Obtaining full-length 16S rRNA gene sequences is important for generating accurate taxonomy assignments of bacteria, which normally is realized via clone library construction. However, the application of clone library has been hindered due to its limitations in sample throughput and in capturing minor populations (<1 % of total microorganisms). To overcome these limitations, a new strategy, two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE can compare microbial communities based on its first-round DGGE profiles and generate partial 16S rRNA gene sequences (8-534 bp, Escherichia coli numbering). Then, strain-specific primers can be designed based on sequence information of bacteria of interest to PCR amplify their remaining 16S rRNA gene sequences (515-1541 bps, E. coli numbering). The second-round DGGE can confirm DNA sequence purity of these PCR products. Finally, the full-length 16S rRNA gene sequences can be ...
Two Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93-95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria , which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid.
A novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity |99·5 %, gyrB gene sequence similarity |97·8 %), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97·1-97·3 %, gyrB gene sequence similarity 84·4-85·0 %). Chemotaxonomic data (major menaquinone MK7; major fatty acids C16 : 0 and C18 : 1 ω9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4T (
A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2T, was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0-5 % (w/v) NaCl and at 10-37 °C, with optimal growth occurring with 1 % NaCl and at 28-30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum DSM 20166T (98.4 %). Levels of similarity with the type strains of all other recognized species of the genus Microbacterium were less than 98.0 %. DNA-DNA hybridization experiments with strain 0704C9-2T and its closest relative, M. testaceum DSM 20166T, revealed a low reassociation value of 42.9 %. The DNA G+C content of strain 0704C9-2T was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were
A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA-DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces
Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level
INTRODUCTION. The genus Bacillus is a phenotypically large, diverse collection of Gram-positive or Gram-variable staining, endospore-forming, aerobic or facultatively anaerobic, rod-shaped bacteria that have undergone considerable reclassification as advances in molecular biology have revealed a high phylogenetic heterogeneity (5, 21). The genus Bacillus and related genera are distributed widely in nature and include thermophilic, psychrophilic, acidophilic, alkalophilic and halophilic bacteria that utilize a wide range of carbon sources for heterotrophic growth or grow autotrophically.. The investigations on phylogenetic divergence of the genus Bacillus and its mesophilic and thermophilic members indicated the need for further and extensive studies to place some of these bacilli in appropriate taxonomic levels (1, 23, 21). With the accumulation of further 16S rRNA gene sequence data, Bacillus has been divided into more manageable and better-defined groups (16). According to Ludwig et al. (2007) ...
Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is the most rigorous. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the ability of the method to properly represent the distances between the sequences is more important. Methods. Our analysis implemented five de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and the open and closed-reference methods. Using two previously published datasets we used the Matthews Correlation Coefficient (MCC) to assess the stability and
The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of ...
A bacterial strain, B5-2(T), was isolated from an ice core drilled from Muztagh Glacier, China. Strain B5-2(T) was a Gram-stainnegative, short rod-shaped, motile by polar flagella, aerobic bacterium. The major fatty acids of strain B5-2(T) were summed feature 8 (C-18 : 1 omega 7c and/ or C-18 : 1 omega 6c) and iso-C-13 : 0. The G+C content of the DNA from strain B5-2(T) was 69.3 mol%. The predominant isoprenoid quinone of strain B5-2(T) was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified phospholipid and sulfoquinovosyldiacylglycerol. Comparative 16S rRNA gene sequence analysis revealed that the novel strain B5-2(T) shared highest similarity (96.7 %) with Aureimonas altamirensis S21B(T). On the basis of the results of this polyphasic study, strain B5-2(T) represents a novel species of the genus Aureimonas, for which the name Aureimonas glaciei sp. nov. is ...
Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea - archaeal diversity;16S rRNA gene;marine group;Ulleung Basin;East Sea;
In a recent study, rich clinical assessment and longitudinal study design are combined with host gene expression and microbial sequencing analyses to develop a framework for exploring disease etiology and outcomes in the context of human inflammatory disease. See related article: http://dx.doi.org/10.1186/s13059-015-0637-x
An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain ...
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S
The PyroTRF-ID bioinformatics methodology (http://bbcf.epfl.ch/PyroTRF-ID/) was developed to combine pyrosequencing and T-RFLP for describing microbial communities and identifying T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same biological samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised pyrosequencing datasets. Sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested on bacterial communities found in chloroethene-contaminated groundwater samples and in granular biofilms from lab-scale wastewater treatment systems. PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, multiple datasets comprising ca. ...
