Universal Bacterial Primers Research Articles

Detection of specific periodontal microorganisms from bacteraemia samples after periodontal therapy using molecular-based diagnostics

The aim of this study was to assess the presence of subgingival pathogens in peripheral blood samples from periodontitis patients before and after scaling and root planing (Sc/RP) using nested polymerase chain reaction (nested PCR). Peripheral blood samples were obtained from 42 patients with severe generalized chronic or aggressive periodontitis. In each patient, four samples of peripheral blood were drawn at different times: immediately before the Sc/RP procedure; immediately after Sc/RP; 15 and 30 min. post-Sc/RP. Blood samples were analysed for bacteraemia with anaerobic culturing and nested PCR, using universal bacterial primers that target the 16S-rRNA gene of most bacteria, subsequently re-amplified with specific primers to Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Eikenella corrodens, Campylobacter rectus and Prevotella intermedia, using a modified phenol-chloroform method for DNA extraction. Presence of specific periodontal pathogens in peripheral blood after treatment was detected in 54.8% of the patients, in 47.6% with anaerobic culturing and in 19% with nested PCR. In 16.6%, the periodontal pathogens were detected before Sc/RP. P. gingivalis and A. actynomicetemcomitans were the pathogens most frequently detected in the bloodstream before and after Sc/RP. Nested PCR demonstrated the presence of DNA from periodontal pathogens in blood samples in severe periodontitis patients before, during and after periodontal therapy. The use of these molecular-based techniques may improve the accuracy from the results obtained by haemoculture.

First Report of Bacterial Wilt Caused by Ralstonia solanacearum on Mesona chinensis in China.

Jellywort (Mesona chinensis Benth) is an herbaceous plant in the Lamiaceae (mint) family. The plant is referred to as 'Xiancao' (weed from angels) in Chinese and primarily used to make grass jelly, a popular refreshing drink. Currently, Xiancao cultivation is a fast-growing industry with a high profit margin in southern China. An estimated 7,000 ha is grown with a value of more than $50 million USD. In June, 2009, a wilting disease of Xiancao was observed in Guangdong and the neighboring Guangxi and Fujian provinces with incidence up to 50% in the severest case. Affected plants initially show withering symptoms on apical leaves during the daytime with recovery at night. As the disease develops, withering leaves spread downward, eventually encompassing the whole plant. Leaves lose vigor but remain green. After 3 to 4 days, wilting becomes irreversible. Roots and basal stem tissues blacken and rot, leading to plant death. Longitudinal sectioning of the basal stem shows browning of vascular tissues with whitish ooze visible when compressed. To investigate the disease etiology, 12 Xiancao plants from three cultivars showing typical wilting symptoms were collected from a production field in Zengcheng City of Guangdong Province in June 2010. A total of 27 bacterial isolates showing large, elevated, and fluidal colonies with a pale red center were isolated from vascular tissue on tripheny tetrazolium chloride medium (3) after incubation at 30° for 2 days. Fifteen 45-day-old Xiancao plants (cv. Zhengcheng 1) were inoculated by injection of 20 μl of bacterial suspension (1 × 108 CFU/ml) into the middle stem. Sterile water was used as a negative control. After 4 to 6 days of incubation in a greenhouse (28 to 30°), all (15 of 15) inoculated plants developed wilting symptoms as described above. The same bacterium was reisolated from inoculated plants. The five negative control plants did not show any wilting symptoms. With the same artificial inoculation procedure, this bacterium also caused similar wilting disease in tobacco, potato, tomato, pepper, and eggplant. An inoculation test with a tomato strain of Ralstonia solanacearum resulted in similar symptoms. On the basis of symptomatology and bacterial culture characteristics, R. solanacearum (formerly Pseudomonas solanacearum) was suspected as the causal agent. For confirmation, the universal bacterial 16S rDNA primer set E8F/E1115R (1) was used to amplify DNA from pure culture. A 1,027-bp DNA sequence was obtained and deposited in GenBank with Accession No. HQ159392. BLAST search against the current version of GenBank database showed 100% similarity with the 16S rDNA sequences of 26 R. solanacearum strains. Furthermore, primer set 759/760 (4) amplified a specific 280-bp fragment. Along with the result from multiplex PCR (2), the bacterium was identified as R. solanacearum Phylotype I. To our knowledge, this is the first report of a disease caused by R. solanacearum on M. chinensis.

