scholarly journals Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

1999 ◽  
Vol 65 (8) ◽  
pp. 3287-3292 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Chih-Ching Chien ◽  
Bruce J. Paster ◽  
Rebecca L. Ericson ◽  
Roger P. Orcutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
Single Species ◽  
Rapid Identification ◽  
Sequence Information ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified asLactobacillus acidophilus (strain ASF 360),Lactobacillus salivarius (strain ASF 361), andBacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus andLactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in theCytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipesphylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes,Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster,Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.

scholarly journals Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) Encoding a Putative Manganese-Oxidizing Enzyme in Bacillus Species

2008 ◽  
Vol 74 (23) ◽  
pp. 7265-7271 ◽  
Author(s):  
Lisa E. Mayhew ◽  
Elizabeth D. Swanner ◽  
Andy P. Martin ◽  
Alexis S. Templeton
Keyword(s):  
16S Rrna ◽  
Gene Loss ◽  
Sequence Similarity ◽  
Bacillus Species ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Vertical Inheritance ◽  
Mn Oxide ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Several Bacillus and Paenibacillus species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the mnxG gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in Bacillus species. Seven of eight Bacillus species were capable of Mn(II) oxidation; however, the mnxG gene was detected in only one isolate. Using sequences of known Bacillus species both with and without amplifiable mnxG genes and Henderson Mine isolates, the 16S rRNA and mnxG gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable mnxG gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable mnxG gene in the isolates. The data revealed a complex phylogenetic distribution of the mnxG gene in which vertical inheritance and gene loss influence the distribution of the gene among the Bacillus species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the mnxG gene within the Bacillus clade.

scholarly journals Isolation and identification of marine bacteria from marine mud in Vietnam with antimicrobial activity

2012 ◽  
Vol 3 (2) ◽  
pp. 71-75 ◽  
Author(s):  
Tuyen Do Thi ◽  
Quyen Le Dinh ◽  
Thi Quyen Dinh ◽  
Cuong Pham Van
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Bacterial Strains ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
E Coli ◽  
Escherichia Coli Jm109 ◽  
Marine Mud ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Seventeen bacterial strains were isolated from 9 marine mud samples from the inshore environments of the East Sea. Four bacterial strains showed an inhibition against all tested microorganisms Staphylococcus aureus ATCC10832, Escherichia coli JM109, and Fusarium oxysporum. 16S rRNA sequences of four bacterial strains were obtained by PCR using specific primers. PCR products were cloned into E. coli DH5a using pJET1.2 blunt vector. The recombinant plasmids were sequenced and the lengths of these 16S rRNA sequences were ~930bp. The 16S rRNA sequence from the four bacterial DB1.2, DB1.2.3, DB4.2 and DB5.2 strain showed a high identity of 97 to 99% with the 16S rRNA sequence from Photobacterium sp., Oceanisphaera sp., Shigella sp., Stenotrophomonas sp, respectively. Mười bảy chủng vi khuẩn đã được phân lập từ 9 mẫu bùn biển từ các vùng ven bờ biển Việt Nam. Bốn chủng vi khuẩn được ghi nhận có khả năng ức chế mạnh sự sinh trưởng và phát triển của các chủng vi khuẩn Staphylococcus aureus ATCC10832, Escherichia coli JM109, và thậm chí cả nấm Fusarium oxysporum. Trình tự gene 16S rRNA của bốn chủng vi khuẩn này đã được khuếch đại bằng PCR sử dụng cặp mồi đặc hiệu. Sản phẩm PCR được nối ghép vào vector pJET1.2 blunt sử dụng T4 ligase, hình thành plasmid tái tổ hợp và biến nạp vào E. coli DH5. Khuẩn lạc có plasmid mang phân đoạn DNA chèn được nuôi cấy và tách plasmid. Trình tự 16S rRNA từ 4 chủng DB1.2, DB1.2.3, DB4.2 and DB5.2 chỉ ra có sự tương đồng 97 ÷ 99% so với trình tự 16S rRNA tương ứng của các chủng vi sinh vật biển trên ngân hàng gene thế giới là Photobacterium sp., Oceanisphaera sp., Shigella sp., và Stenotrophomonas sp.

