16S rDNA Gene Sequence Research Articles

Enriquecimiento diferencial de Pseudomonas spp. en el rizoplano de distintas especies cultivadas

In contrast to rhizobia-legume symbiosis, the specificity for root colonization by pseudomonads seems to be less strict. However, several studies about bacterial diversity in the rhizosphere highlight the influence of plant species on the selective enrichment of certain microorganisms from the bulk soil community. In order to evaluate the effect that different crops have on the structure of pseudomonad community on the root surface, we performed plant trap experiments, using surface-disinfected maize, wheat or soybean seeds that were sown in pots containing the same pristine soil as substrate. Rhizoplane suspensions were plated on a selective medium for Pseudomonas, and pooled colonies served as DNA source to carry out PCR-RFLP community structure analysis of the pseudomonads-specific marker genes oprF and gacA. PCR-RFLP profiles were grouped by plant species, and were distinguished from those of bulk soil samples. Partial sequencing of 16S rDNA genes of some representative colonies of Pseudomonas confirmed the selective enrichment of distinctive genotypes in the rhizoplane of each plant species. These results support the idea that the root systems of agricultural crops such as soybean, maize and wheat, select differential sets of pseudomonads from the native microbial repertoire inhabiting the bulk soil.

Phylogenetic Analysis of Wolbachia from Folsomia Candida (Collembola: Isotomidae) via Sequences from WspB and Ribosomal Protein Genes

Folsomia candida (Collembola: Isotomidae), a springtail that occurs commonly in soils throughout the world, is widely used in soil pollution and ecotoxicological studies. F. candida typically reproduces by parthenogenesis, which is widely believed to result from Wolbachia infection. Wolbachia is a cytoplasmically transmitted alpha‐proteobacterium that induces diverse reproductive alterations in its invertebrate hosts. Wolbachia is currently divided into six supergroups (A to F). Wolbachia from F. candida (wCan) is defined as a member of supergroup E based on sequences of 16S rDNA and ftsZ genes. Unexpectedly, however, no additional gene sequences have been described since wCan was first discovered in 1999. We have observed that recovery of undegraded DNA from springtails can be difficult. The objective of this study is to obtain additional gene sequences for wCan phylogenetic studies. We optimized recovery of DNA by lysing springtail eggs in the presence of 20mM EDTA, followed by extraction of undegraded DNA from agarose gels after electrophesis. Characterization of a nuclease that co‐purifies with springtail DNA is in progress. We used purified genomic DNA as template to amplify Wolbachia surface protein B (wspB) gene and five ribosomal protein genes by polymerase chain reaction (PCR). A concatenated phylogenetic tree based on these six gene sequences from wCan, together with corresponding sequences from nine additional Wolbachia strains, shows a closer relationship with supergroup B relative to supergroup A. Our study expands the DNA sequencing information of wCan and sheds light on its phylogeny.

Biological control of Botrytis cinerea and plant growth promotion potential by Penicillium citrinum in chickpea (Cicer arietinum L.)

A total of 48 fungi were characterised for their antagonistic potential against Botrytis cinerea causing Botrytis Gray Mold (BGM) disease in chickpea by dual culture and metabolite production assays. The culture filtrate of the most promising isolate, VFI-51, was purified by various chromatographic techniques and identified as ‘citrinin’ by nuclear magnetic resonance and mass spectrometry studies. The efficacy of citrinin was demonstrated to control BGM in chickpea under greenhouse conditions. The sequences of 18S rDNA gene of the VFI-51 matched with Penicillium citrinum in BLAST analysis. The VFI-51 produced siderophore, hydrocyanic acid, indole-3-acetic acid, lipase, protease and β-1,3-glucanase; grew well in NaCl (up to 15%), at pH between 7 and 11 and temperatures between 20°C and 40°C; and was compatible with fungicides bavistin and thiram. Under greenhouse and field conditions, VFI-51 significantly enhanced the nodule number, nodule weight, root and shoot weight and stover and grain yield over the un-inoculated control. In the rhizosphere, VFI-51 also significantly enhanced total N, available P and OC over the un-inoculated control. Scanning electron microscopy analysis revealed that VFI-51 colonised on the roots of chickpea. This study concluded that VFI-51 has the potential for biocontrol of BGM and plant growth promotion in chickpea.