Isolation, Molecular and Biochemical Identification of Paraoxon-Metabolizing Pseudomonas Species

Seven soil borne bacterial isolates were collected from locations throughout the Houston metropolitan area. All isolatesproved capable of degrading the pesticide paraoxon to p-nitrophenol in carbon limited media and showed a high degree of tolerance to an environment exposed to increasing concentrations of the pesticide. A combination of 16S rRNA sequencing and fatty acid methyl ester analysis (FAME) analysis was used to identify the unknown bacterial species. Universal bacterial primers were used for 16S rRNA analysis to tentatively identify all seven isolates as species belonging to the genus Pseudomonas. Sequencing results coupled with FAME analysis resolved the species identity of the seven isolates as either Pseudomonas aeruginosa or Pseudomonas putida. The results of this study demonstrate that a combination of molecular and biochemical analysis provide sufficient resolution to identify paraoxon degrading microbial populations.

A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments

A major obstacle in the culture-independent estimation of the abundance of bacteria associated with plants is contamination with plant organelles, which precludes the use of universal rRNA bacterial primers in quantitative PCR applications. We present here a PCR-based method that allows a priori determination of the degree of chloroplast and mitochondrial contamination in DNA samples from plant environments. It is based on differential digestibility of chloroplast, mitochondrial and bacterial small subunit rRNA gene amplicons with the restriction enzymes AfeI and BbvCI. Using this method, we demonstrated for field-grown lettuce plants that even a gentle washing protocol, designed to recover the microbial community and its metagenome from the leaf surface, resulted in substantial contamination with chloroplast DNA. This finding cautions against the use of universal primer pairs that do not exclude chloroplast DNA from amplification, because they risk overestimation of bacterial population sizes. In contrast, contamination with mitochondrial 18S rRNA was minor in the lettuce phyllosphere. These findings were confirmed by real-time PCR using primer sets specific for small subunit rRNA genes from bacteria, chloroplasts, and mitochondria. Based on these results, we propose two primer pairs (534f/783r and mito1345f/mito1430r) which between them offer an indirect means of faithfully estimating bacterial abundances on plants, by deduction of the mito1345f/mito1430r-based mitochondrial count from that obtained with 534f/783r, which amplifies both bacterial and mitochondrial DNA but excludes chloroplast. In this manner, we estimated the number of total bacteria on most leaves of field-grown lettuce to be between 10 5 and 10 6 g − 1 of leaf, which was 1–3 orders of magnitudes higher than the number of colony-forming units that were retrieved from the same leaf surfaces on agar plates.

Molecular characterization of the cloacal microbiota of wild and captive parrots

The gastrointestinal microbiota plays a fundamental role in health and disease. Only limited data are available about the composition of the intestinal microbiota of captive animals compared to those of wild animals. The aim of the present study was to characterize the cloacal microbiota of apparently healthy wild and captive parrots. A total of 16 parrots, 8 wild and 8 captive, belonging to 3 different species, were used in this study. Cloacal material was collected via cloacal swabbing. DNA was extracted and 16S rRNA genes were amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. A total of 518 clones were analyzed, and 49 operational taxonomic units (OTUs) were identified. The OTUs were classified in 4 bacterial phyla: Firmicutes (72.9%), Proteobacteria (14.9%), Actinobateria (12%), and Bacteroidetes (0.2%). Bacterial diversity was significantly lower in wild birds than in captive birds. Principal component analysis based on the Unifrac distance metric indicated that the cloacal microbiota differed between wild and captive parrots. Staphylococcus saprophyticus was significantly more abundant in wild birds, while Escherichia coli was significantly more abundant in captive birds. In conclusion, wild and captive parrots appear to have differences in the composition of their cloacal bacterial microbiota. The clinical significance of these differences remains to be determined.