scholarly journals Phylogeny and Identification In Situ ofNevskia ramosa

1998 ◽  
Vol 64 (5) ◽  
pp. 1895-1901 ◽  
Author(s):  
Frank Oliver Gl�ckner ◽  
Hans-Dietrich Babenzien ◽  
Rudolf Amann
Keyword(s):  
16S Rrna ◽  
Cloning And Sequencing ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Bacterial Populations ◽  
Freshwater Habitats ◽  
Related Group ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT An enrichment of the neuston bacterium Nevskia ramosawas investigated by the cultivation-independent rRNA approach. N. ramosa was first described by Famintzin in 1892 as a rod-shaped, slightly bent bacterium forming typical flat rosettes on the surface of shallow freshwater habitats by unilateral slime formation. PCR in combination with cloning and sequencing was used for retrieving 21 partial and 5 nearly full-length 16S rRNA sequences forming three tight clusters. In situ hybridization with rRNA-targeted oligonucleotide probes allowed us to assign the three sequence clusters to three distinct bacterial populations abundant in the enrichment. The two probes that unambiguously identified the N. ramosamorphotype were derived from a 16S rRNA sequence that had similarities of 87.9 to 88.9% to the rRNA sequences of the most closely related group in the database, Xanthomonas sp. and relatives.N. ramosa currently is the only representative of an independent, deep branch of the gamma subclass of the classProteobacteria. The two other populations abundant in the enrichment were affiliated with the alpha subclass of the classProteobacteria. They were most closely related toBlastobacter sp. (97.2% similarity) and Mycoplana bullata (97.6% similarity) and might represent new species in the respective genera.

scholarly journals Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

2004 ◽  
Vol 186 (9) ◽  
pp. 2629-2635 ◽  
Author(s):  
Silvia G. Acinas ◽  
Luisa A. Marcelino ◽  
Vanja Klepac-Ceraj ◽  
Martin F. Polz
Keyword(s):  
16S Rrna ◽  
Thermophilic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Genomes ◽  
16S Rrna Sequence ◽  
Thermoanaerobacter Tengcongensis ◽  
Copy Numbers ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16S rRNA-based methods. Furthermore, the occurrence of widespread horizontal gene transfer (HGT) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. For this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16S rRNA sequences were evaluated. Bacterial genomes display up to 15 operons and operon numbers up to 7 are commonly found, but ∼40% of the organisms analyzed have either one or two operons. Among the Archaea, a single operon appears to dominate and the highest number of operons is five. About 40% of sequences among 380 operons in 76 bacterial genomes with multiple operons were identical to at least one other 16S rRNA sequence in the same genome, and in 38% of the genomes all 16S rRNAs were invariant. For Archaea, the number of identical operons was only 25%, but only five genomes with 21 operons are currently available. These considerations suggest an upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment; however, the inclusion of genomes with a single rrn operon may lower this correction factor to ∼2.5. Divergence among operons appears to be small overall for both Bacteria and Archaea, with the vast majority of 16S rRNA sequences showing <1% nucleotide differences. Only five genomes with operons with a higher level of nucleotide divergence were detected, and Thermoanaerobacter tengcongensis exhibited the highest level of divergence (11.6%) noted to date. Overall, four of the five extreme cases of operon differences occurred among thermophilic bacteria, suggesting a much higher incidence of HGT in these bacteria than in other groups.

Cleaning and Handling Implements as Potential Reservoirs for Bacterial Contamination of Some Ready-to-Eat Foods in Retail Delicatessen Environments

2007 ◽  
Vol 70 (12) ◽  
pp. 2878-2883 ◽  
Author(s):  
C. A. CHRISTISON ◽  
D. LINDSAY ◽  
A. von HOLY
Keyword(s):  
South Africa ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Bacterial Populations ◽  
16S Rrna Sequence Analysis ◽  
And Staphylococcus Aureus ◽  
Disposable Plastic