The appeal of using MinION for 16S rRNA sequencing is the portability, the potential to get near full-length 16S rRNA reads, and the ability for rapid (same day) sequence data. The capital costs are also low (a laptop), which is a step forward in the democratization of sequencing. While there are many potential applications, some may include sample screening prior to sequencing on another platform, sequencing in the field, or sequencing in the clinic for patient monitoring. The obvious challenge is the error rate.. To initially evaluate the potential of this technology, we sequenced 16S rRNA sequences from pure-culture E. coli and P. fluorescens, as well as a low-diversity sample from hydraulic fracturing produced water that we had previously analyzed using Illumina sequencing. We actually evaluated many more samples, but were forced to exclude them due to sample carryover between washes, which I discuss below.. We attempted to cluster the pure-culture reads into Operational Taxonomic Units ...
Bacterial community composition, as revealed by deep 16S sequence analyses, is argued to contribute to diverse human health and disease states (10). While the microbial community structure has been shown to influence susceptibility to infection in models of gastrointestinal disease (2, 4, 5, 34), the application of this concept to the female urinary tract has not been pursued. To define the existence and compositions of bladder bacterial communities in human females without the confounding factor of possible vulvo-vaginal contamination, we carefully sampled urine directly from female bladders using TUC and SPA. Deep 16S rRNA gene sequencing of these samples revealed that bacterial bladder communities of different types do exist in women, although not in all individuals. These data confirm and extend results of earlier studies (17, 21-23), clearly showing that urine specimens reported to clinicians as "culture-negative" or "insignificant growth" can contain varied bacterial communities that can ...
Widdel 1981) Kuever 2006 may be the type and only species of the genus and the order GEBAproject. class represents a separate lineage within the which is only distantly related to most other members of this class. The closest relatives based on 16S rRNA gene sequence similarity values are the type strains of (87.6% sequence identity) and (87.2%) both belonging to the family within the order [9]. The most similar cloned 16S rRNA gene EUB-42 [10] shared only 95.5% sequence similarity with and was retrieved from anaerobic sludge. Strain 2st14T WYE-354 represents the only stress of this varieties obtainable from a tradition collection so far. Available data from cultivation 3rd party studies (environmental testing and genomic studies) didnt surpass 86% series similarity indicating that people of this varieties are limited to specific habitats which are undersampled generally in most conditions or are in low great quantity (status Oct 2010). The solitary genomic 16S rRNA series of stress 2st14T was ...
Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2(T) as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2(T) (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da ...
Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets of the rhizospheric microbiota can colonize the root surface (rhizoplane) and the root interior (endosphere), forming an intimate relationship with the host plant. Compositional analysis of these communities is important to develop tools in order to manipulate root-associated microbiota for increased crop productivity. Due to the reduced cost and increasing throughput of next-generation sequencing, major advances in deciphering these communities have recently been achieved, mainly through the use of amplicon sequencing of the 16S rRNA gene. Here we first present a protocol for dissecting the microbiota from various root compartments, developed using rice as a
An international consortium of scientists has proposed a new, updated method for assigning scientific names to uncultivated bacteria and archaea.
This module is in beta. Its interface or its results may change in a future update.. Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the taxonomy nodes, e.g. gg123, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons.. The latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies about 4MB of memory once parsed into a Bio::DB::Taxonomy::greengenes object. The taxonomy files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this module can use are available from http://www.secondgenome.com/go/2011-greengenes-taxonomy/.. ...
TY - JOUR. T1 - PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. AU - Greisen, K.. AU - Loeffelholz, M.. AU - Purohit, A.. AU - Leong, D.. PY - 1994/1/1. Y1 - 1994/1/1. N2 - A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a universal bacterial probe, a gram-positive probe, a Bacteroides- Flavobacterium probe, and two probes for other gram-negative species. The second series was designed to detect PCR products from seven major bacterial species or groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The third series was designed for the detection of DNA from species or genera ...
