0 and 89.0 % similarities based on the 16S rRNA and groEL genes, respectively. From both phylogenetic and phenotypic evidence, the four isolates formed two distinct clonal groups and are suggested to represent novel species of the genus Streptococcus . The names proposed for these organisms are Streptococcus orisasini sp. nov. (type strain NUM 1801T = JCM 17942T = DSM 25193T) and Streptococcus dentasini sp. nov. (type strain NUM 1808T = JCM 17943T = DSM 25137T).

scholarly journals Streptococcus loxodontisalivarius sp. nov. and Streptococcus saliviloxodontae sp. nov., isolated from oral cavities of elephants

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3288-3292 ◽  
Author(s):  
Masanori Saito ◽  
Noriko Shinozaki-Kuwahara ◽  
Masatomo Hirasawa ◽  
Kazuko Takada
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies

Four Gram-stain-positive, catalase-negative, coccoid-shaped organisms were isolated from elephant oral cavities. The isolates were tentatively identified as streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus . Two isolates (NUM 6304T and NUM 6312) were related most closely to Streptococcus salivarius with 96.8 % and 93.1 % similarity based on the 16S rRNA gene and the RNA polymerase β subunit encoding gene (rpoB), respectively, and to Streptococcus vestibularis with 83.7 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates (NUM 6306T and NUM 6318) were related most closely to S. vestibularis with 97.0 % and 82.9 % similarity based on the 16S rRNA and groEL genes, respectively, and to S. salivarius with 93.5 % similarity based on the rpoB gene. Based on phylogenetic and phenotypic evidence, these isolates are suggested to represent novel species of the genus Streptococcus , for which the names Streptococcus loxodontisalivarius sp. nov. (type strain NUM 6304T = JCM 19287T = DSM 27382T) and Streptococcus saliviloxodontae sp. nov. (type strain NUM 6306T = JCM 19288T = DSM 27513T) are proposed.

scholarly journals Streptococcus ursoris sp. nov., isolated from the oral cavities of bears

2011 ◽  
Vol 61 (1) ◽  
pp. 40-44 ◽  
Author(s):  
Noriko Shinozaki-Kuwahara ◽  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Extracellular Polysaccharide ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Streptococcal Species ◽  
Rrna Gene Sequencing ◽  
Streptococcus Ratti

Three Gram-positive, catalase-negative, coccus-shaped organisms were isolated from the oral cavities of bears. The isolates were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the new isolates was Streptococcus ratti ATCC 19645T (98.6 %), however, DNA–DNA hybridization analysis showed that the isolates displayed less than 15 % DNA–DNA relatedness with the type strain of S. ratti. Colonies of the novel strains grown on mitis salivarius agar showed an extracellular polysaccharide-producing colony morphology. Based on phenotypic and phylogenetic evidence, it is proposed that the novel isolates are classified in the genus Streptococcus as Streptococcus ursoris sp. nov. The type strain of S. ursoris is NUM 1615T (=JCM 16316T=DSM 22768T).

Biodegradation of Kraft Lignin by a Bacterial Strain Sphingobacterium sp. HY-H

2014 ◽  
Vol 955-959 ◽  
pp. 548-553 ◽  
Author(s):  
Jing Duan ◽  
Ji Dong Liang ◽  
Wen Jing Du ◽  
Dong Qi Wang
Keyword(s):  
Degradation Products ◽  
Treatment Plant ◽  
Kinetic Studies ◽  
16S Rrna Gene Sequencing ◽  
Paper Mill ◽  
Kraft Lignin ◽  
Rrna Gene ◽  
Vanillyl Alcohol ◽  
Biochemical Tests ◽  
Degrading Bacterium

A lignin-degrading bacterium was isolated on mineral salt medium amended by lignosulfonate (L-MSM) agar from the activated sludge of a pulp and paper mill wastewater treatment plant and identified as Sphingobacterium sp. HY-H by biochemical tests and 16S rRNA gene sequencing. The maximum kraft lignin (KL) degradation capability of strain HY-H was determined to be 28.2% on a COD basis under the optimal conditions of pH 7.0, temperature 30°C, and KL to nitrogen (as NH4Cl) ratio of 2 by mass. Moreover, growth kinetic studies showed the KL tolerance of strain HY-H was relatively high and the analysis of KL degradation products by GC-MS revealed the formation of low-molecular-weight aromatic compounds (LMWACs), such as guaiacol, vanillin and vanillyl alcohol, indicating that the strain HY-H can oxidize guaiacyl (G) units and syringyl (S) units in lignin structure. In addition, some low molecular ketone compounds such as 4-hydroxy-2-butanone and methyl vinyl ketone were detected in the inoculated sample after 48h, further validating the partial but possible degradation of KL by strain HY-H.

scholarly journals Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan

2007 ◽  
Vol 57 (7) ◽  
pp. 1599-1602 ◽  
Author(s):  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Yayoi Sakiyama ◽  
Shigeaki Harayama
Keyword(s):  
Sugar Cane ◽  
16S Rrna Gene Sequencing ◽  
Treatment Method ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Actinomycete Strain ◽  
Pre Treatment ◽  
Rrna Gene Sequencing ◽  
Type Strains

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).

scholarly journals Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1486-1490 ◽  
Author(s):  
Dominique Clermont ◽  
Laurence Motreff ◽  
Virginie Passet ◽  
José-Carlos Fernandez ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).

scholarly journals Comparative molecular studies of halophilic bacteria from saline water and soil in the Saudi environment

2020 ◽  
Vol 36 (3) ◽  
Author(s):  
Mohamed Ahmed ◽  
Md. Mohibul Alam Khan ◽  
Saleh M. S. Al-Garni ◽  
Roop Singh Bora ◽  
Saleh A. Kabli
Keyword(s):  
Red Sea ◽  
Saline Water ◽  
Halophilic Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Industrial Applications ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Biochemical Tests ◽  
Water And Soil Samples

Halophilic bacteria are a microorganism that grows optimally in the presence of the very high concentration of sodium chloride. Halophiles are vital sources of various enzymes including hydrolases, which are very stable and catalytically highly efficient at high salt concentration and other extreme conditions such as high temperature, pH and presence of organic solvents.  Several hydrolases such as amylases, proteases, and lipases have been obtained from halophilic bacteria and are commonly used for various industrial applications. We initiated a screening project to isolate and characterize the halophilic bacteria from the Red Sea, which is one of the saltiest bodies of water in the world. Water and soil samples, collected from the Red Sea coast, Jeddah, Saudi Arabia, were screened for isolation of halophilic bacteria. Ten bacterial isolates were obtained, which were characterized by biochemical tests and 16S rRNA gene sequencing. Hydrolase producing bacteria among the isolates were screened by plate assay on starch and gelatin agar plates for amylase and protease, respectively.  Two bacterial isolates i.e Bacillus haynesii and Enterobacter cloacae subsp. were found to possess significant amylase and protease activity. Further characterization of both the strains is in progress.

scholarly journals Mycobacterium branderi from Both a Hand Infection and a Case of Pulmonary Disease

2000 ◽  
Vol 38 (10) ◽  
pp. 3896-3899 ◽  
Author(s):  
Joyce Wolfe ◽  
Christine Turenne ◽  
Michelle Alfa ◽  
Godfrey Harding ◽  
Louise Thibert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Performance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Human Pathogen ◽  
Mycobacterial Species ◽  
Biochemical Tests ◽  
Complementary Method ◽  
Hand Infection

Mycobacterium branderi, a potential human pathogen first characterized in 1995, has been isolated from respiratory tract specimens. We report here a case in which M. branderi was the only organism isolated upon culture from a hand infection. This isolate, along with a second isolate from a bronchial specimen, was subjected to conventional identification tests for mycobacterial species. Further analysis by high-performance liquid chromatography (HPLC) of mycolic acids and 16S rRNA gene sequencing was performed, and the antibiotic susceptibility profile was determined for both strains. Biochemical tests and the HPLC pattern were consistent with that ofM. branderi and M. celatum, which are very similar. The 16S rRNA gene sequence of both strains corresponded to that of M. branderi and enabled us to confidently differentiate this organism from other closely related species such asM. celatum. This contributes to a further understanding of the status of this species as a potential human pathogen as well as illustrating the need for molecular diagnostics as a complementary method for the identification of rare mycobacterial species.

Whole-Genome Analysis of KPC-Producing Klebsiella Pneumoniae Isolates From Hospital Acquired Post-Neurosurgical Meningitis

2021 ◽  
Author(s):  
Mingyue Sun ◽  
Weiqiang Xiao ◽  
Qingxia Xu
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
16S Rrna Gene Sequencing ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genomic Study ◽  
Neurosurgical Patients

Abstract Background: Nosocomial bacterial infections from carbapenem-resistant Klebsiella pneumoniae (CRKP) are associated with high mortality in neurosurgical patients. This study examined the post-neurosurgical meningitis outbreak caused by CRKP of patients with nervous system tumours，and analysed the molecular characteristics of the causative strain.Methods: Neurosurgical cancer patients with meningitis caused by CRKP between 2017–2019 were retrospectively analysed. Identification of strains and antimicrobial susceptibilities was conducted using BD Phoenix-100, 16S rRNA gene sequencing and broth microdilution. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to identify the subtypes of K. pneumoniae. The genotype correlation, resistance genes and plasmid of isolates were assessed by whole-genome sequencing (WGS).Results: Isolates were resistant to almost all of the tested antimicrobial agents except polymyxin and tigecycline. The PFGE and MLST revealed all isolates were the same strain - ST11–while WGS phylogenetic analysis indicated they were closely related. The isolates harboured blaKPC-2 and an IncFII-type plasmid; the blaKPC-2 gene had a similar genetic environment across isolates.Conclusions: The results of molecular analysis showed that ST11 and IncFII-type plasmid in CRKP have close correlations and indicate a long-term retrospective genomic study throughout the hospital for KPC-producing K. pneumoniae is necessary.

scholarly journals Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

2005 ◽  
Vol 55 (1) ◽  
pp. 433-436 ◽  
Author(s):  
Hideki Yamamura ◽  
Masayuki Hayakawa ◽  
Youji Nakagawa ◽  
Tomohiko Tamura ◽  
Tetsuro Kohno ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Reference Strain ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Physiological And Biochemical

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

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