This study assessed the association of bacteria with cleaning tools, such as floor mops (n = 25) and cleaning cloths (n = 39), and handling devices, such as disposable plastic gloves (n = 20), used during filled baguette and assorted salad preparation in four selected retail delicatessens in Johannesburg, South Africa. Samples of each cleaning or handling tool were prepared for aerobic (APC), coliform (CC), Escherichia coli (EC), Bacillus cereus (BCC), and Staphylococcus aureus (SAC) counts, as well as tested for the incidence of Listeria monocytogenes (LM) and Salmonella (SALM) by standard plating methods. Bacterial populations attached to the cleaning and handling tools were observed by scanning electron microscopy (SEM). Ten selected gram-positive isolates were further analyzed by 16S rRNA sequence analysis and compared with isolates from filled baguettes and assorted salads. The floor mops consistently yielded the highest APCs, CCs, and ECs (5.7, 4.1, and 3.0 log CFU/g, respectively), while gloves had the lowest corresponding counts (3.6, 2.0, and 1.0 log CFU/g, respectively). Low BCCs and SACs were recorded in this study (ca. 1.2 log CFU/g), while SALM and LM were each detected in five cleaning tool samples. SEM showed rods and cocci attached to handling and cleaning tools. Furthermore, results of 16S rRNA sequence analysis indicated that several gram-positive isolates were identified as S. aureus, Staphylococcus pasteuri, Staphylococcus sciuri, and Enterococcus faecalis. Genetically similar strains (100% similarity) were isolated from cleaning and handling tools and associated ready-to-eat (RTE) foods. Cleaning and handling tools may act as reservoirs of contamination for RTE foods during preparation in retail delicatessens in South Africa. The transfer of potential pathogens, such as S. aureus, to foods from cleaning and handling tools may hold food safety implications.

scholarly journals Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the γ-Proteobacteria active in alkane and aromatic hydrocarbon degradation

2004 ◽  
Vol 54 (4) ◽  
pp. 1203-1207 ◽  
Author(s):  
Norberto J. Palleroni ◽  
Ava M. Port ◽  
Hung-Kuang Chang ◽  
Gerben J. Zylstra
Keyword(s):  
New Jersey ◽  
16S Rrna ◽  
Environmental Pollutants ◽  
Single Species ◽  
Fuel Oil ◽  
Striking Similarity ◽  
Solid Media ◽  
Degrading Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Novel alkane-degrading strains of bacteria were isolated from soil contaminated with fuel oil from a leaking underground tank in New Jersey, USA. Two phenotypically similar strains (designated AP102 and AP103T) possessed 16S rRNA sequences unique among the majority of known hydrocarbon-degrading bacteria. The 16S rRNA sequences showed a moderate but distant relationship to the genus Nevskia and a substantial similarity to strains that had previously been isolated for growth on phenol (in Japan) and on toluene (in Canada) by other researchers. The hydrocarbon-degrading strains from Japan, Canada and New Jersey showed no resemblance to the typical morphology of Nevskia but did share a striking similarity among themselves in cell morphology, in the unusual appearance of colonies on various solid media and in various physiological properties. A full taxonomic analysis was performed, including DNA–DNA hybridization and nutritional screening with 117 organic compounds as sole sources of carbon and energy. The strains are active in the degradation of important environmental pollutants, and their phenotypic, physiological, metabolic and genomic properties suggest that they are members of a novel taxon in the γ-Proteobacteria, for which the name Hydrocarboniphaga gen. nov. is proposed, with the single species Hydrocarboniphaga effusa sp. nov. The type strain is AP103T (=ATCC BAA-332T=DSM 16095T).

The “Nostocoida limicola” story: resolving the phylogeny of this morphotype responsible for bulking in activated sludge

2002 ◽  
Vol 46 (1-2) ◽  
pp. 105-110 ◽  
Author(s):  
R.J. Seviour ◽  
J.-R. Liu ◽  
E.M. Seviour ◽  
C.A. McKenzie ◽  
L.L. Blackall ◽  
...  
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Pure Culture ◽  
Sequence Analyses ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Culture Studies ◽  
Gram Positive Bacteria ◽  
Morphological Variants

