scholarly journals Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments

2007 ◽  
Vol 73 (10) ◽  
pp. 3272-3282 ◽  
Author(s):  
Erin A. Gontang ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
New Taxa ◽  
Marine Sediments ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
The Republic ◽  
Republic Of Palau ◽  
High Degree

ABSTRACT Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of ≥98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

scholarly journals Prevalence of Gram-Positive Bacteria Isolated from Nasal Swabs and Hands of Healthy Army Trainees in the Republic of Korea

2020 ◽  
Vol 26 (3) ◽  
pp. 244-248
Author(s):  
Dae-Seong Yu ◽  
Sung-Bae Park ◽  
Heechul Park ◽  
Jun Seong Kim ◽  
Jiyoung Lee ◽  
...  
Keyword(s):  
Republic Of Korea ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Nasal Swabs ◽  
The Republic

scholarly journals Identification of the microflora from the oral cavity of exotic snakes kepth as pets

2020 ◽  
Vol 12 (2) ◽  
pp. 56-63
Author(s):  
Marko Naumovski ◽  
Ivamaria Jovanovska ◽  
Kakja Popovska ◽  
Vesna Velikj Stefanovska ◽  
Gordana Mirchevska
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Oral Cavity ◽  
Gram Negative Bacteria ◽  
Proteus Vulgaris ◽  
Gram Positive ◽  
Providencia Rettgeri ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Venomous Snakes ◽  
The Republic

In recent years, snakes have become suitable pets for people with little spare time. By buying these animals people ignore the fact that they carry many microorganisms that are pathogenic for humans. The idea of ​​this study was to identify the microorganisms from the oral cavity of exotic snakes kept as pets in the Republic of North Macedonia, which can help in the treatment of bite infections if they occur. The study comprised 30 snakes of 9 species, from 3 families of non-venomous snakes: Pythonidae, Boidae and Colubridae. Snakes are part of the 5 largest collections of exotic snakes in the Republic of North Macedonia. Only one swab from the oral cavity was taken from each snake. The brushes were cultured and microscopically analyzed at the Institute of Microbiology and Parasitology at the Faculty of Medicine in Skopje. From 59 isolated microorganisms from the oral cavity of 30 exotic snakes, 37.3% were Gram-positive bacteria, 61.01% were Gram-negative bacteria and 1.69% were fungi. Of the total number of microorganisms, Pseudomonas aeruginosa was predominant with 27.11%, Providencia rettgeri / Proteus vulgaris with 18.64% and KONS / Micrococcus luteus with 16.94%. Pseudomonas aeruginosa was present in all three snake families, with 62.5% of the snake in the fam. Pythonidae; 50% in the fam. Boidae and 50% in the fam. Colubridae. The isolate Providencia rettgeri / Proteus vulgaris was most frequently found in the fam. Colubridae with 71.43%, followed by fam. Pythonidae with 12.5%, but was not isolated in any specimen of the fam. Boidae. The microbiome of the non-venomous snakes is composed of Gram-positive bacteria in healthy snakes, but also in snakes kept in inadequate hygienic conditions. Gram-negative bacteria were predominant, of which the most significant was the presence of multiple drug resistance Pseudomonas aeruginosa. Snakes as pets require proper knowledge of terms and conditions.

scholarly journals A New Bacteroides Conjugative Transposon That Carries an ermB Gene

2003 ◽  
Vol 69 (11) ◽  
pp. 6455-6463 ◽  
Author(s):  
Anamika Gupta ◽  
Hera Vlamakis ◽  
Nadja Shoemaker ◽  
Abigail A. Salyers
Keyword(s):  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
Gram Positive ◽  
Amino Acid Sequence Level ◽  
Conjugative Transposon ◽  
Pulsed Field ◽  
Gram Positive Bacteria ◽  
Ermb Gene