Description of two new species of Indo-Pacific Thylacoplethus and a new record of Thompsonia japonica (Rhizocephala: Akentrogonida: Thompsoniidae) from hermit, porcelain, and mud crabs (Decapoda) based on morphological and molecular data

Rhizocephalans of the order Akentrogonida are parasitic barnacles that infest decapods, stomatopods, peracarids, and other cirripedes. Within this order, Thompsoniidae is found in decapods and stomatopods, and is a family comprised of species characterized by having multiple globular reproductive bodies (externae) erupting from the host’s extremities and abdominal surface, and connected internally by a root-like system. Two of the four genera currently accepted within Thompsoniidae, Thompsonia and Thylacoplethus, contain perhaps the most morphologically derived species within Akentrogonida. Herein we describe two new species of Thylacoplethus, T. porcellanus and T. umanguvatus, from the porcellanid and hermit crabs Petrolisthes scabriculus (Dana, 1852) and Calcinus morgani Rahayu and Forest, 1999, respectively. We also redescribe Thompsonia japonica Hafele, 1911 from a xanthid brachyuran crab based on morphological characters and DNA sequences of the nuclear 18S rDNA gene. The new species from the porcellanid crab comprises the first record of an akentrogonid rhizocephalan parasitizing a species of Porcellanidae. We reconstruct a molecular phylogeny of Akentrogonida using new and published DNA sequences, and we discuss our findings within an evolutionary context of host speciation. All species in the four thompsoniid genera are briefly reviewed, and a replacement name is proposed for the preoccupied Pottsia Hoeg and Lutzen, 1993.

Potentially novel Ehrlichia species in horses, Nicaragua.

Ehrlichia sp. DNA was amplified from 4 Ehrlichia-seroreactive horses from Mérida, Nicaragua. Sequencing of 16S rDNA, sodB, and groEL genes indicated that the bacterium is most likely a novel Ehrlichia species. The tick vector and the potential for canine and human infection remain unknown.

Microbial contamination in the indoor environment of tanneries in Leon, Mexico

Manufacturing environment in tanning industry has been associated with human diseases caused by biological agents. This paper reports the microbiological contamination of the indoor environment at a group of tanneries in León, Guanajuato, México. The microorganisms present in the indoor environment of the tannery industry has been quantified and identified. The bacteria and fungi concentration in almost all cases exceeded the acceptable levels as dictated by Swedish standard and the limit values proposed by the American Industrial Hygiene Association. The indoor/outdoor ratio was determined, revealing poor air quality at the studied sites. This study has illustrated the presence of pathogens, hazardous to humans in indoor environments of tanneries. The identified bacteria by sequencing of 16S rDNA gene, belonged to families: Bacillaceae, Corynebacteriaceae, Enterobacteriaceae, Moraxellaceae, Nocardiopsaceae, Pseudomonadaceae, Staphylococcaceae. Some of which can be categorized as pathogens such as Acinetobacter calcoaceticus, Acinetobacter johnsonii, Nocardiopsis dassonvillei, Pantoea agglomerans, Pseudomonas putida and Staphylococcus gallinarum. In addition, Fungi genuses identified by microscopy were Aspergillus and Penicillium. The yeasts presumptively identified by ChromAgar medium were Candida krusei and Candida glabrata. Some of these identified microorganisms have been correlated with adverse human health effects, especially in individuals with immunocompromised system.

Identification and Characterization of Lactic Acid Bacteria Involved in Natural and Lactic Acid Bacterial Fermentations of Pastes of Soybeans and Soybean-Maize Blends Using Culture-Dependent Techniques and Denaturing Gradient Gel Electrophoresis

Pastes of soybeans and soybean-maize blends were fermented with inoculum through back-slopping using lactic acid bacteria (LAB) fermented cereal gruel, thobwa and without inoculum (naturally). LAB involved in the fermentations were characterized using culture-dependent and culture-independent analyses. Decreases in pH from 6.4 to 3.9–4.2 and from 6.9 to 5.4–5.8 after 72 h were observed in LAB fermented pastes (LFP) and in naturally fermented pastes (NFP), respectively. LAB increased from 5.0 to 8.7–9.6 log10 cfu/g in NFP and from 8.1 to 9.3 log10 cfu/g in LFP. LAB in both fermentations were heterofermentative lactobacilli (82.4%) and homofermentative cocci (17.6%), of which 44.7% and 42.9% were exopolysaccharide producers, respectively. Principal component analysis based on carbohydrate fermentation, CO2 production and arginine hydrolysis showed four clusters dominated by Lactobacillus fermentum, Weissella confusa, Lactobacillus brevis 1 and Pediococcus pentosaceus, respectively. Sequencing of 16S rDNA gene confirmed Lb. fermentum, W. confusa/W. cibaria, and P. pentosaceus as identities of species in three clusters. Denaturing gradient gel electrophoresis (DGGE) confirmed these species as the dominant microbiota. DGGE showed higher similarity in microbial profiles of LFP throughout fermentation and low similarity in NFP during early and late stages of fermentation.

