scholarly journals Phylogenetic Diversity of Symbiotic Methanogens Living in the Hindgut of the Lower Termite Reticulitermes speratus Analyzed by PCR and In Situ Hybridization

1999 ◽  
Vol 65 (2) ◽  
pp. 837-840 ◽  
Author(s):  
Naoya Shinzato ◽  
Tadao Matsumoto ◽  
Ikuo Yamaoka ◽  
Tairo Oshima ◽  
Akihiko Yamagishi
Keyword(s):  
Phylogenetic Analysis ◽  
In Situ Hybridization ◽  
Phylogenetic Diversity ◽  
Small Subunit ◽  
Hybridization Analysis ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Reticulitermes Speratus ◽  
Lower Termite

ABSTRACT A phylogenetic analysis of the sequences of 60 clones of archaeal small-subunit rRNA genes amplified from the termiteReticulitermes speratus revealed that most of them (56 clones) clustered in the genus Methanobrevibacter. Three clones were classified in the order Thermoplasmales. TheMethanobrevibacter-related symbionts were detected by in situ hybridization analysis.

scholarly journals Specificity of Associations between Bacteria and the Coral Pocillopora meandrina during Early Development

2012 ◽  
Vol 78 (20) ◽  
pp. 7467-7475 ◽  
Author(s):  
Amy Apprill ◽  
Heather Q. Marlow ◽  
Mark Q. Martindale ◽  
Michael S. Rappé
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Roseobacter Clade ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Sterile Seawater ◽  
Show Evidence ◽  
Coral Health

ABSTRACTRelationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coralPocillopora meandrinawas investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of theAlphaproteobacteria, aPseudoalteromonasspecies of theGammaproteobacteria, and aSynechococcusspecies of theCyanobacteriaphylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination ofP. meandrinaplanulae by fluorescencein situhybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains ofPseudoalteromonasand Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade andSynechococcusdid not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

scholarly journals α-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora

2006 ◽  
Vol 73 (1) ◽  
pp. 303-311 ◽  
Author(s):  
Christine M. Anderson ◽  
Margo G. Haygood
Keyword(s):  
Phylogenetic Analysis ◽  
In Situ Hybridization ◽  
16S Rrna ◽  
Fluorescence In Situ Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Symbionts ◽  
California Coast ◽  
Specific Fluorescence

ABSTRACT Bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan Watersipora arcuata in the 1980s. In this study, we used PCR and sequencing of 16S rRNA genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of “W. subtorquata” and “W. arcuata” from several locations along the California coast are actually closely related α-Proteobacteria, not mollicutes. We propose the names “Candidatus Endowatersipora palomitas” and “Candidatus Endowatersipora rubus” for the symbionts of “W. subtorquata” and “W. arcuata,” respectively.

scholarly journals Protocol for Rapid Fluorescence In Situ Hybridization of Bacteria in Cryosections of Microarthropods

2003 ◽  
Vol 69 (5) ◽  
pp. 2875-2878 ◽  
Author(s):  
Torsten Thimm ◽  
Christoph C. Tebbe
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Bacterial Colonization ◽  
Small Subunit ◽  
Folsomia Candida ◽  
Small Subunit Rrna ◽  
Paraffin Embedding

ABSTRACT A protocol was developed to detect bacteria inhabiting microarthropods by means of small-subunit rRNA-targeted fluorescence in situ hybridization and microscopy. The protocol is based on cryosections of whole specimens. In contrast to more commonly applied paraffin-embedding techniques, the protocol is quicker and reduces the number of manipulations which might damage the microscopic material. The method allowed the study of the bacterial colonization of Folsomia candida (Collembola) and the detection of bacteria in both the gut and tissue.

scholarly journals Phylogenetic Analysis of CryptosporidiumParasites Based on the Small-Subunit rRNA Gene Locus

