scholarly journals Phylogenetic Analysis of 16S rDNA Sequences Manifest Rumen Bacterial Diversity in Gayals (Bos frontalis) Fed Fresh Bamboo Leaves and Twigs (Sinarumdinaria)

2007 ◽  
Vol 20 (7) ◽  
pp. 1057-1066 ◽  
Author(s):  
Weidong Deng ◽  
Metha Wanapat ◽  
Songcheng Ma ◽  
Jing Chen ◽  
Dongmei Xi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Rdna Sequences ◽  
Bamboo Leaves ◽  
16S Rdna Sequences

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.

Degradation of morpholine, piperidine, and pyrrolidine by mycobacteria: evidences for the involvement of a cytochrome P450

1999 ◽  
Vol 45 (3) ◽  
pp. 209-216 ◽  
Author(s):  
P Poupin ◽  
J J Godon ◽  
E Zumstein ◽  
N Truffaut
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome P450 ◽  
16S Rdna ◽  
Mycobacterium Smegmatis ◽  
Energy Sources ◽  
Mycobacterium Fortuitum ◽  
Bacterial Strains ◽  
Cyclic Amines ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Nine bacterial strains that grew on morpholine and pyrrolidine as sole carbon, nitrogen, and energy sources were isolated from three different environments with no known morpholine contamination. One of these strains could also degrade piperidine. These bacteria were identified as Mycobacterium strains. A phylogenetic analysis based on the partial 16S rDNA sequences indicated that the isolated strains clustered within the fast growing group of mycobacteria. When the above-mentioned cyclic amines were used as growth substrates, the synthesis of a soluble cytochrome P450 was induced in all these bacteria. Other laboratory strains, Mycobacterium fortuitum and Mycobacterium smegmatis mc2155, were tested for their abilities to degrade morpholine. Neither of them degraded morpholine but could use pyrrolidine and piperidine. The growth of M. fortuitum and M. smegmatis mc2155 on these compounds involved a soluble cytochrome P450, suggesting that mycobacterial strains are naturally able to use pyrrolidine and have developed a similar enzymatic pathway to metabolize this amine.Key words: mycobacteria, morpholine, piperidine, pyrrolidine, cytochrome P450.

scholarly journals Secondary Intracellular Symbiotic Bacteria in Aphids of the GenusYamatocallis (Homoptera: Aphididae: Drepanosiphinae)

2001 ◽  
Vol 67 (11) ◽  
pp. 5315-5320 ◽  
Author(s):  
Takema Fukatsu
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Natural Populations ◽  
Symbiotic Bacterium ◽  
Nucleotide Substitution Rate ◽  
Diagnostic Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Phylogenetic

ABSTRACT A novel secondary intracellular symbiotic bacterium from aphids of the genus Yamatocallis (subfamily Drepanosiphinae) was characterized by using molecular phylogenetic analysis, in situ hybridization, and diagnostic PCR detection. In the aphid tissues, this bacterium (tentatively designated YSMS [Yamatocallis secondary mycetocyte symbiont]) was found specifically in large cells surrounded by primary mycetocytes harboringBuchnera cells. Of nine drepanosiphine aphids examined, YSMS was detected in only two species of the same genus,Yamatocallis tokyoensis and Yamatocallis hirayamae. In natural populations of these aphids, YSMS was present in 100% of the individuals. Phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences demonstrated that YSMS ofY. tokyoensis and Y. hirayamae constitute a distinct and isolated clade in the γ subdivision of the classProteobacteria. No 16S rDNA sequences of secondary endosymbionts characterized so far from other aphids showed phylogenetic affinity to YSMS. Based on these results, I suggest that YSMS was acquired by an ancestor of the genus Yamatocallisand has been conserved throughout the evolution of the lineage. By using the nucleotide substitution rate for 16S rDNA ofBuchnera spp., the time of acquisition of YSMS was estimated to be about 13 to 26 million years ago, in the Miocene epoch of the Tertiary period.

scholarly journals Saccharothrix algeriensis sp. nov., isolated from Saharan soil

2004 ◽  
Vol 54 (4) ◽  
pp. 1377-1381 ◽  
Author(s):  
A. Zitouni ◽  
L. Lamari ◽  
H. Boudjella ◽  
B. Badji ◽  
N. Sabaou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Detailed Analysis ◽  
16S Rdna ◽  
Type Strain ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Saharan Soil ◽  
Rdna Sequences ◽  
Soil Isolate ◽  
16S Rdna Sequences

The taxonomic position of a soil isolate, strain SA 233T, recovered from Saharan soil from Algeria was established using a polyphasic approach. This isolate has been previously reported to produce three novel dithiolopyrrolone antibiotics, and preliminary chemotaxonomic and morphological characteristics suggested that it was representative of a member of the genus Saccharothrix. Phylogenetic analysis of the strain from 16S rDNA sequences, along with a detailed analysis of morphological, chemotaxonomic and physiological characteristics, indicates that it belongs to the genus Saccharothrix and represents a novel species that is readily distinguished from all recognized Saccharothrix species. The name Saccharothrix algeriensis sp. nov. is proposed for the isolate, with type strain SA 233T (=NRRL B-24137T=DSM 44581T).

scholarly journals Phylogenetic Analysis of the GenusBifidobacteriumand Related Genera Based on 16S rDNA Sequences

1998 ◽  
Vol 42 (10) ◽  
pp. 661-667 ◽  
Author(s):  
Taeko Miyake ◽  
Koichi Watanabe ◽  
Tsugio Watanabe ◽  
Hiroshi Oyaizu
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.

2004 ◽  
Vol 54 (3) ◽  
pp. 929-933 ◽  
Author(s):  
Jung-Sook Lee ◽  
Yu-Ryang Pyun ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Pcr Primers ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Paenibacillus Ehimensis

The taxonomic status of Bacillus ehimensis and Bacillus chitinolyticus was examined, based on their 16S rDNA sequences, DNA–DNA hybridization and other taxonomic characteristics. A phylogenetic analysis using 16S rDNA sequences revealed that the two species belong to the genus Paenibacillus. In particular, B. ehimensis KCTC 3748T and B. chitinolyticus KCTC 3791T were found to be phylogenetically closely related to Paenibacillus koreensis YC300T (98·3 % sequence similarity) and Paenibacillus chinjuensis WN9T (95·2 % sequence similarity), respectively. DNA–DNA hybridization values between B. ehimensis KCTC 3748T and P. koreensis YC300T were less than 26 %. An experiment using Paenibacillus-specific PCR primers, PAEN515F and 1377R, revealed that B. ehimensis and B. chitinolyticus had the same amplified 16S rDNA fragment as members of the genus Paenibacillus. Accordingly, it is proposed that B. ehimensis and B. chitinolyticus be transferred to the genus Paenibacillus as Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov., respectively.

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