Intestinal Microbiome in Transporter Null Mouse Models

A growing interest exists in the interrelation between host organism and bacteria colonization as exemplified by the NIH Human Microbiome Project. This study sought to determine the effect of altered intestinal ion transport on the luminal micobiome in mice. Ammonia is both used and produced by gastrointestinal bacteria. Changes in ammonia have been associated with shifts in bacteria species in vitro. Thus changes in transport function likely influence bacterial location and quantity. NKCC1 and cH/K‐ATPase are both implicated in epithelial cell ammonia transport. Universal, family specific, and species specific bacterial primers based on 16S ribosomal DNA were used with real time PCR to quantify bacterial populations from luminal flushes of mouse terminal ileum, ceacum, proximal and distal colon. Flushes from NKCC1−/− and cH/K‐ATPase−/− mice showed no change in total bacteria present when compared to wild type littermates. Using family specific primers, Bacteroides and Firmicutes family members were also unchanged. Interestingly however, Bifidobacterium, a probiotic bacteria, was decreased in both ileum and ceacum of null mice, yet unchanged in colon. These data suggests that long term differences in intestinal ion transport can result in a decrease of “good” bacterial species which may increase the susceptibility of the host to intestinal dysfunction. Supported by NIH DK079979.

Microbial community of the chemocline of the meromictic Lake Shunet (Khakassia, Russia) during summer stratification

The spatio-temporal organization of the bacterial community inhabiting the chemocline of the stratified meromictic Lake Shunet (Khakassia, Russia) was investigated from May to September 2005 by means of microscopy, analysis of photosynthetic pigments, and PCR-DGGE with subsequent 16S rDNA analysis. The samples were collected with a multisyringe stratification sampler, sampling being performed every 5 cm. It was demonstrated that, during the period of investigation, there were no large changes in the bacterial community of the chlemocline, at least among the detected forms. During the whole period of study, purple sulfur bacteria related to Lamprocystis purpurea (Chromatiaceae) were predominant in the chemocline. Beneath the layer of purple bacteria, green sulfur bacteria were revealed that were phylogenetically distant from strain ShNPel02, which was previously isolated from this lake. Development of phytoflagellates of the genus Cryptomonas was observed in the upper zone of the chemocline. In the chemocline of Lake Shunet, the numbers of picoplankton cyanobacteria of the genus Synechococcus increased from May to September. It was demonstrated that the application of universal bacterial primers for DGGE resulted in the same qualitative distributional pattern of predominant species as microscopic studies.

Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus)

The aim of this study was to describe the microbial communities in the distal gut of wild wolves (Canis lupus). Fecal samples were collected from three healthy unrelated adult wolves captured at the nearby of Dalai Lake Nature Reserve in Inner Mongolia of China. The diversity of fecal bacteria was investigated by constructing PCR-amplified 16S rRNA gene clone libraries using the universal bacterial primers 27 F and 1493 R. A total of 307 non-chimeric near-full-length 16S rRNA gene sequences were analyzed and 65 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified. Seventeen OTUs (26%) showed less than 98% sequence similarity to 16S rRNA gene sequences were reported previously. Five different bacterial phyla were identified, with the majority of OTUs being classified within the phylum Firmicutes (60%), followed by Bacteroidetes (16.9%), Proteobacteria (9.2%), Fusobacteria (9.2%) and Actinobacteria (4.6%). The majority of clones fell within the order Clostridiales (53.8% of OTUs). It was predominantly affiliated with five families: Lachnospiraceae was the most diverse bacterial family in this order, followed by Ruminococcaceae, Clostridiaceae, Peptococcaceae and Peptostreptococcaceae.

