scholarly journals Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis

2004 ◽  
Vol 70 (5) ◽  
pp. 2786-2790 ◽  
Author(s):  
S. A. Burke ◽  
J. D. Wright ◽  
M. K. Robinson ◽  
B. V. Bronk ◽  
R. L. Warren
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Type Strain ◽  
Molecular Diversity ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Rrna Gene ◽  
Bacillus Atrophaeus

ABSTRACT Phenotypically, Bacillus atrophaeus is indistinguishable from the type strain of Bacillus subtilis except by virtue of pigment production on certain media. Several pigmented variants of B. subtilis have been reclassified as B. atrophaeus, but several remain ambiguous in regard to their taxonomic placement. In this study, we examined strains within the American Type Culture Collection originally deposited as Bacillus globigii, B. subtilis var. niger, or Bacillus niger using 16S rRNA gene sequencing and amplified fragment length polymorphism (AFLP) analysis to determine the level of molecular diversity among these strains and their relationship with closely related taxa. The 16S rRNA gene sequences revealed little variation with one base substitution between the B. atrophaeus type strain ATCC 49337 and the other pigmented bacilli. AFLP analysis produced high-quality DNA fingerprints with sufficient polymorphism to reveal strain-level variation. Cluster analysis of Dice similarity coefficients revealed that three strains, ATCC 31028, ATCC 49760, and ATCC 49822, are much more closely related to B. atrophaeus than to B. subtilis and should be reclassified as B. atrophaeus. A very closely related cluster of B. atrophaeus strains was also observed; this cluster was genetically distinct from the type strain. The level of variation between the two groups was approximately the same as the level of variation observed between members of the two B. subtilis subspecies, subtilis and spizizenii. It is proposed that the cluster of strains typified by ATCC 9372 be designated a new subspecies, B. atrophaeus subsp. globigii.

scholarly journals Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces

2003 ◽  
Vol 69 (2) ◽  
pp. 1251-1262 ◽  
Author(s):  
Koji Nagashima ◽  
Takayoshi Hisada ◽  
Maremi Sato ◽  
Jun Mochizuki
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Restriction Fragment Length

ABSTRACT New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (Escherichia coli positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with RsaI plus BfaI or with BslI. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with RsaI and BfaI digestion and 14 predominant OTUs were detected with BslI digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.

scholarly journals Fecal Bacterial Diversity in a Wild Gorilla

2006 ◽  
Vol 72 (5) ◽  
pp. 3788-3792 ◽  
Author(s):  
Julie C. Frey ◽  
Jessica M. Rothman ◽  
Alice N. Pell ◽  
John Bosco Nizeyi ◽  
Michael R. Cranfield ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Gene Clone ◽  
Rrna Gene ◽  
Restriction Fragment Length

ABSTRACT We describe the bacterial diversity in fecal samples of a wild gorilla by use of a 16S rRNA gene clone library and terminal-restriction fragment length polymorphism (T-RFLP). Clones were classified as Firmicutes, Verrucomicrobia, Actinobacteria, Lentisphaerae, Bacteroidetes, Spirochetes, and Planctomycetes. Our data suggest that fecal populations did not change temporally, as determined by T-RFLP.

scholarly journals Rapid Identification of Campylobacter,Arcobacter, and Helicobacter Isolates by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene

1999 ◽  
Vol 37 (12) ◽  
pp. 4158-4160 ◽  
Author(s):  
Stephen M. Marshall ◽  
Pasquale L. Melito ◽  
David L. Woodward ◽  
Wendy M. Johnson ◽  
Frank G. Rodgers ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Restriction Fragment Length

A rapid two-step identification scheme based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 16S rRNA gene was developed in order to differentiate isolates belonging to theCampylobacter, Arcobacter, andHelicobacter genera. For 158 isolates (26 reference cultures and 132 clinical isolates), specific RFLP patterns were obtained and species were successfully identified by this assay.

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