Perspectives. (i) Recommendation for future experiments.Our experiments demonstrated the need to include many different kinds of controls, at different steps, in order to avoid data misinterpretation. In particular, alien positive controls are important for establishing threshold values for OTU positivity. These alien positive controls should include taxa that are distant enough from those of potential pathogens to avoid potential confusion between sequences of alien controls and sequences that result from actual infection of rodent samples. Ideally, one should choose alien positive controls from bacterial genera which are not able to infect the studys host species. In our study, the use of Mycoplasma and Borrelia species as alien positive controls was not ideal because both genera are potential rodent pathogens. Thankfully, the species used as alien controls could be easily distinguished from the species found in rodents on the basis of the phylogenetic analyses of the V4 sequences. However, ...
Aerobic and anaerobic cultivation techniques, 16S rDNA-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates (river snow) obtained from the river Elbe. In the course of the year the river snow community changed. It was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and winter. In all river snow samples, more than 70% of the bacteria counted with the general DNA stain DAPI also hybridized with the Bacteria-specific probe EUB338. In situ analysis of the bacterial river snow community with a comprehensive suite of specific rRNA-targeted probes revealed population dynamics to be governed by seasonal factors. During all seasons, beta-Proteobacteria constituted the numerically most important bacterial group forming up to 54% of the total cell counts. In contrast to this, the ...
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A denitrifying bacterium, designated strain FS(T), was isolated from anoxic digested sludge on oestradiol [17beta-oestra-1,3,5(10)-triene-3,17-diol] or testosterone (17beta-hydroxyandrost-4-en-3-one) as the sole source of carbon and energy with nitrate as the electron acceptor. Strain FS(T) represents the first known bacterium to grow anaerobically on both oestradiol (C-18) and testosterone (C-19). Steroidal hormones were degraded completely by nitrate reduction to dinitrogen monoxide, which was further reduced to dinitrogen in stationary-phase cultures. Gram-negative cells were slightly curved rods, 0.3-0.5 x 0.6-1.6 microm in size, motile, non-fermentative, non-spore-forming and catalase- and oxidase-positive, showing optimal growth at pH 7.0, 28 degrees C and 0.1% (w/v) NaCl. Beside steroidal hormones, the bacterium utilized only a narrow range of organic substrates with nitrate as the electron acceptor, including several fatty acids and glutamate. No aerobic or anaerobic growth occurred on ...
The resolution of the OFRG analysis was evaluated by examining the nucleotide sequences of the clones in six clusters distributed throughout the UPGMA tree (Fig. 3A, clusters 1 and 4 to 8). Clusters 2 and 3 (Fig. 3A) were not used for this analysis because only two clones from these groups were fully sequenced. For each cluster, pairwise sequence analysis showed that clones with an average sequence identity of 97% were grouped in the same cluster. The range of identities was 92.7 to 100%, and 79% of the values were between 96 and 98%. Thus, this OFRG analysis approximated species level resolution because DNA-DNA reassociation experiments have been used to show that bacterial rDNA with sequence identities of 97% or more are likely to come from the same species (25). In general, the resolution of OFRG depends on probe set properties, such as the number of probes, their discriminatory power, and the suitability of the set for a specific environment. Further refinements of probe selection algorithms ...
Estimating the diversity of life is a persistent challenge in biology. In microbiology, the task is complicated by the fact that the subjects of the census are not visible to the naked eye or easily differentiated morphologically, and they are estimated to number over 1030 individual bacteria worldwide (30). The properties of microorganisms necessitate the use of indirect analysis, involving culturing or 16S rRNA gene sequence analysis, to conduct a census of prokaryotes. Previous estimates of the number of bacterial species in the world range from 107 to 109 (6, 7). Although it is well accepted that the number of prokaryotic species in the world is immense and that our efforts to sample them have been inadequate, there has been no systematic analysis to assess how well we have sampled the bacterial world.. Estimating microbial phylogenetic diversity is intrinsically interesting to many microbiologists, but it also plays a crucial role in the functional analysis of microbial communities. ...
Estimating the diversity of life is a persistent challenge in biology. In microbiology, the task is complicated by the fact that the subjects of the census are not visible to the naked eye or easily differentiated morphologically, and they are estimated to number over 1030 individual bacteria worldwide (30). The properties of microorganisms necessitate the use of indirect analysis, involving culturing or 16S rRNA gene sequence analysis, to conduct a census of prokaryotes. Previous estimates of the number of bacterial species in the world range from 107 to 109 (6, 7). Although it is well accepted that the number of prokaryotic species in the world is immense and that our efforts to sample them have been inadequate, there has been no systematic analysis to assess how well we have sampled the bacterial world.. Estimating microbial phylogenetic diversity is intrinsically interesting to many microbiologists, but it also plays a crucial role in the functional analysis of microbial communities. ...
