scholarly journals Multiple metal tolerance of Paenibacillus dentritiformis isolated from metal contaminated soils west Godavari district (Andhra Pradesh)

2019 ◽  
Vol 11 (2) ◽  
pp. 486-491
Author(s):  
V. Sridevi ◽  
M. Raghuram
Keyword(s):  
Bacterial Strain ◽  
Contaminated Soils ◽  
Metal Tolerance ◽  
Industrial Effluents ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Paenibacillus Sp ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Metal Tolerant Bacteria

Sugar industrial effluents possess high amounts of toxic pollutants and contaminate the receiving sites. Treatment of contaminated sites by using microorganisms provides an alternate to conventional methods hence demands in the identification of metal tolerant microorganisms has been increasing day by day. Therefore in this study soil samples collected from Tanuku sugar factory residual effluent point (bank of Gosthani river), west Godavari district A.P were analyzed for the bacterial tolerance to Copper (Cu), Zinc (Zn) and Lead (Pb) in their chloride forms. Additionally, the study was carried out to identify the metal tolerant bacteria by morphological, biochemical and 16S rRNA gene sequencing studies. Four potential bacterial isolates were selected to analyze metal tolerance against CuCl2, ZnCl2, and PbCl2. The sequences were compared with those in NCBI and submitted in gene bank with accession numbers MK100333 (Paenibacillus cookie), MK100334 (Bacillus cereus), MK100335 (Aneurini bacillus sp) and MK100387 (Paenibacillus sp.). A Phylogenetic tree was constructed to Paenibacillus sp. the highly efficient bacterial strain among the four isolates using MEGA 7 soft ware. The results of this study showed that P. dentritiformis had multiple metal tolerances (Cu, Zn and Pb) up to 500mg/L after 72 hrs.  The identified bacterial strain proved to be the strong heavy metal tolerant bacterial strain. Hence, its usage will be helpful in the treatment of heavy metals specifically Cu, Zn and Pb contaminated soils and further optimization of these cultures is required to improve its metal resistant capacity.

scholarly journals Campylobacter insulaenigrae sp. nov., isolated from marine mammals

2004 ◽  
Vol 54 (6) ◽  
pp. 2369-2373 ◽  
Author(s):  
Geoffrey Foster ◽  
Barry Holmes ◽  
Arnold G. Steigerwalt ◽  
Paul A. Lawson ◽  
Petra Thorne ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Marine Mammals ◽  
16S Rrna Gene Sequencing ◽  
Single Species ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Phylogenetic Studies ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Campylobacter Lari

Phenotypic and phylogenetic studies were performed on four Campylobacter-like organisms recovered from three seals and a porpoise. Comparative 16S rRNA gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus Campylobacter, associated with a subcluster containing Campylobacter jejuni, Campylobacter coli and Campylobacter lari. DNA–DNA hybridization studies confirmed that the bacteria belonged to a single species, for which the name Campylobacter insulaenigrae sp. nov. is proposed. The type strain of Campylobacter insulaenigrae sp. nov. is NCTC 12927T (=CCUG 48653T).

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).

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 The Evolution of Multidrug Resistance in an Isolated Pseudomonas Strain

2020 ◽  
Vol 17 (3) ◽  
pp. 41-50
Author(s):  
Allison Grodnick ◽  
Ashley Fink ◽  
Timothy Johnson ◽  
David Mitchell
Keyword(s):  
Multidrug Resistance ◽  
Bacterial Strain ◽  
Acquired Resistance ◽  
16S Rrna Gene Sequencing ◽  
Multidrug Resistant ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Forest Environment ◽  
Antibiotic Drugs ◽  
Rrna Gene Sequencing

