Bacterial Communities in Various Conditions of the Composting Reactor Revealed by 16S rDNA Clone Analysis and DGGE

2009 ◽  
pp. 165-177 ◽  
Author(s):  
Keiko Watanabe ◽  
Norio Nagao ◽  
Tatsuki Toda ◽  
Norio Kurosawa
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Clone Analysis ◽  
Rdna Clone

Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library

2005 ◽  
Vol 39 (20) ◽  
pp. 3687-3695 ◽  
Author(s):  
Pierre-Alain Maron ◽  
David P.H. Lejon ◽  
Esmeralda Carvalho ◽  
Karine Bizet ◽  
Philippe Lemanceau ◽  
...  
Keyword(s):  
Genetic Structure ◽  
16S Rdna ◽  
Dna Fingerprinting ◽  
Clone Library ◽  
Bacterial Communities ◽  
16S Rdna Clone Library ◽  
Genetic Structure And Diversity ◽  
Rdna Clone

Analysis of bacterial communities on aging flue-cured tobacco leaves by 16S rDNA PCR–DGGE technology

2007 ◽  
Vol 73 (6) ◽  
pp. 1435-1440 ◽  
Author(s):  
Mingqin Zhao ◽  
Baoxiang Wang ◽  
Fuxin Li ◽  
Liyou Qiu ◽  
Fangfang Li ◽  
...  
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Tobacco Leaves ◽  
16S Rdna Pcr

scholarly journals Assessment of Spoilage Bacterial Communities in Food Wrap and Modified Atmospheres-Packed Minced Pork Meat Samples by 16S rDNA Metagenetic Analysis

2020 ◽  
Vol 10 ◽  
Author(s):  
Emilie Cauchie ◽  
Laurent Delhalle ◽  
Bernard Taminiau ◽  
Assia Tahiri ◽  
Nicolas Korsak ◽  
...  
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Pork Meat ◽  
Modified Atmospheres ◽  
Meat Samples

scholarly journals Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Fumika Hotta ◽  
Hiroshi Eguchi ◽  
Takeshi Naito ◽  
Yoshinori Mitamura ◽  
Kohei Kusujima ◽  
...  
Keyword(s):  
Case Report ◽  
16S Rdna ◽  
Clone Library ◽  
16S Rdna Clone Library ◽  
Clone Library Analysis ◽  
Rdna Clone ◽  
Buckle Infection

scholarly journals Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

2006 ◽  
Vol 55 (1) ◽  
pp. 101-107 ◽  
Author(s):  
Daniel Saito ◽  
Renato de Toledo Leonardo ◽  
Jorge Luiz Mazza Rodrigues ◽  
Siu Mui Tsai ◽  
José Francisco Höfling ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Significant Proportion ◽  
Oral Bacteria ◽  
Clone Libraries ◽  
Root Canals ◽  
Gram Positive Bacteria ◽  
Identification Of Bacteria ◽  
Endodontic Infections ◽  
Rdna Clone

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65·2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10·9 %), Spirochaetes (4·3 %), Bacteroidetes (6·5 %), Actinobacteria (2·2 %) and Deferribacteres (2·2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Denaturing Gradient Gel Electrophoresis Polymorphism for Rapid 16S rDNA Clone Screening and Microbial Diversity Study.

2002 ◽  
Vol 93 (1) ◽  
pp. 101-103 ◽  
Author(s):  
WEN-TSO LIU ◽  
CHUN-LIN HUANG ◽  
JIANG YONG HU ◽  
LIANGFA SONG ◽  
SAY LEONG ONG ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
16S Rdna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gradient Gel Electrophoresis ◽  
Diversity Study ◽  
Rdna Clone

Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

scholarly journals Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

2002 ◽  
Vol 68 (1) ◽  
pp. 219-226 ◽  
Author(s):  
Christine F. Favier ◽  
Elaine E. Vaughan ◽  
Willem M. De Vos ◽  
Antoon D. L. Akkermans
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Colonization ◽  
Molecular Monitoring ◽  
Fecal Samples ◽  
16S Rdna Sequence Analysis ◽  
Rdna Sequences ◽  
Gradient Gel Electrophoresis

ABSTRACT The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes. DGGE profiles of the dominant populations in the intestines of the infants were obtained by analyzing daily or weekly fecal samples. After delivery, the germfree infant gastrointestinal tracts were rapidly colonized, and the succession of bacteria in each ecosystem was monitored. During the first few days of life the profiles were simple, but they became more complex as the bacterial diversity increased with time in both babies. Clone libraries of amplified 16S rDNA fragments from baby feces were constructed, and these libraries allowed identification of the bacterial types by comparative DNA sequence analysis; the bacteria identified included members of the genera Bifidobacterium, Ruminococcus, Enterococcus, Clostridium, and Enterobacter. Species most closely related to the genera Bifidobacterium and Ruminococcus in particular dominated the intestinal microbiota based on the stability over time and the numbers, as estimated by the intensities of the bands. However, 19 of the 34 cloned rDNA sequences exhibited less than 97% identity with sequences of known bacteria or cloned sequences in databases. This study showed that using PCR-DGGE and 16S rDNA sequence analysis together resulted in a dynamic description of bacterial colonization in the infant intestinal ecosystem and allowed visualization of bacteria that are difficult to cultivate or to detect by other methods.

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