If your groups gene sequencing didnt work well, omit the exercise described in this paragraph.)If your soil samples 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on your cultured isolates. This analysis should identify your cultured soil community members. Do these bacteria belong to the genus or family you expected from the morphologic and metabolic information you have gathered? You can use Wellesleys electronic version of The Procaryotes found at [1] and/or Bergeys Manualfound at [2] to look up the bacteria identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses of your isolates.Do you have evidence for phylogenetic diversity as different form of richness in the community? Create a phylogenetic tree of your community members and selected non-members ...
The five most frequent keywords within the labels of environmental samples which yielded hits were microbi (9.4%), hypersalin (9.1%), http://www.selleckchem.com/products/pazopanib.html mat (8.6%), len, miniprim, new, view, world (8.5%) and food (3.4%). The single most frequent keyword within the labels of environmental samples which yielded hits of a higher score than the highest scoring species was hypersalin, len, mat, microbi, miniprim, new, view, world (12.5%). These key words are in line with the ecology and the niche from where strains of H. praevalens have been isolated. Figure 1 shows the phylogenetic neighborhood of H. praevalens GSLT in a 16S rRNA gene based tree.. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to five nucleotides, and differ by up to five nucleotides from the previously published 16S rRNA gene sequence ("type":"entrez-nucleotide","attrs":"text":"AB022034″,"term_id":"4127263″,"term_text":"AB022034″AB022034). ...
Dish one containing the swabbed doorknob bacteria grew three distinctive colonies. A dark yellow colony that was a rougher outside circle, a lighter yellow colony with a smooth outside circle, and finally a white colony which was round and smooth. Dish two containing the swabbed phone before sterilization grew the same colonies as dish one. Dish three containing the swabbed phone after sterilization grew four distinctive colonies. A dark yellow colony that was a rougher outside circle, a lighter yellow colony with a smooth outside circle, a white colony which was round and smooth, and finally a red colony that was a smooth circle that resided directly inside of the dark yellow colony ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The SeqRank project aims are to develop approaches for automatic selection of high-quality molecular sequences for microbial strains, through the use of modern ranking techniques. Currently, the SeqRank algorithm can automate the process of selecting a high-quality 16S rRNA gene sequence for any given prokaryotic strain, based on a series of quality statistics, the latest status of taxonomy and the latest sequence information from the INSDC databases. The extended SeqRank workflow applies SeqRank to all type strains of a given prokaryotic genus or family, adds an automatically chosen outgroup sequence, and infers a phylogenetic tree from the resulting list of sequences.. Contact: [email protected] or the StrainInfo team (see contact). ...
Lineage: cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Ruminiclostridium; Ruminiclostridium ...
In order for the development of antibiotics and vaccines to be successful, the lifecycle and infection pattern of a pathogen must be studied well. In this paper, we study the rate of replication and the pattern of infection in a homogeneous population, which may or may not have an effective immunity or immunization program against the pathogen. We utilize three functions: one will determine the rate with which the pathogen replicates; the second will show the result of an infection by a single individual of a susceptible population without a removal rate; and the third will include the removal rate and its dependent factor, intensity.
Singleton, D.R., M. Hunt, S.M. Powell, R. Frontera-Suau and M.D. Aitken. (2007) Stable isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. Journal of Microbiological Methods: 69:180-187 ...
Lineage: cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Alkaliphilus; Alkaliphilus ...
Gene sequencing is the process of identifying the base nucleotides in an organisms DNA. Practical applications of gene sequencing...
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.. ...
Our understanding of thermophile diversity is based predominantly on PCR studies of community DNA. Universal and domain-specific rRNA gene PCR primers have historically been used for the assessment of microbial diversity ...