Detection of indigenous endophytic bacteria in Eucalyptus urophylla in vitro conditions

The presence of indigenous endophytic bacteria in aseptically grown seedlings of Eucalyptus urophylla germinated from surface sterilized seeds was investigated using dilution plating, microscopy, and PCR detection. No culturable endophytic bacteria could be detected in suspensions of ground plant tissue incubated on solid or in liquid cultivation media. However, a large number of endophytic bacterial cells, mostly rod-shaped and measured 2–3 μm×0.5–0.8 μm, were observed in in vitro cultured seedlings of E. urophylla using both light and electron microscopy. Using the universal bacterial 16S rDNA primers, a predicted 190-bp fragment was amplified from total DNA isolated from the seedlings of E. urophylla. We concluded that the endophytic bacteria originated from the seed were present in seedlings of E. urophylla. However, the bacterial cells observed appeared to be nonculturable.

Characterization of fecal microbiota in cats using universal 16S rRNA gene and group-specific primers for Lactobacillus and Bifidobacterium spp.

The diversity of the feline intestinal microbiota has not been well elucidated. The aim of this study was to characterize fecal microbiota of cats by comparative sequence analysis with universal bacterial 16S rRNA gene and group-specific primers for Bifidobacterium and Lactobacillus spp. Using universal bacterial primers, a total of 133 non-redundant 16S rRNA gene sequences were identified in fecal samples obtained from 15 healthy pet cats. The majority of these sequences were assigned to the phylum Firmicutes, followed by Proteobacteria and Bacteroidetes. Further classification showed that Firmicutes were predominantly affiliated with Clostridium clusters XI, XIVa, and I. Using group-specific primers for Bifidobacterium and Lactobacillus spp., 364 clones were analyzed in fecal samples obtained from 12 additional cats and these bacterial genera were observed in 100% and 92% of cats, respectively. These detection rates differed from those obtained using universal bacterial primers, where Bifidobacterium and Lactobacillus spp. were each detected in 2 cats (13.3%). Overall, 23 different Lactobacillus-like and 11 Bifidobacterium-like sequences were identified. We observed marked differences in the prevalence of the various lactic acid bacteria in individual cats. In conclusion, the use of a combination of universal and group-specific primers allows a more detailed characterization of lactic acid bacteria in the feline intestine. While Bifidobacterium and Lactobacillus spp. are prevalent in feline fecal samples, individual animals show a unique species distribution.

Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing.

The preferential detection of cells with intact membranes by sample treatment with propidium monoazide (PMA) in combination with PCR amplification is gaining in popularity. This study evaluates the effect of PMA on 454 pyrosequencing profiles of environmental water samples from a canal in Amsterdam and seawater (with sediment) left untreated or exposed to elevated temperatures (50, 60, or 85 °C) for 10 min. Community analysis was based on the extraction of genomic DNA followed by PCR amplification of 16S rRNA genes using universal bacterial primers. Whereas the highest temperature in combination with PMA treatment completely suppressed PCR amplification, PCR products from the other samples were subjected to massively parallel tag sequencing. PMA treatment did not substantially affect the sequence profiles of non-heated samples, but heat exposure resulted in a clear difference in the relative proportions of certain groups. This difference was significantly more pronounced in heated seawater than in heated canal water. The effect of the chosen experimental conditions on the membrane integrity of cells was supported by BacLight LIVE/DEAD staining in combination with flow cytometry, which confirmed an increase in the uptake of propidium iodide in samples exposed to high temperatures.

Molecular Analysis of the Microbial Communities of Mars Analog Lakes in Western Australia

Unique, shallow interdune lakes and groundwaters with extremely low pH and high salinity exist in Australia, along with nearby lakes that possess higher pH values. These acidic hypersaline environments are possibly the best modern terrestrial analogues for past martian environments. However, no previous microbiological analyses of these lakes have been conducted. During the Australian winter of 2005, water samples were taken from several hypersaline lakes located in southern Western Australia that possessed acidic to slightly alkaline pH. These samples were subjected to molecular analysis to identify bacterial communities. DNA extraction and polymerase chain reaction (PCR) amplification of the 16S rRNA gene sequences, by using universal bacterial primers, were also performed on the samples. Extracted DNA was amplified with 1070 forward and 1392 GC-clamped reverse primers and analyzed by using denaturant gradient gel electrophoresis (DGGE). In addition, libraries were developed from DNA retrieved from four lakes, including a marginal marine neutral lake, an inland neutral lake, and two inland acid lakes, and selected clones with distinct operational taxonomic units were sequenced. The DGGE profiles and clone sequence data indicate that there are distinct, abundant, and diverse microbial populations in these Australian hypersaline environments, especially the acidic ones. These results are significant for two reasons: (1) they provide the first microbiological survey of natural acid saline lakes and (2) they hint at the possibility that there could have been a diverse microbial population in acidic hypersaline environments on Mars.

