16S-23S rRNA Intergenic Spacer Region Research Articles

Study of the diversity of 16S-23S rDNA internal transcribed spacer (ITS) typing of Escherichia colistrains isolated from various biotopes in Tunisia.

We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.

Variability in microcystin quotas during a Microcystis bloom in a eutrophic lake.

Microcystis is a bloom-forming genus of cyanobacteria with some genotypes that produce highly toxic microcystin hepatotoxins. In waterbodies where biological and physical factors are relatively homogenous, toxin quotas (the average amount of toxin per cell), at a single point in time, are expected to be relatively constant. In this study we challenged this assumption by investigating the spatial distribution of microcystin quotas at a single point in time on two separate occasions in a lake with a major Microcystis bloom. Microcystis cell concentrations varied widely across the lake on both sampling occasions (730- and 137-fold) together with microcystin quotas (148- and 362-fold). Cell concentrations and microcystin quotas were strongly positively correlated (R2 = 0.89, P < 0.001, n = 28; R2 = 0.67, P < 0.001, n = 25). Analysis of Microcystis strains using high-throughput sequencing of the 16S-23S rRNA intergenic spacer region showed no relationship between microcystin quota and the relative abundance of specific sequences. Collectively, the results of this study indicate an association between microcystin production and cell density that magnifies the potential for bloom toxicity at elevated cell concentrations.

Maize (Zea mays L.): A New Host for Ligustrum witches' Broom Phytoplasma.

In the 2019–2020 growing season, two corn fields located in İmamoğlu town (Adana Province, Turkey) were surveyed following the appearance of phytoplasma-like symptoms on maize plants. A total of 40 samples were collected and tested in first-round and nested PCR using universal primer pairs P1/P7 and R16F2n/R16R2, respectively. All maize-diseased plants reacted positively, whilst no PCR amplifications were obtained from asymptomatic plants. Blast sequence analysis of R16F2n/R16R2-primed amplicons from different maize isolates showed 99.2% to 100% of identity with the 16S rRNA gene of Ligustrum witches’ broom phytoplasma (LiWBP). To gain additional molecular information on the 16S ribosomal RNA and 23S rRNA intergenic spacer region of LiWBP, not identified previously, the P1/P7-primed amplicons were also sequenced and analyzed. The results show that maize isolates from Turkey share 99.6% to 100% of identity among them, whereas the highest identity found (91%) was with members of groups 16SrII and 16SrXXV (peanut and tea witches’ broom groups, respectively). This distant relationship between LiWBP and members of 16SrII and XXV was also confirmed by RFLP and phylogenetic analyses. This is the first finding of LiWBP on maize in nature, where it was found responsible for phyllody disease of corn plants in Turkey. The additional molecular information acquired in this study on the 16S–23S rRNA intergenic spacer region of LiWBP further corroborates its distant relationship to any other phytoplasma groups.

Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Salmonella spp. in Terms of Sensitivity and Applicability

Salmonella spp. are important food-borne pathogens that can cause diseases in humans. Many detection methods have been established in Salmonella spp. using loop-mediated isothermal amplification (LAMP) or reverse transcription loop-mediated isothermal amplification (RT-LAMP). The detection limits of these assays varied from 1 CFU/reaction to 104 CFU/reaction, from 100 fg genomic DNA/reaction to 10 pg genomic DNA/reaction, or from 2.0×101 CFU/mL to 107 CFU/mL for food samples. In this study, LAMP assays were developed using genomic DNA for the detection of Salmonella spp. Two sets of LAMP primers were designed using the invA gene and the 16S-23S rRNA intergenic spacer region (ITS) of S. enterica as the target sequences for two LAMP assays. The detection limits of the two methods were respectively 20 pg S. enterica DNA/reaction and 10 pg S. enterica DNA/reaction at the optimized temperature, and the LAMP methods were of high repeatability and specificity for S. enterica detection. This study provides a baseline for the application of LAMP for the detection of food-borne pathogenic bacteria.

Genomic Insights Into the Mycobacterium kansasii Complex: An Update.

Only very recently, has it been proposed that the hitherto existing Mycobacterium kansasii subtypes (I–VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, a monophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.

Are Cowpea-Nodulating Bradyrhizobial Communities Influenced by Biochar Amendments in Soils? Genetic Diversity and Symbiotic Effectiveness Assessment of Two Agricultural Soils of Brazilian Drylands

The objective of this study was to evaluate the influence of biochar amendment on the bacterial genetic diversity and symbiosis in cowpea-nodulating rhizobial communities in two agricultural soils of Brazilian drylands. Vertisol and Ultisol surface layer soil samples were collected in the Brazilian semiarid region. The soils were mixed with biochar and cowpea seeds (BRS Marataoa) and sown in pots. Forty-five days after plant emergence, the nodule bacteria were isolated. The genetic variability of the nodule bacteria was evaluated by means of restriction fragment length polymorphism of 16S-23S rRNA intergenic spacer region (IGS-RFLP), and those that shared identical IGS-RFLP profiles were fingerprinted by BOX-PCR. By selecting of representative isolates in the genetic clusters, 27 bacteria were identified by 16S-23S IGS sequencing and symbiotically assessed. The IGS-RFLP dendrogram of the 73 isolates had 20 clusters; the multivariate correspondence analysis grouped both Vertisol treatments, and the Ultisol treatments were placed far away in the biplot. Ultisol showed higher bradyrhizobial diversity than the Vertisol. The fingerprinting indicated the presence of only three clonal colonies, showing high intraspecific diversity. The 16S-23S IGS sequences indicated the prevalence of bacteria related to Bradyrhizobium guangxiense in the Vertisol and Bradyrhizobium zhanjiangense in the Ultisol, in addition to the presence of three putative Microvirga spp. in the Ultisol. The symbiotic efficiency of 22 out of 27 bacteria was comparable with that of the inoculant strain Bradyrhizobium yuanmingense BR 3267. The genetic diversity of the cowpea-nodulating bradyrhizobia was not primarily affected by the biochar application in two agricultural soils of Brazilian drylands. Both soils harbored symbiotically efficient bacteria, without the influence of biochar amendment .

Mycoplasma nasistruthionis sp. nov. and Mycoplasma struthionis sp. nov. isolated from ostriches with respiratory disease

Twelve Mycoplasma (M.) strains isolated from the nose, the trachea, and the lung of ostriches (Struthio camelus) displaying respiratory disease were investigated. Analysis of 16S rRNA gene sequences placed five of these strains within the M. synoviae cluster, and seven strains within the M. hominis cluster of genus Mycoplasma, which was further confirmed by analyses of the 16S-23S rRNA intergenic spacer region, and partial rpoB gene and amino acid sequences. Genomic information as well as phenotypic features obtained by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry analysis and serological reactions indicated that the strains examined are representatives of two hitherto unclassified species of genus Mycoplasma, for which the names Mycoplasma nasistruthionis sp. nov., with type strain 2F1AT (= ATCC BAA-1893T = DSM 22456T), and Mycoplasma struthionis sp. nov., with type strain 237IAT (= ATCC BAA-1890T = DSM 22453T), are proposed.

Soymilk bio-enrichment by indigenously isolated riboflavin-producing strains of Lactobacillus plantarum

Lactobacilli (n = 68) isolated from human feces and fermented milk products were screened for the production of riboflavin (vitamin B2) by culturing into riboflavin assay medium (RAM). Cell-free culture supernatants from positive isolates (BBC32A, BBC32B, BBC33 and BIF43) were transferred onto RAM agar pre-seeded with Enterococcus faecalis MTCC2729 (a riboflavin auxotroph). The enhanced growth of B2-auxotroph confirmed the bioavailability of produced vitamin. Isolate BBC32B produced the highest riboflavin (319 ± 36 μg/l), followed by BBC33 (304 ± 91 μg/l), BBC32A (276 ± 8 μg/l) and BIF43 (257 ± 91 μg/l). All four isolates contained riboflavin genes ribG, ribB, ribA and ribH. Sequencing of DNA fragments amplified from the 16S–23S rRNA intergenic spacer region and areas flanking the 23S rRNA gene grouped these isolates within the species Lactobacillus plantarum. Identifications were confirmed by sequencing 1300-bp of amplified 16S rDNA fragments. Fermentation of soymilk by single cultures of L. plantarum BBC32B, BBC33 and BIF43 yielded 49.05%, 38.97% and 35.94% riboflavin enrichment respectively, which is more than 18.75% recorded in literature for Lactobacillus fermentum MTCC8711. Maximum levels of riboflavin were obtained within 12 h of fermentation in soymilk. Lactobacillus plantarum BBC32B may be used as starter culture for developing of riboflavin-enriched soymilk.

Genetic diversity of Streptococcus equi subsp. zooepidemicus isolated from horses

Streptococcus equi subsp. zooepidemicus (SEZ) is an opportunistic and zoonotic pathogen of horses. In this study, genetic intraspecies variability of SEZ obtained mainly from respiratory and genital samples of horses was investigated by analysis of the 16S–23S rRNA intergenic spacer region (ISR) and of the 16S rRNA gene. 16S–23S ISR rRNA type A1 was predominant, although a high rate of multiple products (30.5%) was obtained. Phylogenetic analysis of the 16S rRNA gene detected three genogroups (I, II and III). 16S rRNA variable regions V1 and V2 are the most important regions for evaluating SEZ intraspecies variability, but at least V1-V5 regions should be considered to avoid mistakes. Analysis of all 16S rRNA sequences available in databases assigned human SEZ to groups I and III but not to group II. These results show a high genetic variability in SEZ collected from different specimens of horses from various regions of Italy.

Molecular epidemiology and genetic characterisation of carbapenem-resistant Acinetobacter baumannii isolates from Guangdong Province, South China.

Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a worldwide issue. This study aimed to characterise the epidemiology and genetic relationships of A. baumannii isolates in Guangdong Province, China. CRAB isolates were collected from five municipal hospitals from June-December 2017. The 16S-23S rRNA intergenic spacer region was used for confirmation of strain identity. Antimicrobial susceptibility testing and the CarbAcineto NP test were performed to analyse the resistance spectrum and carbapenemase production of the isolates. PCR-based assays were used to detect β-lactamase genes and related mobile genetic elements. Genetic diversity among the isolates was analysed by enterobacterial repetitive intergenic consensus (ERIC)-PCR, multilocus sequence typing (MLST) and multiplex PCR. A total of 122 isolates were confirmed as A. baumannii; all were resistant to the tested antibiotics except for tigecycline and colistin. The CarbAcineto NP test showed that 93.4% of the isolates produced a carbapenemase. blaOXA-23-like and extended-spectrum β-lactamase-encoding genes were found by PCR in 94.3% and 91.8% of the isolates, respectively. Furthermore, the genetic environment of blaOXA-23-like was mainly associated with transposons Tn2008 (46.1%), Tn2006 (27.0%) and Tn2009 (20.9%). MLST identified six existing sequence types (STs) and three novel STs, of which ST195 (35.7%) and ST208 (32.1%) were the most common, belonging to clonal group 92 and European clone II. This study suggests that co-production of β-lactamases was the major resistance mechanism of CRAB isolates. Dissemination of blaOXA-23-like may be facilitated by transposable elements. ST195 and ST208 were the predominant epidemic types of A. baumannii in Guangdong Province.

Examination of 16S-23S rRNA intergenic spacer region (ISR) heterogeneity in a population of clinical Streptococcus pneumoniae- a new laboratory epidemiological genotyping tool to aid outbreak analysis

Streptococcus pneumoniae (pneumococci) are the most frequent cause of bacterial pneumonia of people of all ages, as well as an important cause of meningitis and otitis media. Although enormous effo...

Diversity and prevalence of Bartonella species in small mammals from Slovakia, Central Europe.

Wild-living rodents are important hosts for zoonotic pathogens. Bartonella infections are widespread in rodents; however, in Slovakia, knowledge on the prevalence of these bacteria in small mammals is limited. We investigated the prevalence and diversity of Bartonella species in the spleens of 640 rodents of six species (Apodemus flavicollis, Apodemus sylvaticus, Myodes glareolus, Microtus arvalis, Microtus subterraneus, and Micromys minutus) and in the European mole (Talpa europaea) from three different habitat types in south-western and central Slovakia. Overall, the prevalence of Bartonella spp. in rodents was 64.8%; a rate of 73.8% was found in natural habitat (deciduous forest), 56.0% in suburban forest park and 64.9% in rural habitat. Bartonella spp. were detected in 63.0% of A. flavicollis, 69% of My. glareolus and 61.1% of M. arvalis and in T. europaea. However, Bartonella were not found in the other examined rodents. Molecular analyses of the 16S-23S rRNA intergenic spacer region revealed the presence of four different Bartonella spp. clusters. We identified B. taylorii, B. rochalimae, B. elizabethae, B. grahamii and Bartonella sp. wbs11 in A. flavicollis and My. glareolus. Bartonella genotypes ascribed to B. taylorii and B. rochalimae were found in M. arvalis. B. taylorii was identified in T. europaea. Questing Ixodes ricinus ticks that were collected at the study sites were not infected with Bartonella. This study improves our understanding of the ecoepidemiology of Bartonella spp. in Europe and underlines the necessity for further research on Bartonella-host-vector associations and their consequences on animal and human health in Slovakia.

Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities.

Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S–23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters.

Trueperella pyogenes isolated from a brain abscess of an adult roebuck (Capreolus capreolus).

The present study was designed to characterize phenotypically and genotypically a Trueperella pyogenes strain isolated from a brain abscess of an adult roebuck (Capreolus capreolus). The species identity could be confirmed by phenotypical investigations, by MALDI-TOF MS analysis, and by sequencing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rRNA intergenic spacer region (ISR); by sequencing the target genes rpoB, gap, and tuf; and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay. The T. pyogenes strain could additionally be characterized by PCR-mediated amplification of several known and putative virulence factor-encoding genes which revealed the presence of the genes plo encoding pyolysin and nanH and nanP encoding neuraminidases; the genes fimA, fimC, and fimE encoding the fimbrial subunits FimA, FimC, and FimE; and the gene cbpA encoding collagen-binding protein CbpA. The present data give a detailed characterization of a T. pyogenes strain isolated from a brain abscess of a roebuck. However, the route of infection of the roebuck remains unclear.

Involvement of multiple Chlamydia suis genotypes in porcine conjunctivitis.

Chlamydia suis has been detected in numerous disease conditions of pigs, particularly in eye infections. This study examined recurring conjunctivitis cases in five commercial pig farms in Japan. 40.5% of the cases were identified as Chlamydia positive using impression cytology of ocular smears and a genus-specific direct fluorescent antibody. C.suis was detected in 59.5% of the samples using PCR tests targeting 16S-23S rRNA intergenic spacer region (ISR) and ompA gene. Genetic analysis of PCR amplicons revealed nine sequence variants of 16S-23S rRNA ISR and 20 sequence variants within ompA gene. Among C.suis-positive conjunctivitis cases, 36.4% showed concurrent infection with 2-4 varied ompA sequence types and 9.1% showed multiple 16S-23S rRNA ISR sequence types of C.suis. Multiple genotypes were found circulating in four of five farms. All 20 detected strains and 25 previously reported C.suis strains were grouped into four clusters. Japanese C.suis strains were closely related to American and European strains indicating wide distribution of these genetically variant strains. This study is the first to show multiple and genetically diverse C.suis strain associations in pig conjunctivitis.

Prevalence of Bartonella species infections in cats in Southern Germany

Bartonella species are zoonotic pathogens, and infections in cats are common. However, prevalence in cats in Southern Germany is still unknown. Therefore, prevalence of Bartonella species DNA in blood of...

Genetic characterization and antimicrobial resistance of Staphylococcus aureus isolated from bovine milk in Tunisia.

This paper describes the characteristics ofStaphylococcus aureus isolated from bulk tank and individual cow milk in Tunisia. All strains were genotyped by spa typing and RS-PCR, a method based on the amplification of the 16S-23S rRNA intergenic spacer region, and multiplex PCRs for 22 virulence genes. A selected subsample of strains was also genotyped by multilocus sequence typing. All strains were tested for antimicrobial resistance. Our study evidences a predominance of strains belonging to Clonal Complex 97. Methicillin-resistant strains were not detected, and overall low level of antimicrobial resistance was reported.

Porphyromonas loveana sp. nov., isolated from the oral cavity of Australian marsupials.

An obligatory anaerobic, Gram-stain-negative coccobacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic and molecular criteria showed that this bacterium was a distinct species within the genus Porphyromonas, and was closely related to Porphyromonas gingivalis and Porphyromonas gulae. This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterization by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight MS showed that this putative novel species could be differentiated phenotypically from P. gingivalis and P. gulae. Definitive identification by 16S rRNA gene sequencing showed that this bacterium belonged to a unique monophyletic lineage, phylogenetically distinct from P. gingivalis (94.9 % similarity) and P. gulae (95.5 %). This also was supported by 16S-23S rRNA intergenic spacer region and glutamate dehydrogenase gene sequencing. A new species epithet, Porphyromonas loveana sp. nov., is proposed for this bacterium, with DSM 28520T (=NCTC 13658T=UQD444T=MRK101T), isolated from a musky rat kangaroo, as the type strain.

EFFECTIVE IDENTIFICATION OF LACTOBACILLUS PARACASEI SSP. PARACASEI-1 BY 16S-23S rRNA INTERGENIC SPACER REGION SEQUENCING

Fermentation profiling is a common tool to identify Lactobacillus paracasei from other related members of Lactobacillus genus. Because of the proximate biochemical characteristics, identification based on the fermentation pattern within L. casei group (L. casei, L. paracasei and L. rahmnosus) has considerable limitation. On the other hand, members of L. casei group are genetically very closely related and sequencing of signature region is the most reliable and rapid method of differentiation. In this study, instead of sequencing entire 16S or 23S ribosomal RNA gene, we have sequenced 16s-23s rRNA intergenic spacer region and compared them across the members of L. casei group. We also compiled thirteen signature sequences within 16s-23s ISR rRNA gene of L. casei group members. Our isolated strain (L. paracasei ssp. paracasei-1) resembled 100% and 99% similarity when compared with 16s-23s rRNA intergenic spacer region of L. paracasei and L. casei respectively. Our study summarizes that sequencing of short 16s-23s rRNA intergenic spacer region carries great significance in identification of closely related probiotic bacteria such as the members of L. casei group. The findings of this research could be very much helpful for food and pharmaceutical industries who are dealing with probiotic bacteria.

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

BackgroundTo date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition profiles and evaluate indicators for BV using three molecular methods.MethodsEvaluation of indicators for BV was carried out by 16S rRNA amplicon sequencing of the V5-V7 region, a tailor-made 16S rRNA oligonucleotide-based microarray, and a PCR-based profiling technique termed IS-profiling, which is based on fragment variability of the 16S-23S rRNA intergenic spacer region. An inventory of vaginal bacterial species was obtained from 40 females attending a Dutch sexually transmitted infection outpatient clinic, of which 20 diagnosed with BV (Nugent score 7–10), and 20 BV negative (Nugent score 0–3).ResultsAnalysis of the bacterial communities by 16S rRNA amplicon sequencing revealed two clusters in the BV negative women, dominated by either Lactobacillus iners or Lactobacillus crispatus and three distinct clusters in the BV positive women. In the former, there was a virtually complete, negative correlation between L. crispatus and L. iners. BV positive subjects showed cluster profiles that were relatively high in bacterial species diversity and dominated by anaerobic species, including Gardnerella vaginalis, and those belonging to the Families of Lachnospiraceae and Leptotrichiaceae. Accordingly, the Gini-Simpson index of species diversity, and the relative abundance Lactobacillus species appeared consistent indicators for BV. Under the conditions used, only the 16S rRNA amplicon sequencing method was suitable to assess species diversity, while all three molecular composition profiling methods were able to indicate Lactobacillus abundance in the vaginal microbiota.ConclusionAn affordable and simple molecular test showing a depletion of the genus Lactobacillus in combination with an increased species diversity of vaginal microbiota could serve as an alternative and practical diagnostic method for the assessment of BV.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-1513-3) contains supplementary material, which is available to authorized users.