Prázdniny skončili! Je tu čas na formovanie postavy a budovanie kondície!. Od 17. septembra štartujeme vo všetkých našich prevádzkach skupinové cvičenia podľa nových jesenných rozvrhov. Vyskúšajte novinky podľa Vašej chuti, a vyberte si z množstva cvičení, ktoré Vám zaručene spríjemnia nadchádzajúce chladné dni! Čaká vás výborná atmosféra, profesionálny prístup, ale aj tie správne posilňovačky, makačky, naťahovačky i tancovačky!. Teší sa na Vás tím inštruktorov Golem Clubu!. Nový rozvrh v Eurovei nájdete tu,. Nový rozvrh v Auparku nájdete tu,. Nový rozvrh v Avione nájdete tu,. Nový rozvrh v Toweri nájdete tu,. OTVÁRACIE HODINY OD 17.9.2012 DO 15.6.2013. Golem club Aupark. Pondelok - Piatok: 6:00 - 22:00. Sobota - Nedeľa: 8:00 - 22:00. Počas sviatkov: 8:00 - 22:00. Zodpovedný vedúci: Ing. Zuzana Polanská. Kontakt:0917 571 100 Golem club Avion. Pondelok - Piatok: 6:00 - 22:00. Sobota - Nedeľa: 8:00 - 22:00. Počas sviatkov: 8:00 - ...
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COMPARISON OF THE POTENCY OF POLYVALENT ANTIMENINGOCOCCUS SERUM PRODUCED WITH FOUR AND SIX REPRESENTATIVE STRAINS AND THAT PRODUCED WITH SIXTY STRAINS, AS DETERMINED BY THE AGGLUTINATION ...
Thermobaculum terrenum ATCC ® BAA-798D-5™ Designation: Genomic DNA from Thermobaculum terrenum strain YNP1 (ATCC ® BAA-798™) TypeStrain=False Application:
Define punch: a tool usually in the form of a short rod of steel that is variously shaped at one end for different operations… - punch in a sentence
Axygen™ GEN3™ Multi-Barrier Pipette Tips 20uL multi-barrier pipette tip Axygen™ GEN3™ Multi-Barrier Pipette Tips Filtered Universal Pipette Tips
Parablechnum roraimense and P. paucipinna spp. nov. (Blechnaceae: Polypodiopsida), lectotypification of P. stuebelii , and citation corrections in the family
Jak jsou nov trendy v hubnut a diet ch, co je zdrav a inn , co pom h ? Jak diety mohou naopak u kodit? Dozv te se na Ona.idnes.cz
Nov m gener ln m editelem esk pobo ky Vodafonu se stal Petr Dvo k, kter byl od poloviny ledna pov en zen m firmy. Na pozici gener ln ho editele st d Ji ho B u.
Hello all!! Ive been waiting and WAITING for a new thread to start with Oct/Nov/Dec this year.... So I decided to start one myself. Im really wary about posting here already, as Im prone to miscarriage, but while Im pregnant, Im going
TCDRVDCK (*) OWC Drive Dock with USB-C (USB 3.1 Gen 2) Dual Drive Bay Solution. Add up to two 2.5" and 3.5" SATA drives. Connect via USB 3.1 Gen 2 (up to 10Gb/s). Internal power with independent power switches. *New, Open Box*
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As discussed in this http://www.daz3d.com/forums/discussion/58379/v4-uvs-for-g3f/ thread. Heres my method for converting textures to Gen3
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... FIGURA 4-3 Vias de sinalização e funções do TLRs. Os TLRs 1, 2, 5 e 6 utilizam a proteína adaptadora MyD88 e
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Strains VIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were isolated from marine sediments collected from the Xisha Islands in the South China Sea. All three isolates were able to grow optimally at pH 7.0, 28-37 degrees C and 0-3% (w/v) NaCl. Comparison of 16S rRNA gene sequences showed that these strains are members of the genus Streptomyces, exhibiting moderately high 16S rRNA gene sequence similarities of 97.0-98.8% to members of the most closely related Streptomyces species. Morphological characteristics, physiological characteristics and compositions of whole-cell sugars and phospholipids are consistent with the diagnostic characteristics of the genus Streptomyces, but still allowed differentiation amongst the three strains and their neighbours. Based on 16S rRNA gene sequence analysis, DNA DNA relatedness, phenotypic characteristics and chemotaxonomic data, strains VIM M 10366(T), VIM M 10378(T) and VIM M 10400(T) were identified as members of three novel species of the genus ...