Identification and Phylogenetic Analysis of Bacterial Isolates from Litopenaeus vannamei Shrimp Culture System and Gut Environment Based on 16SrRNA Gene Sequence Data

Selected bacterial isolates from a Litopenaeus vannamei shrimp culture system and gut environment were assessed using 16S rRNA gene sequencing method to identify their identity and to construct their phylogenetic relationship. In a preliminary study, a total of 19 isolates were selected as probiotics. These isolates were prepared using freeze and heat-shock method to obtain the DNA template. PCR amplification of 16S ribosomal RNA gene of isolates was carried out using bacterial universal primers 9F and 1510R and was sequenced using an automated DNA sequencer. These gene sequences were compared with other gene sequences in the GenBank database (NCBI) using a BLAST search to find closely related sequences. Alignment of these sequences with sequences available from GenBank database was carried out to construct a phylogenetic tree for these bacteria. Most of the isolates obtained, i.e. 17 out of the 19 isolates, belonged to different species of Bacillus, sharing 95 to 99% 16S ribosomal RNA identity with the respective type-strain, whereas the remaining 2 isolates belonged to Micrococcus sp. and Micrococcus luteus, with 97 to 99% 16S rRNA homology, consecutively. Key words: Bacillus, Micrococcus, PCR amplification of 16S rRNA gene, phylogeny

Isolation, molecular and biochemical characterization of oil degrading bacteria from contaminated soil at an oil refinery

Biodegradation using microorganisms is considered to be cost-effective and environmentally friendly treatment of oil-contaminated sites. Oil-biodegrading bacterial strains were isolated, identified and characterized from oil contaminated soil samples at oil refinery in Zarqa (Jordan). Thirty four bacterial isolates were grown on mineral salt media supplemented with crude oil, but 16 showed positive biodegradation of diesel. All the 34 bacterial isolates were characterized at the molecular and bio-chemical levels, and showed positive polymerase chain reaction (PCR) amplification product size of 1500 bp when 16s rDNA bacterial universal primers were used. Eighteen bacterial isolates showed positive PCR amplification product size of 150 bp specific for the genus Pseudomonas and 3 bacterial isolates showed positive amplification product size of 1500 bp specific for the genus Acinetobacter. Biochemical and physiological characterization performed on the 34 bacterial isolates, revealed the presence of oil biodegrading bacterial genera and species of Pseudomonas Acidovorans, P. aerugi-nosa, P. alcaligenes, P. fluorescens, P. cepacia, P. mallei, P. maltophilia, P. oleovorans, P. putida, P. stutzeri P. vesicularis, Acinetobacter calcoaceticus, Ac. lowffii, Micro-ococcus luteus , M. varians, M. lylae, M. roseus, Alcaligenes denitrificians, Bacillus megaterium, Comamonas sp., Moraxella sp., Bordetella sp., P. putida, P. stutzeri and P. mallei.

Low‐temperature (9°C) AMD treatment in a sulfidogenic bioreactor dominated by a mesophilic Desulfomicrobium species