ABSTRACT The erythromycin resistance gene ermB has been found in a variety of gram-positive bacteria. This gene has also been found in Bacteroides species but only in six recently isolated strains; thus, the gene seems to have entered this genus only recently. One of the six Bacteroides ermB-containing isolates, WH207, could transfer ermB to Bacteroides thetaiotaomicron strain BT4001 by conjugation. WH207 was identified as a Bacteroides uniformis strain based on the sequence of its 16S rRNA gene. Results of pulsed-field gel electrophoresis experiments demonstrated that the transferring element was normally integrated into the Bacteroides chromosome. The element was estimated from pulsed-field gel data to be about 100 kb in size. Since the element appeared to be a conjugative transposon (CTn), it was designated CTnBST. CTnBST was able to mobilize coresident plasmids and the circular form of the mobilizable transposon NBU1 to Bacteroides and Escherichia coli recipients. A 13-kb segment that contained ermB was cloned and sequenced. Most of the open reading frames in this region had little similarity at the amino acid sequence level to any proteins in the sequence databases, but a 1,723-bp DNA segment that included a 950-bp segment downstream of ermB had a DNA sequence that was virtually identical to that of a segment of DNA found previously in a Clostridium perfringens strain. This finding, together with the finding that ermB is located on a CTn, supports the hypothesis that CTnBST could have entered Bacteroides from some other genus, possibly from gram-positive bacteria. Moreover, this finding supports the hypothesis that many transmissible antibiotic resistance genes in Bacteroides are carried on CTns.

scholarly journals Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov.

2006 ◽  
Vol 56 (12) ◽  
pp. 2837-2842 ◽  
Author(s):  
Yoshihide Matsuo ◽  
Atsuko Katsuta ◽  
Satoru Matsuda ◽  
Yoshikazu Shizuri ◽  
Akira Yokota ◽  
...  
Keyword(s):  
Gene Tree ◽  
Distinct Group ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Marine Lakes ◽  
The Republic ◽  
Republic Of Palau ◽  
Type Strains

A study was carried out to clarify the taxonomy of four Gram-positive, heterotrophic mesophiles isolated from marine lakes in the Republic of Palau. The strains, designated YM3-251T, YM3-653, YM3-671 and YM11-542T, formed aerial and substrate mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of their genomic DNA was approximately 45 mol%. The major fatty acid was iso-C15 : 0 and the major isoprenoid quinone was MK-9. The strains formed a distinct group in the 16S rRNA gene tree and shared a range of phenotypic properties that distinguished them from members of related genera in Thermoactinomycetaceae fam. nov. The name proposed to accommodate the new isolates is Mechercharimyces gen. nov., comprising two species based on genotypic and phenotypic criteria, including comparative gyrB and DNA–DNA relatedness data. The names proposed for these taxa are Mechercharimyces mesophilus sp. nov., the type species, and Mechercharimyces asporophorigenens sp. nov., with the type strains YM3-251T (=MBIC06230T=DSM 44894T) and YM11-542T (=MBIC06487T=DSM 44955T), respectively.

Bacterial diversity associated with subalpine fir (Abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central British Columbia

2002 ◽  
Vol 48 (7) ◽  
pp. 611-625 ◽  
Author(s):  
Madhukar B Khetmalas ◽  
Keith N Egger ◽  
Hugues B Massicotte ◽  
Linda E Tackaberry ◽  
M Jill Clapperton
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Abies Lasiocarpa ◽  
Gram Positive ◽  
Salvage Logging ◽  
Gram Positive Bacteria ◽  
Significant Difference

To assess the effect of fire and salvage logging on the diversity of mycorrhizal–bacterial communities, bacteria associated with Cenococcum, Thelephora, Tomentella, Russulaceae, and E-strain ectomycorrhizae (ECM) of Abies lasiocarpa seedlings were characterized using two approaches. First, bacteria were isolated and characterized by Biolog©, gas chromatography fatty acid methyl ester (GC-FAME), and amplified 16S rDNA restriction analysis (ARDRA). The bacterial communities retrieved from ECM from both sites were dominated by Proteobacteria (groups gamma and beta). Pseudomonas was the most common genus isolated, followed by Variovorax, Burkholderia, and Xanthomonas. Gram-positive isolates (mostly high-G+C Gram-positive bacteria) were more frequently retrieved on the burned-salvaged site, many commonly associated with the two ascomycete ECM, Cenococcum and E-strain. Pseudomonas species were retrieved more frequently from Thelephora. Although actinomycetes were isolated from all sites, almost no actinomycetes or other Gram-positive bacteria were isolated from either Thelephora or Tomentella. Second, amplified 16S rRNA gene sequences were amplified directly from root tips and then cloned into the plasmid vector pAMP1, followed by restriction analysis. This technique distinguished more genotypes than isolates retrieved by culturing methods, but generally, results were similar in that the largest proportion of the bacteria were putatively Gram-negative; putative Gram-positive bacteria were fewer and most were from the burned–salvaged site. Direct cloning resulted in many patterns that did not match any identified isolates, suggesting that a large proportion of clones were unique or not culturable by the methods used. Analysis for both protocols showed no significant difference in bacterial diversity between the burned–salvaged and unburned sites. Key words: rhizosphere bacteria, ARDRA, 16S rDNA, Biolog©, GC-FAME.

