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1.
The phylogenetic diversity of a sediment microbial community from two ponds having different salinities, 150–200 g/l (M2) and 250–300 g/l (TS38), of an Sfax (Tunisia) solar saltern, was investigated using 16S rRNA clone libraries. The 16S rRNA genes from 135 bacterial clones and 105 archaeal clones were sequenced and phylogenetically analyzed. 32 operational taxonomic units (OTUs) were generated for Bacteria and 64 for Archaea. The bacterial community in M2 sediment was affiliated only with Bacteroidetes, while that in TS38 sediment was dominated by clones affiliated with Bacteroidetes, (gamma, alpha, delta) Proteobacteria and unclassified bacteria; these represented 56.52, 26.08, 4.34, 4.34 and 8.7% of the OTUs, respectively. In the M2 and TS38 sediments, 44.44 and 43.47% of the bacterial OTUs, respectively, were novel. All archaeal sequences fell into the Euryarchaeota phylum. In both sediments, 38.46 and 72.55% of the OTUs had less than 97% 16S rRNA sequence identity, representing novel OTUs. Two sequences, retrieved from TS38 sediment, were found to be affiliated with the candidate division MSBL-1 defining two OTUs. The sediment phylogenetic study revealed the presence of a highly diverse microbial population in highly salty media.  相似文献   

2.
The diversity and temporal dynamics of bacterial communities in pristine snow around two Russian Antarctic stations was investigated. Taxonomic analysis of rDNA libraries revealed that snow communities were dominated by bacteria from a small number of operational taxonomic units (OTUs) that underwent dramatic swings in abundance between the 54th (2008–2009) and 55th (2009–2010) Russian Antarctic expeditions. Moreover, analysis of the 55th expedition samples indicated that there was very little, if any, correspondence in abundance of clones belonging to the same OTU present in rDNA and rRNA libraries. The latter result suggests that most rDNA clones originate from bacteria that are not alive and/or active and may have been deposited on the snow surface from the atmosphere. In contrast, clones most abundant in rRNA libraries (mostly belonging to Variovorax, Janthinobacterium, Pseudomonas, and Sphingomonas genera) may be considered as endogenous Antarctic snow inhabitants.  相似文献   

3.
Bacteria influence site‐specific disease etiology and the host's ability to metabolize xenobiotics, such as polycyclic aromatic hydrocarbons (PAHs). Lung cancer in Xuanwei, China has been attributed to PAH‐rich household air pollution from burning coal. This study seeks to explore the role of lung microbiota in lung cancer among never smoking Xuanwei women and how coal burning may influence these associations. DNA from sputum and buccal samples of never smoking lung cancer cases (n = 8, in duplicate) and controls (n = 8, in duplicate) in two Xuanwei villages was extracted using a multi‐step enzymatic and physical lysis, followed by a standardized clean‐up. V1‐V2 regions of 16S rRNA genes were PCR‐amplified. Purified amplicons were sequenced by 454 FLX Titanium pyrosequencing and high‐quality sequences were evaluated for diversity and taxonomic membership. Bacterial diversity among cases and controls was similar in buccal samples (P = 0.46), but significantly different in sputum samples (P = 0.038). In sputum, Granulicatella (6.1 vs. 2.0%; P = 0.0016), Abiotrophia (1.5 vs. 0.085%; P = 0.0036), and Streptococcus (40.1 vs. 19.8%; P = 0.0142) were enriched in cases compared with controls. Sputum samples had on average 488.25 species‐level OTUs in the flora of cases who used smoky coal (PAH‐rich) compared with 352.5 OTUs among cases who used smokeless coal (PAH‐poor; P = 0.047). These differences were explained by the Bacilli species (Streptococcus infantis and Streptococcus anginosus). Our small study suggests that never smoking lung cancer cases have differing sputum microbiota than controls. Further, bacteria found in sputum may be influenced by environmental exposures associated with the type of coal burned in the home. Environ. Mol. Mutagen. 55:643–651, 2014. © 2014 Wiley Periodicals, Inc.  相似文献   