Actinobacteria occurrence and their metabolic characteristics in the nickel-contaminated soil sample

AbstractHeavy metals are a significant source of pollution in soils that have been demonstrated to exert significant toxic effect on soil microbial assemblages. Here we investigate the occurrence and metabolic characteristics of actinobacteria, which form a predominated component of farmland bacterial community near the town of Sereď in southwest Slovakia, contaminated by close nickel ore facility. Actinobacteria occurred in this environment with high concentrations of nickel (2.109 mg/kg), slightly above the natural occurrence of cobalt (355 mg/kg) and zinc (177 mg/kg), even too low concentration of iron (35.75 mg/kg) for a normal soil and not a toxic amount of copper (32.2 mg/kg) and cadmium (<0.25 mg/kg). The phylogeny was reconstructed using partial sequences of 16S rDNA genes of both, actinobacterial isolates and clones. A total of 105 actinobacterial representatives were divided into 66 species belonging to one order, 7 genera and 5 uncategorized groups. The selected 14 morphologically distinct isolates were able to produce drop collapsing, haemolytic and lipase activities. Whereas only 4 isolates produced dark brown melanin pigment and only 5 of them produced decolourization of the azo dye, all isolates tested were capable of assimilating all 11 sugars tested. All these actinobacterial isolates were resistant to nickel, cobalt, zinc, cadmium, copper, but the level of resistance differed between the individual isolates, and the resistance profiles of antibiotics (gentamycin, ampicillin, ciprofloxacin, chloramphenicol, erythromycin, rifampicin, penicillin-G) varied among them to a certain extent. Our results suggested that actinobacteria in soil contaminated by nickel present a relatively divergent group inside of microbial assemblage.

Plant growth-promoting traits of Pseudomonas geniculata isolated from chickpea nodules.

A bacterium, isolated from nodules of chickpea grown in alluvial soils of Haryana state of India, designated as IC-76 was characterized for in vitro plant growth-promoting (PGP) properties and further evaluated under greenhouse, on-station and on-farm field conditions for PGP activity in chickpea. The isolate IC-76 produced indole acetic acid, siderophore, hydrocyanic acid, cellulase, protease, and β-1,3-glucanase. When the bacterium was evaluated individually for their PGP potential in the greenhouse on chickpea and in combination with five Streptomyces sp. (strains CAI-24, CAI-121, CAI-127, KAI-32, and KAI-90; demonstrated earlier as biocontrol potential against Fusarium wilt disease in chickpea), the traits, including nodule number and weight, shoot, and root weight, pod number and weight, seed number and weight, available phosphorus and % organic carbon were found significantly, enhanced over un-inoculated control. In the on-station and on-farm field conditions, IC-76 significantly enhanced nodule number and weight, shoot, and root weight, stover and grain yield and total dry matter. In the rhizosphere (0–15 cm soil), the bacterium also significantly enhanced the total nitrogen, available phosphorus and % organic carbon. The sequence of 16S rDNA gene of the IC-76 was matched with Pseudomonas geniculata in BLAST analysis. This study demonstrates that IC-76 has the potential for PGP in chickpea.

Carbapenem resistance in a human clinical isolate identified to be closely related to Acinetobacter indicus

Here we report a case of carbapenem resistance in a human clinical isolate that was found to be closely related to the newly described environmental species Acinetobacter indicus. This strain harboured the blaOXA-23 carbapenemase gene located on a conjugative plasmid. Partial sequencing of 16S rDNA and rpoB genes, together with matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) analysis, showed that this strain was distantly related to the Acinetobacter baumannii–calcoaceticus complex and was closely related to A. indicus.