scholarly journals OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

2016 ◽  
Author(s):  
Sarah L. Westcott ◽  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Significant Advance ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Operational Taxonomic Units ◽  
Computational Bottleneck

AbstractAssignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to ten other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6-times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the dataset. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications.

scholarly journals Moderate thermophilic chemoorganoheterotrophic bacterium in surface layer of anthropogenic grounds of industrial estate area of Al-Mafraq, Jordan

2021 ◽  
Vol 19 (3) ◽  
pp. 209-217
Author(s):  
Alexander S. Galushko ◽  
Snezanna K. Ibryaeva ◽  
Anna S. Zhuravleva ◽  
Gayane G. Panova ◽  
Jacob H. Jacob
Keyword(s):  
Thermophilic Bacteria ◽  
Rrna Gene ◽  
Growth Data ◽  
Alkane Degradation ◽  
Gram Positive ◽  
Moderately Thermophilic ◽  
Gram Positive Bacteria ◽  
Industrial Estate ◽  
First Time ◽  
The 16S Rrna Gene

Surface of oil-contaminated soil from Industrial Estate of Al-Mafraq city, Jordan, was investigated for the presence of aerobic oil-degrading moderately thermophilic bacteria. A pure culture of spore forming aerobic chemoorganogeterotrophic rod shaped bacterial isolate, designated as strain j3n, was obtained. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain j3n is closely related to gram-positive bacteria of kaustophilus thermoleovorans cluster of Geobacillus genus. Strain j3n grew aerobically with oil, hexadecane, benzoate and acetate. Growth data indicated that utilization of hexadecane but not of oil and benzoate might be under catabolite repression control. Possibility of a regulation of alkane degradation by acetate in aerobic thermophilic gram-positive bacteria of Geobacillus spp. was shown for the first time.

scholarly journals Functional Identification of Rubber Oxygenase (RoxA) in Soil and Marine Myxobacteria

2013 ◽  
Vol 79 (20) ◽  
pp. 6391-6399 ◽  
Author(s):  
Jakob Birke ◽  
Wolf Röther ◽  
Georg Schmitt ◽  
Dieter Jendrossek
Keyword(s):  
Chemical Reduction ◽  
Three Dimensional ◽  
Visible Spectrum ◽  
Functional Identification ◽  
Gram Positive ◽  
Zone Formation ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Degrading Bacteria ◽  
High Degree

ABSTRACTThe rubber oxygenase (RoxA) ofXanthomonassp. strain 35Y (RoxAXsp) is so far the only known extracellularc-type diheme cytochrome that is able to cleave poly(cis-1,4-isoprene). All other rubber-degrading bacteria described are Gram positive and employ a nonheme protein (latex-clearing protein [Lcp]) for the postulated primary attack of polyisoprene. Here, we identified RoxA orthologs in the genomes ofHaliangium ochraceum,Myxococcus fulvus,Corallococcus coralloides, andChondromyces apiculatus. TheroxAorthologs ofH. ochraceum(RoxAHoc),C. coralloidesBO35 (RoxACco), andM. fulvus(RoxAMfu) were functionally expressed in a ΔroxA Xanthomonassp. 35Y background. All RoxA orthologs oxidatively cleaved polyisoprene, as revealed by restoration of clearing-zone formation and detection of 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) as a cleavage product. RoxAXsp, RoxAMfu, and RoxACcowere purified and biochemically characterized. The optimal temperature of RoxACcoand RoxAMfuwas between 22 and 30°C. All RoxA orthologs as isolated showed an oxidized UV-visible spectrum. Chemical reduction of RoxACcoand RoxAMfuindicated the presence of two slightly different heme centers with absorption maxima between 549 and 553 nm, similar to RoxAXsp. Sequence analysis and modeling of the three-dimensional structures of the RoxA orthologs revealed a high degree of similarity to the recently solved RoxAXspstructure and included several conserved residues, notably, W302, F317, and a MauG motif at about H517. Lcp-like sequences were not detected in the genomes of theXanthomonassp. 35Y,H. ochraceum,M. fulvus, andC. coralloides. No RoxA orthologs were found in Gram-positive bacteria, and this first description of functional RoxA in Gram-negative bacteria other thanXanthomonasproves that RoxA is more common among rubber degraders than was previously assumed.

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