4.
Microbial diversity of mine water at Zhong Tiaoshan copper mine, China   总被引:1,自引:0,他引:1  
Microbial diversity of mine water at Zhong Tiaoshan copper mine, Shanxi province, China, was analyzed using a culture-independent 16S rRNA gene (rDNA) based on cloning approach. A total of 59 Operational Taxonomic Units (OTUs) were obtained from 226 clones from all three samples (8 OTUs from sample SX1, 25 from SX2 and 26 from SX3). 46 of them were representative OTUs and were sequenced. 93.5% of the total clones had sequences that were less than 5% difference from those in the nucleic acids database. The percentage of overlapping OTUs among samples was from 12.1% to 35.3%. Phylogenetic analysis indicated that 60.62% of the clones were affiliated with members of the Proteobacteria (alpha -3.10%, beta -24.78%, gamma -31.41%, delta -1.33%), whereas 29.20% of the clones were closely related to the Nitrospira (Leptospirillum ferrooxidans 20.80%, Leptospirillum ferriphilum 0.88% and Leptospirillum group III 7.52%, respectively). The rest clones were affiliated with the Firmicutes (2.65%) and the Bacteroidetes (7.52%). The results of Principal Component Analysis (PCA) based on the percentages of OTUs and biogeochemical data revealed that biogeochemical properties affected the diversity of microbial communities in mine water. Especially, the pH value, temperature and different concentrations of elements such as lead, zinc, sulfur, iron and copper seemed to be key factors affecting the composition and structure of microbial communities in this study.  相似文献   

5.
Detection of Neisseria gonorrhoeae relies increasingly on nucleic acid amplification tests (NAATs). The specificity of many gonococcal NAATs has been suboptimal and supplementary testing remains recommended in Europe and several additional countries. The novel dual‐target GeneProof Neisseria gonorrhoeae PCR kit, targeting porA pseudogene and 16S rRNA gene, showed a high specificity and sensitivity when isolates of non‐gonococcal Neisseria and related species (n = 144), and gonococci (n = 104) were tested. However, rare gonococcal porA mutants were only detected in the 16S rRNA gene target and two non‐gonococcal isolates showed a low‐level cross‐reactivity in the 16S rRNA gene target. The detection limit for both targets was 1.5 copies per reaction.  相似文献   

6.
Phylogenetic diversity analyses of archaeal 16S rRNA and ammonia monooxygenase subunit A (AamoA) genes were carried out on sediment samples from the Mandovi and Zuari estuaries on the central west coast of India. The 16S rRNA gene libraries revealed quite high diversity of archaea in these sediments compared to previous reports from tropical and temperate estuarine sediments. Uncultured members of Crenarchaeota accounted for ~78% of 433 archaeal 16S rRNA gene clones from both of the estuaries. We detected archaeal 16S and amoA gene-related organisms capable of ammonia oxidation. Among Crenarchaeota, marine group I (MG I) was the most predominant. Clones matching the uncultured methanobacteria were predominant among the ribogroups of Euryarchaeota. Our results indicate that archaeal diversity in tropical estuarine sediments is influenced by the mangrove vegetation bordering the lower stretches of both estuaries. Higher diversity may be related to elevated land drainage during the monsoon, particularly in the Mandovi estuary sediments. Also, the diversity of AamoA sequences was higher in Mandovi sediments than those from Zuari and other tropical and/or temperate estuaries studied previously.  相似文献   

7.
IgG4‐related sclerosing sialadenitis is currently considered as an autoimmune disease distinct from Sjogren’s syndrome (SS) and responds extremely well to steroid therapy. To further elucidate the characteristics of IgG4‐related sclerosing sialadenitis, we analysed VH fragments of IgH genes and their somatic hypermutation in SS (n = 3) and IgG4‐related sclerosing sialadenitis (n = 3), using sialolithiasis (n = 3) as a non‐autoimmune control. DNA was extracted from the affected inflammatory lesions. After PCR amplification of rearranged IgH genes, at least 50 clones per case (more than 500 clones in total) were sequenced for VH fragments. Monoclonal IgH rearrangement was not detected in any cases examined. When compared with sialolithiasis, there was no VH family or VH fragment specific to SS or IgG4‐related sclerosing sialadenitis. However, rates of unmutated VH fragments in SS (30%) and IgG4‐related sclerosing sialadenitis (39%) were higher than that in sialolithiasis (14%) with statistical significance (P = 0.0005 and P < 0.0001, respectively). This finding suggests that some autoantibodies encoded by germline or less mutated VH genes may fail to be eliminated and could play a role in the development of SS and IgG4‐related sclerosing sialadenitis.  相似文献   