The isolation of Balamuthia mandrillaris from environmental sources from Peru

Balamuthia mandrillaris is an opportunistic free-living amoeba that has been reported to cause skin lesions and the fatal Balamuthia amoebic encephalitis (BAE) in humans and other animals. Currently, around 200 human BAE cases have been reported worldwide, although this number is considered to be underestimated. The highest number of BAE cases has been reported in the American continent, mainly in the southwest of the USA. Peru seems to be another hotspot for BAE with around 55 human cases having been identified, usually involving cutaneous infection, especially lesions in the central face area. The isolation of Balamuthia from environmental sources has been reported on only three prior occasions, twice from Californian soils and once from dust in Iran and so it seems that this amoeba is relatively rarely encountered in samples from the environment. We investigated that possibility of finding the amoebae in soil samples from different regions where clinical cases have been reported in Peru. Twenty-one samples were cultured in non-nutrient agar plates and were checked for the presence of B. mandrillaris-like trophozoites and/or cysts. Those samples that were positive for these amoebae by microscopic criteria were then confirmed by PCR amplification and DNA sequencing of the mitochondrial 16S rDNA gene of B. mandrillaris. We have detected the presence of B. mandrillaris in four samples collected in the regions of Piura (3) and Lima (1) where infection cases have been previously reported. We hypothesize that B. mandrillaris is present in Peru in soil and dust which therefore constitutes a source of the infection for the BAE cases previously reported in this country. Further studies should be carried out in the area to confirm the generality of this finding.

Construction of a DNA database for ticks collected in Japan: application of molecular identification based on the mitochondrial 16S rDNA gene

Tick identification is important in control of tick-born diseases because tick-borne pathogens are often transmitted by specific tick species. In this study, we determined partial DNA sequences of the mitochondrial 16S rDNA gene (mt-rrs ) for ticks including 7 genera and 39 species, and these ticks were allocated to 113 sequence types. Of the 39 species of ticks, 36 species (92.3%) were distinguishable by phylogenetic analysis of mt-rrs . This result suggests that species identification of ticks based on mt-rrs is a viable alternative to morphological identification. In order to establish a DNA database for identification of ixodid and argasid ticks in Japan, we deposited all sequence data in GenBank (from AB819156 to AB819268).

Evaluation of Streptomyces strains isolated from herbal vermicompost for their plant growth-promotion traits in rice

Six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140, CAI-155 and KAI-180, isolated from six different herbal vermi-composts were characterized for in vitro plant growth-promoting (PGP) properties and further evaluated in the field for PGP activity in rice. Of the six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140 and CAI-155 produced siderophores; CAI-13, CAI-93, CAI-155 and KAI-180 produced chitinase; CAI-13, CAI-140, CAI-155 and KAI-180 produced lipase; CAI-13, CAI-93, CAI-155 and KAI-180 produced protease; and CAI-13, CAI-85, CAI-140 and CAI-155 produced ß-1-3-glucanase whereas all the six actinomycetes produced cellulase, hydrocyanic acid and indole acetic acid (IAA). The actinomycetes were able to grow in NaCl concentrations of up to 8%, at pH values between 7 and 11, temperatures between 20 and 40°C and compatible with fungicide bavistin at field application levels. In the rice field, the actinomycetes significantly enhanced tiller numbers, panicle numbers, filled grain numbers and weight, stover yield, grain yield, total dry matter, root length, volume and dry weight over the un-inoculated control. In the rhizosphere, the actinomycetes also significantly enhanced total nitrogen, available phosphorous, % organic carbon, microbial biomass carbon and nitrogen and dehydrogenase activity over the un-inoculated control. Sequences of 16S rDNA gene of the actinomycetes matched with different Streptomyces species in BLAST analysis. Of the six actinomycetes, CAI-85 and CAI-93 were found superior over other actinomycetes in terms of PGP properties, root development and crop productivity. qRT-PCR analysis on selected plant growth promoting genes of actinomycetes revealed the up-regulation of IAA genes only in CAI-85 and CAI-93.

Occurrence, characterization and antimicrobial susceptibility of Vibrio alginolyticus in the Eastern Adriatic Sea

In 2007–2008, 162 samples (72 marine water samples, 90 swabs from the gills and skin) were collected from three European seabass fish farms in Eastern Adriatic. The aim of study was to determine the occurrence of Vibrio, to identify the isolated strains and to investigate their antimicrobial resistance. The comparison of the results obtained in spring and autumn periods indicated a higher Vibrio concentration in spring samplings. The greatest prevalence of Vibrio alginolyticus was on gills than on skin, whereas statistically significant differences were obtained between sampling periods with maximal prevalence in spring. Vibrio isolates from the marine water and from swabs of European seabass were analysed by DNA sequencing of partial 16S rDNA and gyrB genes and identified as V. alginolyticus. Isolates were highly susceptible to flumequine, chloramphenicol and oxytetracycline.

