Stenoxybacter acetivorans gen. nov., sp. nov., an Acetate-Oxidizing Obligate Microaerophile among Diverse O2-Consuming Bacteria from Termite Guts

ABSTRACT In termite hindguts, fermentative production of acetate—a major carbon and energy source for the insect—depends on efficient removal of inwardly diffusing oxygen by microbes residing on and near the hindgut wall. However, little is known about the identity of these organisms or about the substrate(s) used to support their respiratory activity. A cultivation-based approach was used to isolate O2-consuming organisms from hindguts of Reticulitermes flavipes. A consistently greater (albeit not statistically significant) number of colonies developed under hypoxia (2% [vol/vol] O2) than under air, and the increase coincided with the appearance of morphologically distinct colonies of a novel, rod-shaped, obligately microaerophilic β-proteobacterium that was <95% similar (based on the 16S rRNA gene sequence) to its closest known relative (Eikenella corrodens). Nearly identical organisms (and/or their 16S rRNA genes) were obtained from geographically separated and genetically distinct populations of Reticulitermes. PCR-based procedures implied that the novel isolates were autochthonous to the hindgut of R. flavipes and comprised ca. 2 to 7% of the hindgut prokaryote community. Representative strain TAM-DN1 utilized acetate and a limited range of other organic and amino acids as energy sources and possessed catalase and superoxide dismutase. On solid medium, the optimal O2 concentration for growth was about 2%, and no growth occurred with O2 concentrations above 4% or under anoxia. However, cells in liquid medium could grow with higher O2 concentrations (up to 16%), but only after proportionately extended lag phases. The genetic and physiological distinctiveness of TAM-DN1 and related strains supports their recognition as a new genus and species, for which the name Stenoxybacter acetivorans gen. nov., sp. nov. is proposed.

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Clover proliferation phytoplasma: ‘Candidatus Phytoplasma trifolii’

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02842-0 ◽

2004 ◽

Vol 54 (4) ◽

pp. 1349-1353 ◽

Cited By ~ 51

Author(s):

Chuji Hiruki ◽

Keri Wang

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Reference Strain ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Beet Leafhopper ◽

Signature Sequences ◽

Elm Yellows ◽

The 16S Rrna Gene

Clover proliferation phytoplasma (CPR) is designated as the reference strain for the CP phylogenetic group or subclade, on the basis of molecular analyses of genomic DNA, the 16S rRNA gene and the 16S–23S spacer region. Other strains related to CPR include alfalfa witches'-broom (AWB), brinjal little leaf (BLL), beet leafhopper-transmitted virescence (BLTV), Illinois elm yellows (ILEY), potato witches'-broom (PWB), potato yellows (PY), tomato big bud in California (TBBc) and phytoplasmas from Fragaria multicipita (FM). Phylogenetic analysis of the 16S rRNA gene sequences of BLL, CPR, FM and ILEY, together with sequences from 16 other phytoplasmas that belong to the ash yellows (AshY), jujube witches'-broom (JWB) and elm yellows (EY) groups that were available in GenBank, produced a tree on which these phytoplasmas clearly clustered as a discrete group. Three subgroups have been classified on the basis of sequence homology and the collective RFLP patterns of amplified 16S rRNA genes. AWB, BLTV, PWB and TBBc are assigned to taxonomic subgroup CP-A, FM belongs to subgroup CP-B and BLL and ILEY are assigned to subgroup CP-C. Genetic heterogeneity between different isolates of AWB, CPR and PWB has been observed from heteroduplex mobility assay analysis of amplified 16S rRNA genes and the 16S–23S spacer region. Two unique signature sequences that can be utilized to distinguish the CP group from others were present. On the basis of unique properties of the DNA from clover proliferation phytoplasma, the name ‘Candidatus Phytoplasma trifolii’ is proposed for the CP group.

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Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000258 ◽

2015 ◽

Vol 65 (Pt_7) ◽

pp. 2320-2325 ◽

Cited By ~ 11

Author(s):

Shih-Yao Lin ◽

Asif Hameed ◽

Cheng-Zhe Wen ◽

You-Cheng Liu ◽

Yi-Han Hsu ◽

...

Keyword(s):

16S Rrna ◽

Sea Urchins ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

The Novel ◽

Moderate Amount ◽

Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

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Overestimation of Streptococcus mutans prevalence by nested PCR detection of the 16S rRNA gene

Journal of Medical Microbiology ◽

10.1099/jmm.0.46280-0 ◽

2006 ◽

Vol 55 (1) ◽

pp. 109-113 ◽

Cited By ~ 14

Author(s):

Ali Al-Ahmad ◽

Thorsten Mathias Auschill ◽

Gabriele Braun ◽

Elmar Hellwig ◽

Nicole Birgit Arweiler

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Streptococcus Mutans ◽

Nested Pcr ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Direct Pcr ◽

Specific Primers ◽

The 16S Rrna Gene

This study was carried out in order to compare two PCR-based methods in the detection of Streptococcus mutans. The first PCR method was based on primers for the 16S rRNA gene and the second method was based on specific primers that targeted the glucosyltransferase gene (gtfB). Each PCR was performed with eight different streptococci from the viridans group, five other streptococci and 17 different non-streptococcal bacterial strains. Direct use of the S. mutans 16S rRNA gene-specific primers revealed that Streptococcus gordonii and Streptococcus infantis were also detected. After amplifying the 16S rRNA gene with universal primers and subsequently performing nested PCR, the S. mutans-specific nested primers based on the 16S rRNA gene detected all tested streptococci. There was no cross-reaction of the gtfB primers after direct PCR. Our results indicate that direct PCR and nested PCR based on 16S rRNA genes can reveal false-positive results for oral streptococci and lead to an overestimation of the prevalence of S. mutans with regards to its role as the most prevalent causative agent of dental caries.

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Molecular taxonomic reassessment of the Cloud Forest’s Bolitoglossa salamanders (Caudata: Plethodontidae) from Cordillera de Mérida (Mérida state, Venezuela)

Zootaxa ◽

10.11646/zootaxa.3356.1.2 ◽

2012 ◽

Vol 3356 (1) ◽

pp. 47 ◽

Cited By ~ 1

Author(s):

GUSTAVO FERMIN ◽

JAVIER GARCÍA-GUTIÉRREZ ◽

MOISÉS ESCALONA ◽

ANDRÉS MORA ◽

AMELIA DÍAZ

Keyword(s):

16S Rrna ◽

Sierra Nevada ◽

16S Rrna Genes ◽

Rrna Genes ◽

Morphological Evidence ◽

Rrna Gene ◽

Putative Species ◽

Salamander Species ◽

The 16S Rrna Gene ◽

Tissue Digestion

Salamanders found at different localities nearby Mérida city, Venezuela, are thus far reported as Bolitoglossa orestes or B.spongai. However, morphological ambiguities among individuals from several populations of both putative species, besidestheir reported disparate geographical distributions, prompted us to clarify the specific identity of these bolitoglossines throughthe sequence analysis of their corresponding 16S rRNA genes. Seventeen specimens belonging to the vertebrates collection ofUniversidad de Los Andes (CVULA), collected at separated cloud forests in Sierra La Culata (San Eusebio, Macho Capaz andSan Javier del Valle) and Sierra Nevada de Mérida (La Mucuy), were used to extract DNA upon tissue digestion. Sequenceanalysis of the 16S rRNA gene supports a biogeographical scenario where, so far, there is only one salamander species for eachsierra: B. orestes, which is widely distributed in Sierra La Culata, and a so far undescribed species of a Venezuelan bolitogloss-ine apparently restricted to Sierra Nevada de Mérida. Based on our molecular results and an examination of morphological evidence, B. spongai should be considered a synonym of B. orestes.

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16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”

Applied and Environmental Microbiology ◽

10.1128/aem.00052-06 ◽

2006 ◽

Vol 72 (7) ◽

pp. 5077-5082 ◽

Cited By ~ 21

Author(s):

Thomas A. Auchtung ◽

Cristina D. Takacs-Vesbach ◽

Colleen M. Cavanaugh

Keyword(s):

16S Rrna ◽

Hot Springs ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Environmental Distribution ◽

Candidate Division ◽

High Level ◽

The 16S Rrna Gene

ABSTRACT The environmental distribution and phylogeny of “Korarchaeota,” a proposed ancient archaeal division, was investigated by using the 16S rRNA gene framework. Korarchaeota-specific primers were designed based on previously published sequences and used to screen a variety of environments. Korarchaeota 16S rRNA genes were amplified exclusively from high temperature Yellowstone National Park hot springs and a 9°N East Pacific Rise deep-sea hydrothermal vent. Phylogenetic analyses of these and all available sequences suggest that Korarchaeota exhibit a high level of endemicity.

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Reassessment of the phylogenetic relationships of Thiomonas cuprina

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65537-0 ◽

2007 ◽

Vol 57 (11) ◽

pp. 2720-2724 ◽

Cited By ~ 22

Author(s):

Donovan P. Kelly ◽

Yoshihito Uchino ◽

Harald Huber ◽

Ricardo Amils ◽

Ann P. Wood

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Significant Similarity ◽

23S Rrna Gene ◽

The 16S Rrna Gene

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.

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Horizontal Transfer of Segments of the 16S rRNA Genesbetween Species of the Streptococcus anginosusGroup

Journal of Bacteriology ◽

10.1128/jb.185.24.7241-7246.2003 ◽

2003 ◽

Vol 185 (24) ◽

pp. 7241-7246 ◽

Cited By ~ 68

Author(s):

Leo M. Schouls ◽

Corrie S. Schot ◽

Jan A. Jacobs

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Horizontal Transfer ◽

Blot Hybridization ◽

Reverse Line Blot ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Streptococcus Anginosus ◽

The 16S Rrna Gene

ABSTRACT The nature in variation of the 16S rRNA gene of members of the Streptococcus anginosus group was investigated by hybridization and DNA sequencing. A collection of 708 strains was analyzed by reverse line blot hybridization. This revealed the presence of distinct reaction patterns representing 11 different hybridization groups. The 16S rRNA genes of two strains of each hybridization group were sequenced to near-completion, and the sequence data confirmed the reverse line blot hybridization results. Closer inspection of the sequences revealed mosaic-like structures, strongly suggesting horizontal transfer of segments of the 16S rRNA gene between different species belonging to the Streptococcus anginosus group. Southern blot hybridization further showed that within a single strain all copies of the 16S rRNA gene had the same composition, indicating that the apparent mosaic structures were not PCR-induced artifacts. These findings indicate that the highly conserved rRNA genes are also subject to recombination and that these events may be fixed in the population. Such recombination may lead to the construction of incorrect phylogenetic trees based on the 16S rRNA genes.

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Molecular characterization of Mycobacterium intracellulare-related strains based on the sequence analysis of hsp65, internal transcribed spacer and 16S rRNA genes

Journal of Medical Microbiology ◽

10.1099/jmm.0.020727-0 ◽

2010 ◽

Vol 59 (9) ◽

pp. 1037-1043 ◽

Cited By ~ 18

Author(s):

Joo-Hee Park ◽

Tae-Sun Shim ◽

Seung-Ae Lee ◽

Hyungki Lee ◽

In-Kyung Lee ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Internal Transcribed Spacer ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Mycobacterium Intracellulare ◽

Epidemiological Features ◽

The 16S Rrna Gene

We investigated the molecular epidemiological features of 94 Mycobacterium intracellulare-related strains, isolated from Korean patients, using sequence analysis targeting 3 independent chronometer molecules, hsp65, the internal transcribed spacer 1 region and the 16S rRNA gene. By collective consideration of these three gene-based approaches, the 94 strains were divided into 5 groups (INT1, INT2, INT3, INT4 and INT5). The frequencies of genotype INT1, 2, 3, 4 and 5 in the 94 isolates were 57.4 % (54), 27.7 % (26), 6.4 % (6), 5.3 % (5) and 3.2 % (3), respectively. When correlations between genotypes and clinical parameters (age, sex, radiological type and the presence of a cavity) were analysed in 78 patients with non-tuberculous mycobacteria pulmonary diseases, no relationships were observed with respect to age, sex and radiological type, but genotype and the presence of a cavity tended to be related (P=0.051).

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Comparative Genetic Diversity of the narG, nosZ, and 16S rRNA Genes in Fluorescent Pseudomonads

Applied and Environmental Microbiology ◽

10.1128/aem.69.2.1004-1012.2003 ◽

2003 ◽

Vol 69 (2) ◽

pp. 1004-1012 ◽

Cited By ~ 29

Author(s):

Sandrine Delorme ◽

Laurent Philippot ◽

Veronique Edel-Hermann ◽

Chrystel Deulvot ◽

Christophe Mougel ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Pairwise Comparison ◽

Fluorescent Pseudomonads ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Bacterial Strains ◽

Good Correspondence ◽

The 16S Rrna Gene

ABSTRACT The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.

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Comparative genomics of the genus Bifidobacterium

Microbiology ◽

10.1099/mic.0.039545-0 ◽

2010 ◽

Vol 156 (11) ◽

pp. 3243-3254 ◽

Cited By ~ 85

Author(s):

Francesca Bottacini ◽

Duccio Medini ◽

Angelo Pavesi ◽

Francesca Turroni ◽

Elena Foroni ◽

...

Keyword(s):

16S Rrna ◽

Genome Structure ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Pan Genome ◽

Single Genome ◽

Phylogenetic Resolution ◽

Functional Analyses ◽

The 16S Rrna Gene

Whole-genome sequencing efforts have revolutionized the study of bifidobacterial genetics and physiology. Unfortunately, the sequence of a single genome does not provide information on bifidobacterial genetic diversity and on how genetic variability supports improved adaptation of these bacteria to the environment of the human gastrointestinal tract (GIT). Analysis of nine genomes from bifidobacterial species showed that such genomes display an open pan-genome structure. Mathematical extrapolation of the data indicates that the genome reservoir available to the bifidobacterial pan-genome consists of more than 5000 genes, many of which are uncharacterized, but which are probably important to provide adaptive abilities pertinent to the human GIT. We also define a core bifidobacterial gene set which will undoubtedly provide a new baseline from which one can examine the evolution of bifidobacteria. Phylogenetic investigation performed on a total of 506 orthologues that are common to nine complete bifidobacterial genomes allowed the construction of a Bifidobacterium supertree which is largely concordant with the phylogenetic tree obtained using 16S rRNA genes. Moreover, this supertree provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. This comparative study of the genus Bifidobacterium thus presents a foundation for future functional analyses of this important group of GIT bacteria.

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