8.
Summary Neurospora crassa wild type genome shows DNA sequences which are homologous to the sequences present in the rRNA processing genes of the yeast Saccharomyces cerevisiae. Five such processing genes from yeast, viz., RNA1 through RNA5, cloned in plasmid pBR322 were transformed in Escherichia coli strain LE392. Southern blots containing DNAs from these clones were restricted with several restriction endonucleases along with DNAs from lambda phage, rice (plant) and neuroblastoma (animal), were hybridized with 32P-labelled nick-translated N. crassa nuclear DNA under very stringent conditions. Autoradiograms of these blots revealed that four yeast rRNA processing genes (RNA1, RNA2, RNA3, and RNA4) showed homology with N. crassa nuclear DNA but such analogs were not found in DNAs representing prokaryotes, phages, higher plants and animals.  相似文献   

9.
Until now, Planctomycetes bacteria were considered as environmental organisms. Nevertheless, some studies detected Planctomycetes DNA from human gut. We therefore explored the human gut Planctomycetes content. Planctomycetes‐specific PCR primers were designed to amplify a 240–bp 16S rRNA gene fragment in human stool specimens from individuals in France and in Senegal and from endocarditis patients receiving antibiotics in France. PCR products were then cloned and sequenced. PCR detection revealed a significantly higher prevalence (1.8% vs 0.4%, p = 0.05) and higher diversity (62 vs 6 phylotypes, p = 0.02) of Planctomycetes 16S rRNA gene in stool specimens collected in Senegal than in France. Also, stool specimens from endocarditis patients exhibited non‐significantly higher prevalence (0.6% vs 0.4%) and the ratio of phylotypes by positive patient (3 vs 1.5) than those collected from untreated French individuals. Gemmata sp. related sequences were found in 6/12 individuals. Planctomycetes organisms are a part of the human digestive tract microbiota. Their diversity varied by environment including the geographical origin of the individual and antibiotics treatment.  相似文献   

10.
The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.  相似文献   

11.
Cloning, sequencing and characterization of nearly full‐length 23S rRNA genes in 12 urease‐positive thermophilic Campylobacter (UPTC) isolates were carried out using two novel PCR primer pairs. Nucleotide sequences of the 23S rRNA genes from the 12 isolates were first shown not to carry any intervening sequences (IVSs) in both the 25 and 45 helix regions. Then, two PCR primer sets were designed in silico for amplification of the helix 25 and 45 regions within 23S rRNA gene sequences from Campylobacter lari. No IVSs were identified within the 23S rRNA genes among a total of 53 isolates of C. lari, following PCR amplification, TA cloning and sequencing procedures. Intact 23S rRNA was identified in all 65 C. lari isolates, resulting in no production of the fragmented 23S rRNA. These data suggest that C. lari may not have any opportunity to interact with any other source of IVSs until now, or has been unable to integrate IVSs into their own genomes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)  相似文献   

12.
Summary: We have isolated several cytotoxic T lymphocyte (CTL) clones from lymphocytes infiltrating a lung carcinoma of a patient with long survival. These clones showed a CD3+, CD8+, CD4, CD28 phenotype and expressed a T‐cell receptor (TCR) encoded either by Vβ8‐Jβ1.5 or Vβ22‐Jβ1.4 rearrangements. Functional studies indicated that these clones mediated a high human leukocyte antigen (HLA)‐A2.1‐restricted cytotoxic activity against the autologous tumor cell line. Interestingly, TCRβ chain gene usage indicated that CTL clones identified in vitro were selectively expandedin vivo at the tumor site as compared to autologous peripheral blood lymphocytes (PBL). These findings provide evidence that an immune response may take place in non‐small cell lung carcinoma and that effector T cells may contribute to tumor regression. Further study indicated that the CTL clones recognized the same decamer peptide encoded by a mutated α‐actinin‐4 gene. Using tetramers of soluble HLA‐A2 molecules loaded with the mutated antigenic peptide, we have derived several anti‐α‐actinin‐4 T‐cell clones from patient PBL. These CTL, recognizing a truly tumor‐specific antigen, may play a role in the clinical evolution of this lung cancer patient. Adoptive transfer of CTL clones in a SCID/NOD mice model transplanted with autologous tumor supported their antitumor effect in vivo.  相似文献   