Rapid molecular diagnosis of the stored-product psocid Liposcelis corrodens (Psocodea: Liposcelididae): Species-specific PCR primers of 16S rDNA and COI

Psocids of the genus Liposcelis (Psocodea: Liposcelididae) are common economically important pests in storage facilities all over the world. Stored-product psocids have small bodies and are difficult to identify to species using external morphological characteristics. Quick and accurate identification methods for psocid species serve as the foundation for pest management, quality control of food products, and settling of legal disputes from quarantine inspection. Liposcelis corrodens (Heymons) is a common stored-product pest distributed in European, American, and Oceania countries but has not been reported as established in China. To facilitate pest management and quarantine inspection to prevent importation and establishment of L. corrodens in China, methods for accurate and rapid identification need to be developed. Based on the sequencing and alignment of mitochondrial 16S rDNA and COI gene of 10 common Liposcelis species, two pairs of species-specific primers were designed according to the variation regions among species. PCR cycling parameters were developed for the amplification of specific fragments of 16S rDNA and COI genes of L. corrodens with lengths of 261 bp and 243 bp, respectively. Both primer sets have high sensitivity in target species detection and successfully identified psocids found by quarantine personnel in China as L. corrodens. The diagnostic method we have developed is reliable for identification of L. corrodens for quarantine and pest management purposes.

Mitochondrial DNA analysis of Rhipicephalus sanguineus sensu lato (Acari: Ixodidae) in the Southern Cone of South America

A genetic analysis of partial sequences of the mitochondrial 16S and 12S rDNA genes of Rhipicephalus sanguineus sensu lato collected in the Southern Cone of South America was carried out. Also, sequences of ticks belonging to this taxon from Europe, Africa and other South American localities were included. TCS networks constructed with 16S rDNA sequences showed two clusters of haplotypes, namely, Southern lineage (ST) and Northern lineage (NT). Haplotypes representing the specimens coming from localities of Argentina, Uruguay and Chile were included in the ST lineage, while haplotypes from Brazil, Paraguay, Colombia, South Africa, Mozambique and from two localities of Northern Argentina were grouped in the NT lineage. The phylogenetic trees obtained with both 16S and 12S sequences showed two distinct clades, one containing R. sanguineus s.l from Argentina, Uruguay, Chile (ST lineage) and Western Europe (Italy and France), and a second clade including R. sanguineus s.l from Argentina, Paraguay, Brazil, Colombia (NT lineage), South Africa and Mozambique. The results herein reported revealed that the taxon R. sanguineus s.l is represented by two lineages in the Southern Cone of South America. According with the genetic comparative analysis, NT lineage and the ticks from Mozambique and South Africa represent a species that is not R. sanguineus s.s, while R. sanguineus s.l ticks from Western Europe and Southern South America (ST lineage) probably represent true R. sanguineus, because the type locality of R. sanguineus s.s is located in France. The taxonomic issue described for R. sanguineus s.l in the South America has epidemiological implications. Difference in the vectorial competence for Ehrlichia canis between the two lineages of R. sanguineus s.l was found in previous works. Further investigations are needed in order to verify a possible different vectorial competence for the other pathogens transmitted by these ticks.

Morphological study of Ornithodoros viguerasi cooley and kohls, 1941 (Acari: Ixodida: Argasidae), with sequence information from the mitochondrial 16S rDNA gene

A morphological and molecular study of Ornithodoros (Subparmatus) viguerasi (Acari: Argasidae) was carried out. Free-living males and females of this tick species were collected in Calcehtok cavern, Yucatán, Mexico. The morphology of the females of O. viguerasi was identical to the holotype female from Cuba. The only difference was related to size; females from Mexico were bigger than the holotype female. The male of O. viguerasi was described for the first time from the specimens collected in Mexico. The diagnostic characters are a combination of a genital aperture covered by a semicircular flap, a central sclerotized plate posterior to genital aperture, a transverse and thin plate anterior to the genital aperture located at the level of the anterior margin of coxae I, a pair of sclerotized plates bordering coxae II, III and IV, basis capituli rectangular in shape and protrusible, a hypostome roughly blunt at the apex with small denticles (it appears to be functionless), and article I of the palpi with a medial integumental extension which has a long setae on the medial margin. A comparative morphological analysis of the male described in this work with the paratype specimens from Cuba was also conducted; we conclude that the nymphs described in the original description of O. viguerasi correspond to males. Sequences of the mitochondrial 16S rDNA gene of both male and female ticks from Mexico were identical. In a phylogenetic analysis, the monophyly of the subgenus Subparmatus could not be resolved.