A Gram-stain-positive, aerobic, non-spore-forming, atrichous and short rod-shaped endophytic actinomycete, designated strain BGMRC 2075 , was isolated from the leaves of Kandelia candel, and was subjected to polyphasic characterization to unravel its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BGMRC 2075 belongs to the genus Nocardioides ,showing the highest 16S rRNA gene sequence similarity to Nocardioides aestuarii JC2056 (96.1 %), Nocardioides agariphilus MSL-28 (95.1 %) andNocardioides islandiensis MSL-26 (95.1 %). The predominant cellular fatty acids of strain BGMRC 2075 were iso-C16 : 0, C17 : 1ω8c and C17 : 0. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of ribose and glucose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, ...
A Gram-staining-positive, cocci, halotolerant bacterial strain, designated as SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurs at temperatures in the range between 25-37 °C (optimum 30 °C), pH 7.0-11.0 (optimum 8.0) and at NaCl concentrations up to 25 .0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids are diphosphatidylglycerol (DPG), phosphatidylinositol (PI) and phosphatidylglycerol (PG). The major cellular fatty acids are iso-C15: 0, anteiso-C15: 0, iso-C17: 0 and anteiso C17: 0. The draft genome of strain SV-16T consisted of 2,591,284 bp with G+C content of 48.7 mol %. On the basis of the phenotypic characteristics and genotypic ...
Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data ...
article{7225551, abstract = {A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676(T), was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8\% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676(T) from all established species of the genus Leuconostoc. Strain LMG 27676(T) (=R-50029(T)=MHB 277(T)=DSM 27776(T)) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.}, author = {Lyhs, Ulrike and Snauwaert, Isabel and Pihlajaviita, Seija and De Vuyst, Luc and Vandamme, Peter}, issn = {1466-5026}, journal = {INTERNATIONAL ...
Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual ...
Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a molecular biology technique for profiling of microbial communities based on the position of a restriction site closest to a labelled end of an amplified gene. The method is based on digesting a mixture of PCR amplified variants of a single gene using one or more restriction enzymes and detecting the size of each of the individual resulting terminal fragments using a DNA sequencer. The result is a graph image where the x-axis represents the sizes of the fragment and the y-axis represents their fluorescence intensity. TRFLP is one of several molecular methods aimed to generate a fingerprint of an unknown microbial community. Other similar methods include DGGE, TGGE, ARISA, ARDRA, PLFA, etc. These relatively high throughput methods were developed in order to reduce the cost and effort in analyzing microbial communities using a clone library. The method was first described by Liu and colleagues in 1997 which employed ...
Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus, Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified, Saccharophagus degradans gen. nov., sp. nov. 2-40(T) (=ATCC 43961(T)=DSM 17024(T)). S. degradans strain 2-40(T) can degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan. S. degradans 2-40(T) shares 90.5% 16S rRNA gene sequence similarity with the type strain of the Microbulbifer type species, Microbulbifer hydrolyticus ...
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The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic
Relative abundance of 16S/18S rRNA gene sequences affiliated to lineages displaying metabolisms favoring carbonate precipitation in Alchichica microbialites. Si
A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6(T), was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereu
Bacteria were isolated from the dental plaques of nine dogs and a sample of pooled saliva from five other dogs and were then identified by comparative 16S rRNA gene sequencing. Among 339 isolates, 84 different phylotypes belonging to 37 genera were identified. Approximately half of the phylotypes were identified to the species level, and 28% of these were considered members of the indigenous oral microbiota of humans. The 16S rRNA gene sequences of the remaining 44 phylotypes were not represented in GenBank, and most of these phylotypes were tentatively identified as candidate new species. The genera most frequently isolated from saliva were Actinomyces (26%), Streptococcus (18%), and Granulicatella (17%). The genera most frequently isolated from plaque were Porphyromonas (20%), Actinomyces (12%), and Neisseria (10%). A comparison of the DNA sequences from this study with sequences of the human microbiota available in GenBank showed that, on average, canine and human microbiotas differed by ...
Abstract: Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., ...
The type species for the genus Skermanella is Skermanella parooens ACM 2042T, which was originally proposed as Conglomeromonas largomobilis subsp. parooensis by Skerman et al. in 1983 [1]. Later, it was transferred to the genus Skermanella (family Rhodospirillaceae) on the basis of phylogenetic evidence and phenotypic characteristics, especially the inability to fix nitrogen [2,3]. At present, this genus comprises four validly published species, Skermanella parooensis [3], Skermanella aerolata [4], Skermanella xinjiangensis [5] and Skermanella stibiiresistens [6], which were isolated from fresh water, air, sandy soil and a coal mine, respectively.. Skermanella was characterized as a Gram-negative, non-spore-forming bacterium with unicellular and multicellular phases of growth, an obligate chemo-organotroph and facultative anaerobe, unable to fix nitrogen, and with a high DNA G+C content. To the best of our knowledge, genome information for Skermanella members is still not available. In this ...
A polyphasic study was designed to determine the taxonomic provenance of three Modestobacter strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates KNN 45-1a, KNN 45-2b(T) and KNN 45-3b, were shown to have chemotaxonomic and morphological properties in line with their classification in the genus Modestobacter. The isolates had identical 16S rRNA gene sequences and formed a branch in the Modestobacter gene tree that was most closely related to the type strain of Modestobacter marinus (99.6% similarity). All three isolates were distinguished readily from Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. The whole genome sequence of isolate KNN 45-2b(T) showed 89.3% average nucleotide identity, 90.1% (SD: 10.97%) average amino acid identity and a digital DNA-DNA hybridization value of 42.4±3.1 against the genome sequence of M. marinus DSM 45201(T), ...
We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity ,90%) in the data ... read more sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97 - 100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in ...
An obligately anaerobic bacterial strain designated T-1-35(T) was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35(T) stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8-1.0 3.5-15.0 m, and motile by means of two to four polar flagella. Cells of strain T-1-35(T) exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 C for 10 min. The temperature range for growth was 15-40 C, with an optimum at 35 C. The pH range for growth was 5.5-9.0, with an optimum at pH 8.0-8.5 (slightly alkaliphilic). Strain T-1-35(T) fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed ...
What: Academic Seminar, Dr. Emma Allen Vercoe, Department of Molecular and Cellular Biology at the University of Guelph Topic: Understanding gut microbial community dynamics using an in vitro bioreactor model When: Monday, August 14, 10:30-11:30 a.m. Where: Robert B. Schultz Lecture Theatre
A novel Gram-positive, aerobic, actinobacterial strain, CF6/1T, was isolated in 2007 during environmental screening of arid desert soil in the Sahara near to Ourba, Chad. The isolate was found to grow best in a temperature range of 20-37 °C and at pH 6.0-8.5 and showed no NaCl tolerance, forming black-coloured and nearly circular colonies on GYM agar. Chemotaxonomic and molecular characteristics determined for the isolate match those previously described for members of the genus Geodermatophilus. The DNA G + C content of the novel strain was determined to be 74.9 mol %. The peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The main phospholipids were determined to be phosphatidylethanolamine, phosphatidylinositol, phosphatidylcholine, diphosphatidylglycerol and traces of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose as the diagnostic sugar. The major cellular fatty acids were found to be the branched-chain ...
Ward, N.L., Rainey, F.A., Hedlund, B.P., Staley, J.T., Ludwig, W., and Stackebrandt, E. Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny. Int. J. Syst. Evol. Microbiol. (2000) 50:1965-1972 ...
Using high resolution molecular fingerprinting techniques like random amplification of polymorphic DNA, repetitive extragenic palindromic PCR and multilocus enzyme electrophoresis, a high bacterial diversity below the species and subspecies level (microdiversity) is revealed. It became apparent that bacteria of a certain species living in close association with different plants either as associated rhizosphere bacteria or as plant pathogens or symbiotic organisms, typically reflect this relationship in their genetic relatedness. The strain composition within a population of soil bacterial species at a given field site, which can be identified by these high resolution fingerprinting techniques, was markedly influenced by soil management and soil features. The observed bacterial microdiversity reflected the conditions of the habitat, which select for better adapted forms. In addition, influences of spatial separation on specific groupings of bacteria were found, which argue for the occurrence of ...
Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut.
We isolated 59 strains of cyanobacteria from the benthic microbial mats of 23 Antarctic lakes, from five locations in two regions, in order to characterize their morphological and genotypic diversity. On the basis of their morphology, the cyanobacteria were assigned to 12 species that included four Antarctic endemic taxa. Sequences of the ribosomal RNA gene were determined for 56 strains. In general, the strains closely related at the 16S rRNA gene level belonged to the same morphospecies. Nevertheless, divergences were observed concerning the diversity in terms of species richness, novelty, and geographical distribution. For the 56 strains, 21 operational taxonomic units (OTUs, defined as groups of partial 16S rRNA gene sequences with more than 97.5% similarity) were found, including nine novel and three exclusively Antarctic OTUs. Sequences of Petalonema cf. involvens and Chondrocystis sp. were determined for the first time. The internally transcribed spacer (ITS) between the 16S and the 23S ...
Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was ...
Citation: Labeda, D.P., Kroppenstedt, R.M. 2008. Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov. International Journal of Systematic and Evolutionary Microbiology. 58:1472-1475. Interpretive Summary: Gene sequence-based molecular analyses for reassessment of evolutionary relationships of microoganisms at the species, genus, or higher taxonomic levels can sometimes reveal unexpected problems with existing classification of microbial species where conclusions based incomplete morphological or chemical composition data resulted in incorrect decisions. The microorganism that produces the antiviral antibiotic cycloviracin was described as a species of the genus Kibdelosporangium in 1993 based on data available to the researchers at that time. A molecular systematic analysis of the 16S ribosomal RNA gene sequences of all members of the bacterial family ...
Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively. Gene-targeted assays enumerating the TMA-producing community by quantitative PCR and characterizing its composition via Illumina sequencing were developed and applied on human fecal samples (n = 50) where all samples contained
In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At ...
Synonyms for coccobacilli in Free Thesaurus. Antonyms for coccobacilli. 4 words related to coccobacillus: Brucella, eubacteria, eubacterium, true bacteria. What are synonyms for coccobacilli?
Enorma timonensis strain GD5T (= CSUR P900 = DSM 26111) is the type strain of E. timonensis sp. nov. This bacterium was isolated from the stool of a 53-year-old French woman hospitalized for 3 months into an intensive care unit for a Guillain-Barre syndrome, as part of a culturomics study aiming at cultivating individually all species within human feces [1-3]. It is a Gram-positive, anaerobic, non-endospore forming, indole-negative, rod-shaped bacillus.. The human gut microbiota consists of billions of microorganisms that outnumber the human cells [4]. Advances in DNA sequence-based technologies and the development of 16S ribosomal RNA sequence-based metagenomic methods have been used to explore the complex gut microbial population, which has a crucial role in human health and disease development [5,6]. The currently used strategy for determining the taxonomic status of a bacterial isolate includes comparing it to its phylogenetically closest neighbors in terms of 16S rRNA gene similarity, G + C ...
article{157352, author = {Boon, Nico and De Windt, Wim and Verstraete, Willy and Top, Eva}, issn = {0168-6496}, journal = {FEMS MICROBIOLOGY ECOLOGY}, language = {eng}, number = {2}, pages = {101--112}, title = {Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.}, volume = {39}, year = {2002 ...
... : Phylogram (neighbor-joining method) showing genetic relationship between strain ETL-1982 and other microorganisms based on the 16S rRNA gene sequence analysis ...
The General Community Profile is new for the 2016 Census. It replaces the Basic and Expanded Community Profiles and has been created by merging elements of both these profiles. It consists of 59 tables containing key Census characteristics on persons, families and dwellings. The data are based on place of usual residence. The General Community Profile will be released in three phases. First release tables are those containing classifications which are relatively easy to process and will be available on release day. Second release tables contain Labour Force classifications which require more complex processing and will be available on the second release day. In third release the final geography area for Remoteness will be available. ...
The General Community Profile is new for the 2016 Census. It replaces the Basic and Expanded Community Profiles and has been created by merging elements of both these profiles. It consists of 59 tables containing key Census characteristics on persons, families and dwellings. The data are based on place of usual residence. The General Community Profile will be released in three phases. First release tables are those containing classifications which are relatively easy to process and will be available on release day. Second release tables contain Labour Force classifications which require more complex processing and will be available on the second release day. In third release the final geography area for Remoteness will be available. ...
Ben Hanelt, D. Van Schyndel, C. M. Adema, L. A. Lewis, E. S. Loker. The Phylogenetic Position of Rhopaluva ophiocomae (Orthonectida) Based on 18s Ribosomal DNA Sequence Analysis. -Molecular Biology and Evolution, 1996,. 13 (9), lk 1187-1191. Veebiversioon. ...
Designation of Streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes.: The 16S and 23S rRNA of various Streptomyces species were partia