13.
Ultra‐fine fiber mats of poly(L ‐lactic acid) containing gallic acid were prepared by electrospinning from gallic acid‐containing PLLA solution in 7:3 v/v dichloromethane (DCM)/N,N‐dimethylformamide (DMF). The amount of the as‐loaded gallic acid was 40% w/w (based on the weight of PLLA in the solution) or 28.6 wt.‐% (based on the weight of the resulting fiber mats). Both the neat and the gallic acid‐loaded PLLA fibers were smooth, with the average diameters of 965 and 843 nm, respectively. No aggregates of gallic acid were observed on the fiber surface and the actual amount of gallic acid in the gallic acid‐loaded PLLA fiber mats, determined in the acetate buffer, the citrate‐phosphate buffer, and the normal saline, was 26.3, 27.1, and 24.6 wt.‐%. The cumulative amount of gallic acid released from the gallic acid‐loaded PLLA fiber mats was greatest in the normal saline, followed by those in the citrate‐phosphate and the acetate buffer, respectively. Lastly, the free radical scavenging activity, based on the 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) assay, of the as‐loaded and the as‐released gallic acid remained active.

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14.
Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of EAE, a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short‐chain fatty acid (SCFA) production in CD44 knockout (CD44KO) mice. Fecal transfer from naïve CD44KO but not C57BL/6 wild type (CD44WT) mice, into EAE‐induced CD44WT mice, led to significant amelioration of EAE. High‐throughput bacterial 16S rRNA gene sequencing, followed by clustering sequences into operational taxonomic units (OTUs) and biochemical analysis, revealed that EAE‐induced CD44KO mice showed significant diversity, richness, and evenness when compared to EAE‐induced CD44WT mice at the phylum level, with dominant Bacteroidetes (68.5%) and low Firmicutes (26.8%). Further, data showed a significant change in the abundance of SCFAs, propionic acid, and i‐butyric acid in EAE‐CD44KO compared to EAE‐CD44WT mice. In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs. Furthermore, our studies also demonstrate that the phenotype of gene knock‐out animals may be shaped by gut microbiota.  相似文献   

15.
We investigated the genetic similarities and expression of the MexAB‐OprM efflux pump system in different clones of multiresistant Pseudomonas aeruginosa strains collected from 2002 to 2009 at two intensive care units (ICU). Regulatory and structural genes mexB, mexR, and mexA were found in 99%, 98%, and 94% of tested strains, respectively. The presence of class 1 integron was found in 90% of the strains, while class 2 integron in only one strain (Psa506). Class 3 integron was not found in any of the tested strains. Among the eleven clones identified, only two clones, I and D, exhibited higher levels of mexB gene expression than the other clones. Clone I had the highest expression (FC = 10.36, p < 0.05). The results of our study indicated a high level of MexAB‐OprM pump expression in groups of strains isolated in the years 2008–2009 (FC = 12.92, p < 0.03) and 2002–2006 (FC = 5.14, p < 0.03). There were no statistically significant differences in resistance to all tested antibiotics among the various clones. The high level of antimicrobial resistance may have been due to the coexistence of different resistance mechanisms among the studied P. aeruginosa strains. However, this does not exclude the contribution of the MexAB‐OprM pump, particularly in resistance to meropenem and ciprofloxacin.  相似文献   

16.
Landfills represent a major source of methane in the atmosphere. In a previous study, we demonstrated that earthworm activity in landfill cover soil can increase soil methane oxidation capacity. In this study, a simulated landfill cover soil mesocosm (1 m × 0.15 m) was used to observe the influence of earthworms (Eisenia veneta) on the active methanotroph community composition, by analyzing the expression of the pmoA gene, which is responsible for methane oxidation. mRNA-based pmoA microarray analysis revealed that earthworm activity in landfill cover soil stimulated activity of type I methanotrophs (Methylobacter, Methylomonas, Methylosarcina spp.) compared to type II methanotrophs (particularly Methylocystis spp.). These results, along with previous studies of methanotrophs in landfill cover soil, can now be used to plan in situ field studies to integrate earthworm-induced methanotrophy with other landfill management practises in order to maximize soil methane oxidation and reduce methane emissions from landfills.  相似文献   