As an unintentional result of the extensive use of antibiotics in healthcare and agriculture, antibiotics have become an increasingly prevalent selective pressure on bacteria. This forces bacteria to evolve and acquire antibiotic-resistant genes or mutations in order to survive. Suppose a bacterial strain acquires resistance to three or more antibiotics. In that case, it is deemed multidrug-resistant (MDR), and it becomes a potentially more serious problem to solve in the context of healthcare. This study aims to evaluate the acquisition of resistance to multiple antibiotic drugs by an initially susceptible isolated bacterium from a Minnesota forest environment. The bacterium was found to be Pseudomonas by 16s rRNA gene sequencing. Three antibiotics, neomycin, ciprofloxacin, and imipenem, each from a different drug class, were selected to see if this isolate could become resistant over time and exposure. The bacterial strain developed resistance to the selected antibiotics through a series of sequential exposures to increasing concentrations of each drug in this order. As determined by a disc susceptibility test, the initial isolate acquired resistance to all three selected antibiotics. Single nucleotide polymorphisms (SNPs) between the original isolate and the final resistant strain were identified. These SNPs suggest that mutations to efflux transporters and antibiotic protein targets play a role in acquiring and maintaining antibiotic resistance. KEYWORDS: Multidrug Resistance; Antibiotics; Neomycin; Ciprofloxacin; Imipenem; Pseudomonas; Evolution; MDR; Minnesota Environment

scholarly journals The archives are half-empty: an assessment of the availability of microbial community sequencing data

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Stephanie D. Jurburg ◽  
Maximilian Konzack ◽  
Nico Eisenhauer ◽  
Anna Heintz-Buschart
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Data Reuse ◽  
Data Availability ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Data Archiving ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing

AbstractAs DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.

scholarly journals Loktanella koreensis sp. nov., isolated from sea sand in Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2199-2202 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Jong-Shik Kim ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sand Sample ◽  
Sea Sand ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Taxonomic Characterization

A bacterial strain, GA2-M3T, isolated from a sea-sand sample in Korea, was subjected to polyphasic taxonomic characterization. Cells of strain GA2-M3T were Gram-negative, non-motile, non-spore-forming and short rod- to ovoid-shaped. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium fell within the radiation of the genus Loktanella. Similarity levels between the 16S rRNA gene sequence of strain GA2-M3T and those of type strains of Loktanella species with validly published names were 93.5–96.1 %; highest sequence similarity was with Loktanella rosea. The G+C content of the genomic DNA of strain GA2-M3T was 60.0 mol% and the predominant ubiquinone was Q-10. Major fatty acids were 18 : 1ω7c, 18 : 0 and 18 : 1ω7c 11-methyl. On the basis of the evidence presented, it is proposed that strain GA2-M3T represents a novel species, for which the name Loktanella koreensis sp. nov. is proposed. The type strain is GA2-M3T (=KACC 11519T=DSM 17925T).

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.

scholarly journals Actinomyces dentalis sp. nov., from a human dental abscess

2005 ◽  
Vol 55 (1) ◽  
pp. 427-431 ◽  
Author(s):  
Val Hall ◽  
Matthew D. Collins ◽  
Paul A. Lawson ◽  
Enevold Falsen ◽  
Brian I. Duerden
Keyword(s):  
Novel Species ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Dental Abscess ◽  
Unknown Species ◽  
Sequencing Studies ◽  
Molecular Phylogenetic ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing

A previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8 % with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165T (=CCUG 48064T=CIP 108337T).

scholarly journals Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)

2006 ◽  
Vol 56 (11) ◽  
pp. 2671-2676 ◽  
Author(s):  
Ana I. Vela ◽  
María C. Gutiérrez ◽  
Enevold Falsen ◽  
Eduardo Rollán ◽  
Isabel Simarro ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Callithrix Geoffroyi

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

scholarly journals Streptococcus dentapri sp. nov., isolated from the wild boar oral cavity

2010 ◽  
Vol 60 (4) ◽  
pp. 820-823 ◽  
Author(s):  
Kazuko Takada ◽  
Kazuhiko Hayashi ◽  
Yutaka Sato ◽  
Masatomo Hirasawa
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phylogenetic Studies ◽  
Streptococcus Equi ◽  
Sequencing Studies ◽  
Streptococcal Species ◽  
Rrna Gene Sequencing

Four Gram-stain-positive, catalase-negative, coccoid-shaped isolates were obtained from the oral cavities of wild boars and characterized by phenotypic and phylogenetic studies. On the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organisms are members of the genus Streptococcus, with Streptococcus equi subsp. equi ATCC 33398T as their closest phylogenetic relative (94.7 % similarity). DNA–DNA hybridization analysis showed that the isolates displayed less than 10 % relatedness to Streptococcus equi subsp. equi DSM 20561T. From the phylogenetic and phenotypic evidence, the four isolates represent a novel species of the genus Streptococcus, for which the name Streptococcus dentapri sp. nov. (type strain NUM 1529T =JCM 15752T =DSM 21999T) is proposed.

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