On the basis of 16S rRNA sequence analyses of several isolates of “Nostocoida limicola” from activated sludge plants in Australia and other countries, it is clear that “N. limicola” I, II and III are not three morphological variants of a single bacterium but at least three phylogenetically different bacteria. Data show that “N. limicola” I are members of at least two genera in the low mol% G+C Gram-positive bacteria, while some isolates of “N.limicola” II belong to the high mol% G+C Gram positive bacteria, and “N.limicola” III is a member of the Planctomycetales. Design and application of 16S rRNA targeted probes for each to biomass samples suggests that their phylogeny is more diverse than pure culture studies would suggest.

scholarly journals 16S rRNA Sequences and Differences in Bacteria Isolated from the Muztag Ata Glacier at Increasing Depths

2005 ◽  
Vol 71 (8) ◽  
pp. 4619-4627 ◽  
Author(s):  
Shurong Xiang ◽  
Tandong Yao ◽  
Lizhe An ◽  
Bingliang Xu ◽  
Junxia Wang
Keyword(s):  
16S Rrna ◽  
Ice Core ◽  
Growth Conditions ◽  
Small Subunit ◽  
Bacterial Isolates ◽  
Gram Positive ◽  
Mountain Glacier ◽  
Gram Positive Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Small subunit 16S rRNA sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates recovered under aerobic growth conditions from different regions of a 22-m ice core from the Muztag Ata Mountain glacier on the Pamirs Plateau (China). Only 11% were psychrophiles (grew at 2°C or −2°C up to ∼20°C), although the majority (82%) were psychrotolerant (grew at 2°C or −2°C up to 37°C). The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from 85% to 100% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G+C (HGC) gram-positive bacteria, 23.3% wereγ -Proteobacteria, 14.7% were α-Proteobacteria, 14.7% were Flavobacteria, and 4.7% were low-G+C (LGC) gram-positive bacteria. There were clear differences in the depth distribution, with Proteobacteria, HGC/Cytophaga-Flavobacterium-Bacteroides (CFB), Proteobacteria, LGC/CFB/HGC, Cryobacterium psychrophilum, HGC/CFB, Proteobacteria/HGC/CFB, and HGC/CFB being the predominant isolates from ice that originated from 2.7 to 3.8, 6.2, 7.5, 8.3, 9.0, 9.7, 12.5, and 15.3 m below the surface, respectively. This layered distribution of bacterial isolates presumably reflects both differences in bacteria inhabiting the glacier's surface, differences in bacteria deposited serendipitously on the glacier's surface by wind and snowfall, and nutrient availability within the ice.

scholarly journals Characterization Physiology and Molecular Bacteria Symbiont- Entomopathogenic Nematodes based of Gene Sequences Encoding the 16S rRNA District of Bromo Probolinggo

2017 ◽  
Vol 18 (1) ◽  
pp. 39
Author(s):  
Bagus Setiawan ◽  
Didik Sulistyanto ◽  
Kartika Senjarini
Keyword(s):  
16S Rrna ◽  
Entomopathogenic Nematodes ◽  
Phenotypic Characterization ◽  
Bacterial Symbionts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Gene Encoding ◽  
Bacillus Strain ◽  
Rrna Sequences

This study aims to identify entomopathogenic nematodes symbiotic bacteria phenotypically and based on the gene encoding 16S rRNA sequences. Bacterial symbionts of entomopathogenic nematodes, obtained from isolates from the area Wonokerto (WN01) and isolates Sukapura (SP01), Bromo, Probolinggo, two symbiont bacteria was found in entomopathogenic nematodes Steinernema sp. The method used in this study are: the isolation of entomopathogenic nematodes Steinernema sp. and bacterial symbionts conventionally for the identification of phenotypically, after the characterization of bacterial isolates, the isolation of genomic DNA, 16S rRNA PCR, DNA purification and DNA sequence analysis. The results based on phenotypic characterization showed that isolates WN01 and SP01, yellowish white, gram positive, negative bioluminenscene, catalase positive, can not hydrolyze urea, and also can not produce H2S. The results of the gene encoding 16S rRNA sequence can be deduced WN01 isolates have in common with the bacteria Bacillus strain toyonensis BCT 7112, while the SP01 isolates have in common with the bacteria Bacillus strain cereus ATCC 14 579.

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