17.
Diazotrophs diversity in soybean is a topic requiring thorough investigation since the previous researches have focused on only rice, forest, grass, water, etc. In this research, iron‐only nitrogenase nifH gene was as genetic marker. PCR‐RFLP was used to investigate the difference of diazotrophs community diversity in the soil from the continuous cropping (CC) (the 5‐yr tilling of soybean) and the rotational cropping (RC) (soybean‐corn) soils in the northeast of China. A total of 36 isolates were genetically characterized. Most of the isolates closely related to Azospirillum and Azotobacter. Eighty‐six unique nifH gene sequences were obtained by cloning of the respective PCR products in two soil samples. It was found that the diversity of nifH genes in CC changed obviously compared with RC. Phylogenetic analysis indicated that most of the clones clustered together in a high homogeneity with some sequence retrieved from environmental representatives. The sequence diversity of nifH genes was high and the members of the Alphaproteobacteria were predominant in both samples. The experimental study also revealed the two non‐proteobacterial diazotrophs, firmicutes and euryarchaeota. Through this study, it can be assumed that different tillage perhaps affected the nifH gene‐containing population diversity. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)  相似文献   

18.
Tuberculosis is a disease caused by the Mycobacterium tuberculosis complex (MTb). In 2011, global mortality due to tuberculosis was 1·4 million individuals. The only available vaccine is the attenuated M. bovis [bacillus Calmette–Guérin (BCG)] strain, which confers variable protection against pulmonary tuberculosis. Some widely distributed non‐tuberculous mycobacteria (NTM), such as M. avium and M. arupense, are also potential pathogens for humans. This work aimed to produce and characterize monoclonal antibodies against the M. bovis BCG Mexico strain of the MTb, M. avium subs. hominissuis and the M. arupense strain from NTM. Hybridomas were produced from splenocytes of BALB/c female mice immunized with radiation‐inactivated mycobacteria, and the immunoglobulin (Ig)G2a antibody‐producing clones with the highest antigenic recognition were selected. The selected clones, Mbv 2A10 for M. bovis BCG Mexico, Mav 3H1 for M. avium and Mar 2D10 for M. arupense, were used in further studies. Enzyme‐linked immunosorbent assay (ELISA) and immune proteomics analyses characterized the clones as having the highest cross‐reactivity with mycobacteria. Using mass spectrometry, a number of proteins recognized by the monoclonal antibody (mAb) clones were identified. These proteins had roles in metabolic processes, hypoxia, cell cycle and dormancy. In addition, a Clustal W and Immune Epitope Database (IEDB) in‐silico analysis was performed in protein sequences that result in the conserved regions within probability epitopes that could be recognized for Mbv2A10 and Mav3H1 clones.  相似文献   

19.
A 1 380-bp intervening sequence within the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum has been sequenced and identified as a group-I intron. This is the first report of an intron in the mt SSU rRNA gene. The intron shows close similarity in secondary structure to the subgroup-IC2 introns from Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has an open reading frame (ORF) that encodes a putative protein of 420 amino acids which contains two copies of the LAGLI-DADG motif. The ORF belongs to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2, and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also similar to a site-specific endonuclease in the chloroplast large subunit ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos. In each clone of S. sclerotiorum examined, including several clones which were sampled over a 3-year period from geographically separated sites, all isolates either had the intron or lacked the intron within the mt SSU rRNA gene. Screening by means of Southern hybridization and PCR amplification detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae, such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous and basidiomycetous fungi.  相似文献   

20.
Cells heterozygously mutant for a ribosomal protein gene, called Minute/+ mutants, are eliminated from epithelium by cell competition when surrounded by wild‐type cells. Whereas several factors that regulate Minute cell competition have been identified, the mechanisms how winner/loser status is determined and thereby triggers cell competition are still elusive. To address this, we established two assay systems for Minute cell competition, namely (i) the CORE (competitive elimination of RpS3‐RNAi‐expressing cells) system in which RpS3‐RNAi‐expressing wing pouch cells are eliminated from wild‐type wing disc and (ii) the SURE (supercompetition of RpS3‐expressing clones in RpS3/+ tissue) system in which RpS3‐over‐expressing clones generated in RpS3/+ wing disc outcompete surrounding RpS3/+ cells. An ectopic over‐expression screen using the CORE system identified Wg signaling as a critical regulator of Minute cell competition. Activation of Wg signaling in loser cells suppressed their elimination, whereas down‐regulation of Wg signaling in loser cells enhanced their elimination. Furthermore, using the SURE system, we found that down‐regulation of Wg signaling in winner cells suppressed elimination of neighboring losers. Our observations suggest that cellular Wg signaling activity is crucial for determining winner/loser status and thereby triggering Minute cell competition.  相似文献   

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