1999 ◽  
Vol 65 (4) ◽  
pp. 1578-1583 ◽  
Author(s):  
Lihua Xiao ◽  
Lillian Escalante ◽  
Chunfu Yang ◽  
Irshad Sulaiman ◽  
Anannias A. Escalante ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Distinct Species ◽  
Small Subunit ◽  
Biological Data ◽  
Rrna Genes ◽  
Recent Analysis ◽  
Species Differentiation ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rock Hyrax

ABSTRACT Biological data support the hypothesis that there are multiple species in the genus Cryptosporidium, but a recent analysis of the available genetic data suggested that there is insufficient evidence for species differentiation. In order to resolve the controversy in the taxonomy of this parasite genus, we characterized the small-subunit rRNA genes of Cryptosporidium parvum,Cryptosporidium baileyi, Cryptosporidium muris, and Cryptosporidium serpentis and performed a phylogenetic analysis of the genus Cryptosporidium. Our study revealed that the genus Cryptosporidium contains the phylogenetically distinct species C. parvum, C. muris, C. baileyi, and C. serpentis, which is consistent with the biological characteristics and host specificity data. The Cryptosporidium species formed two clades, with C. parvum and C. baileyi belonging to one clade and C. muris and C. serpentisbelonging to the other clade. Within C. parvum, human genotype isolates and guinea pig isolates (known asCryptosporidium wrairi) each differed from bovine genotype isolates by the nucleotide sequence in four regions. A C. muris isolate from cattle was also different from parasites isolated from a rock hyrax and a Bactrian camel. Minor differences were also detected between C. serpentis isolates from snakes and lizards. Based on the genetic information, a species- and strain-specific PCR-restriction fragment length polymorphism diagnostic tool was developed.

scholarly journals Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium

1999 ◽  
Vol 65 (1) ◽  
pp. 283-286 ◽  
Author(s):  
Friedrich von Wintzingerode ◽  
Burkhard Selent ◽  
Werner Hegemann ◽  
Ulf B. Göbel
Keyword(s):  
Phylogenetic Analysis ◽  
Microbial Consortium ◽  
Chlorinated Solvents ◽  
Molecular Study ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Bacterial Clone

ABSTRACT A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for Bacteria or Euryarchaeotaand were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating Dehalobacter species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chlorinated solvents (Dojka et al., Appl. Env. Microbiol. 64:3869–3877, 1998).

scholarly journals Phylogenetic Relationships ofCryptosporidium Parasites Based on the 70-Kilodalton Heat Shock Protein (HSP70) Gene

2000 ◽  
Vol 66 (6) ◽  
pp. 2385-2391 ◽  
Author(s):  
Irshad M. Sulaiman ◽  
Una M. Morgan ◽  
R. C. Andrew Thompson ◽  
Altaf A. Lal ◽  
Lihua Xiao
Keyword(s):  
Phylogenetic Analysis ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Distinct Species ◽  
Small Subunit ◽  
Major Group ◽  
Rrna Genes ◽  
Hsp70 Gene ◽  
Small Subunit Rrna ◽  
Heat Shock Protein Hsp70

ABSTRACT We have characterized the nucleotide sequences of the 70-kDa heat shock protein (HSP70) genes of Cryptosporidium baileyi,C. felis, C. meleagridis, C. muris,C. serpentis, C. wrairi, and C. parvum from various animals. Results of the phylogenetic analysis revealed the presence of several genetically distinct species in the genus Cryptosporidium and eight distinct genotypes within the species C. parvum. Some of the latter may represent cryptic species. The phylogenetic tree constructed from these sequences is in agreement with our previous results based on the small-subunit rRNA genes of Cryptosporidium parasites. TheCryptosporidium species formed two major clades: isolates of C. muris and C. serpentis formed the first major group, while isolates of C. felis, C. meleagridis, C. wrairi, and eight genotypes ofC. parvum formed the second major group. Sequence variations were also observed between C. muris isolates from ruminants and rodents. The HSP70 gene provides another useful locus for phylogenetic analysis of the genusCryptosporidium.

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