The possibilities for the treatment of low-temperature mine waste waters have not been widely studied. The amenability of low-temperature sulfate reduction for mine waste water treatment at 9 degrees C was studied in a bench-scale fluidized-bed bioreactor (FBR). Formate was used as the electron and carbon source. The first influent for the FBR was acidic, synthetic waste water containing iron, nutrients, and sulfate, followed by diluted barren bioleaching solution (DBBS). The average sulfate reduction rates were 8 mmol L(-1) day(-1) and 6 mmol L(-1) day(-1) with synthetic waste water and DBBS, respectively. The corresponding specific activities were 2.4 and 1.6 mmol SO(4)(2-) g VSS(-1) day(-1), respectively. The composition of the microbial community and the active species of the FBR was analyzed by extracting the DNA and RNA, followed by PCR-DGGE with the universal bacterial 16S rRNA gene primers and dsrB-primers specific for sulfate-reducing bacteria. The FBR microbial community was simple and stable and the dominant and active species belonged to the genus Desulfomicrobium. In summary, long-term operation of a low-temperature bioreactor resulted in enrichment of formate-utilizing, psychrotolerant mesophilic sulfate reducing bacteria.

Molecular Analysis of Persistent Periradicular Lesions and Root Ends Reveals a Diverse Microbial Profile

Introduction The microbial etiology of periradicular lesions is recognized; however, the bacterial profile of these lesions is not well elucidated. The purpose of this study was to determine the frequency of bacterial colonization in these lesions and to characterize the bacterial community present in root ends and periradicular lesions. Methods Thirty-four adult patients who presented for apicoectomy of persistent periradicular lesions after endodontic therapy were selected for the study and samples of periradicular tissue and resected root ends collected. Total bacterial levels were estimated for 34 paired periradicular lesions and root ends using real-time polymerase chain reaction with universal bacterial primers. Sixteen pairs of these samples were analyzed using ribosomal 16S cloning and sequencing for bacterial identification. Results Bacteria were detected more consistently and at higher levels in root ends. Periradicular lesions exhibited a diverse microbial profile with many uncultivated phylotypes. Enterococcus faecalis and Burkholderia cepacia predominated in both samples. Campylobacter gracilis and Streptococcus gordonii were associated with root ends, whereas Atopobium rimae, Peptostreptococcus micros, Streptococcus genomospecies C8, Dialister sp E2_20 E1, and Eubacterium strain A35MT were associated with periradicular lesions. Conclusions Persistent periradicular lesions are polymicrobial infections with many as-yet-uncultivated and unknown bacterial species. The bacterial load and microbial profile of root ends is significantly different from the soft-tissue lesion, indicating the presence of diverse bacterial populations in these tissues.

Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array

Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S-23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7%, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.

16S rRNA gene phylogenesis of culturable predominant bacteria from diseased Apostichopus japonicus (Holothuroidea, Echinodermata)

Cultured Apostichopus japonicus in China suffers from a kind of skin ulceration disease that has caused severe economic loss in recent years. The disease, pathogens of which are supposed to be bacteria by most researchers, is highly infectious and can often cause all individuals in the same culture pool to die in a very short time. The 16S rRNA gene phylogenesis of the culturable bacteria from the lesions of diseased individuals was conducted to study the biodiversity of the bacterial communities in the lesions and to identify probable pathogen(s) associated with this kind of disease. S. japonica samples were selected from a hatchery located in the eastern part of Qingdao, China. Bacterial universal primers GM5F and DS907R were used to amplify the 16S rRNA gene of bacteria colonies, and touchdown PCR was performed to amplify the target sequences. The results suggest that γ- proteobacteria (Alteromonadales and Vibrionales) of CFB group, many strains of which have been also determined as pathogens in other marine species, are the predominant bacterial genera of the diseased Apostichopus japonicus individuals.

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

Infectious agents and lymphoma development: molecular and clinical aspects

This review is focused on the role of infectious agents in the development of some lymphoma entities. Associations involving bacterial infections mostly regard marginal zone B-cell lymphomas of mucosa-associated lymphoid tissue (MALT)-type. Some paradigmatic examples of these associations include the Helicobacter pylori-related gastric MALT lymphoma and the more recently reported links between Chlamydophila psittaci and ocular adnexal MALT lymphomas and Borrelia burgdorferi and cutaneous MALT lymphomas. The well-documented association between Epstein-Barr virus infection and related lymphoproliferative disorders are analysed as an example of lymphotropic virus with tumourigenic activity. Molecular, biological and clinical features as well as therapeutic implications of these associations are analysed and future perspectives in this field are discussed.