Antimicrobial susceptibility of Enterococcus faecalis and a novel Planomicrobium isolate of bacterimia

During nucleotide sequences of 16SrDNA gene, Enterococcus faecalis was predominant in 322 samples; 11 isolates (100%) were from outpatients' vaginal swabs and 3 isolates (75%) from inpatients' blood samples. The three isolates from the blood showed two frame shift mutations Deletion at sequence positions 21 and 1076 bp to be 100% similar with type strain OG1RF. The isolates totally showed no resistance to gentamycin, streptomycin and erythromycin whereas, there was high resistance to amoxicillin/clavulanic acid (71.4%), methicillin and vancomycin (92.8%, for each). All isolates from the blood were completely resistant to penicillin and ampicillin. The study also detected Planomicrobium mcmeekinii from an inpatients' blood case (containing Gene or Point mutation type Transversion at position 358 bp resulting to 99% sequence identity to ATCC 700539) as first reporting and revealing it to be a new subspecies or species. Key words: Enterococcus faecalis, Planomicrobium mcmeekinii, 16SrDNA and sequencing.

The first case of cutaneous infection with Mycobacterium parascrofulaceum.

The authors present the first, to the best of their knowledge, reported case of cutaneous infection caused by Mycobacterium parascrofulaceum. A 42-year-old woman presented with asymptomatic reddish papules, nodules, plaques, and patches on the right side of her face and on her forehead that had persisted for 5 years, with the lesions gradually increasing in size over that time. No previous intervening medical treatment had been applied. No history or evidence of immunosuppression was found. A skin biopsy was performed for routine histological examination. Samples of lesioned skin were inoculated on Löwenstein–Jensen medium to determine the presence of acid-fast bacilli. Ziehl–Neelsen staining was used to confirm the presence of the organism. In vitro drug susceptibility testing was conducted using the microtiter plate method. Mycobacterium was identified by polymerase chain reaction–restriction fragment length polymorphism analysis and sequencing of the hsp65 and 16S rDNA genes. Cultures for aerobic and anaerobic bacteria, as well as fungus, were also conducted. Routine histopathology revealed granulomatous changes without caseation. Ziehl–Neelsen staining showed that the organisms in both the lesions and the cultures were acid-fast bacilli. The cultured colonies were grown in Löwenstein–Jensen medium and incubated at two different temperatures (32°C and 37°C) for 2–3 weeks, developing pigmentation both in the dark and in the light. In vitro drug susceptibility tests showed that the organism was sensitive to clarithromycin and moxifloxacin. Polymerase chain reaction–restriction fragment length polymorphism analysis and sequencing of the hsp65 and 16S rDNA genes confirmed that the isolated organisms were M. parascrofulaceum. Fungal and other standard bacterial cultures were negative. In conclusion, identification and diagnosis of nontuberculous mycobacteria should be performed promptly to obtain better prognoses. Empirical treatments may be feasible, and drug susceptibility tests are important.

Analysis of the salivary microbiome using culture-independent techniques

BackgroundThe salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated.MethodsWe explored the bacterial community composition in the saliva sample using metagenomic whole genome shotgun (WGS) sequencing, the extraction of 16S rRNA gene fragments from metagenomic sequences (16S-WGS) and high-throughput sequencing of PCR-amplified bacterial 16S rDNA gene (16S-HTS) regions V1 and V3.ResultsThe hierarchical clustering of data based on the relative abundance of bacterial genera revealed that distances between 16S-HTS datasets for V1 and V3 regions were greater than those obtained for the same V region with different numbers of PCR cycles. Datasets generated by 16S-HTS and 16S-WGS were even more distant. Finally, comparison of WGS and 16S-based datasets revealed the highest dissimilarity.The analysis of the 16S-HTS, WGS and 16S-WGS datasets revealed 206, 56 and 39 bacterial genera, respectively, 124 of which have not been previously identified in salivary microbiomes. A large fraction of DNA extracted from saliva corresponded to human DNA. Based on sequence similarity search against completely sequenced genomes, bacterial and viral sequences represented 0.73% and 0.0036% of the salivary metagenome, respectively. Several sequence reads were identified as parts of the human herpesvirus 7.ConclusionsAnalysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen.