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OBJECTIVES It has been suggested that smoking affects the oral microbiome, but its effects on sites other than the subgingival microbiome remain unclear. This study investigated the composition of the salivary and tongue bacterial communities of smokers and nonsmokers in periodontally healthy adults. METHODS The study population included 50 healthy adults. The bacterial composition of resting saliva and the tongue coating was identified through barcoded pyrosequencing analysis of the 16S rRNA gene. The Brinkman index (BI) was used to calculate lifetime exposure to smoking. The richness and diversity of the microbiome were evaluated using the t-test. Differences in the proportions of bacterial genera between smokers and nonsmokers were evaluated using the Mann-Whitney U test. The quantitative relationship between the proportions of genera and the BI was evaluated using Pearson's correlation analysis. RESULTS The richness and diversity of the oral microbiome differed significantly between saliva and the tongue but not between smokers and nonsmokers. The saliva samples from smokers were enriched with the genera Treponema and Selenomonas. The tongue samples from smokers were enriched with the genera Dialister and Atopobium. The genus Cardiobacterium in saliva, and the genus Granulicatella on the tongue, were negatively correlated with BI values. On the other hand, the genera Treponema, Oribacterium, Dialister, Filifactor, Veillonella, and Selenomonas in saliva and Dialister, Bifidobacterium, Megasphaera, Mitsuokella, and Cryptobacterium on the tongue were positively correlated with BI values. CONCLUSIONS The saliva and tongue microbial profiles of smokers and nonsmokers differed in periodontally healthy adults. The genera associated with periodontitis and oral malodor accounted for high proportions in saliva and on the tongue of smokers without periodontitis and were positively correlated with lifetime exposure to smoking. The tongue might be a reservoir of pathogens associated with oral disease in smokers.

Objective Peri-implantitis has been attributed to a myriad of factors, including microleakage at the abutment-implant interface. Implant abutment access channel sealing materials (IACSM) are readily used in implant dentistry, with little evidence on their effect on microleakage. This study aims to evaluate the effect of IACSM on the microbial composition in the implant access channel and the peri-implant sulcus. Methods A total of n=8 patients (64 implants) were included in this single-blinded, randomized controlled trial, whereas four different materials (cotton, Polytetrafluroethylene (PTFE), synthetic foam or Polyvinyl siloxane (PVS)) were randomly placed as an IACSM. Following 6 months, microbial analysis was completed on the IACSM and samples from the peri-implant sulci via PCR and high-throughput sequencing. Bacterial samples on the IACSM and in the peri-implant sulci were classified according to Socransky's microbial complexes. Results There was a preponderance of early colonizing bacteria within the IACSM, while the peri-implant sulci were dominated by Orange complex bacteria. The proportion of Red and Orange complex members on the IACSM was significantly less than in the peri-implant sulci. The proportion of Green, Yellow, and Blue complex members found on the IACSM was significantly greater than in the peri-implant sulci. Atopobium, a diverse species not included in the microbial complexes, was frequently detected in the peri-implant sulcus samples. Conclusions No detectable effects of IACSM on the microbial community in the peri-implant sulcus or on the IACSM were identified. Variation of bacterial species was most dependent on the individual patient. No significant differences were found in the periodontal parameters between the different treatment groups.

The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.

AIM To identify dominant microorganisms in root filled teeth with apical periodontitis by Pan-PCRs in comparison with a culture-dependent approach, focusing on fungal species profiling. METHODOLOGY The root filling material (gutta-percha) removed from 42 teeth with periapical radiolucencies undergoing root canal retreatments was analysed by molecular genetics techniques. Real-Time Pan-PCRs were conducted for the diagnosis of predominant bacteria (targeting 16S rDNA) and fungi (targeting ITS1-2 region). Identification of microorganisms was performed by Sanger sequencing of the PCR products and BLAST analysis. Additionally, subgingival plaque samples were collected and cultured to review the composition of the microbial flora. The McNemar test and the repeated measures anova were used for statistical analyses (significance level was set at P

Objective Determine the associations between factors and sexual practices and the composition of the vaginal microbiome (VM) of women treated for bacterial vaginosis (BV). Design Prospective cohort study. Setting The Melbourne Sexual Health Centre, Melbourne, Australia. Population Seventy-five reproductive-age women diagnosed with clinical BV, treated with first-line antibiotics and followed for up to 6 months. Methods Women self-collected vaginal swabs and completed questionnaires at enrolment, the day following antibiotics and monthly for up to 6months until BV recurrence or no BV recurrence (n = 430 specimens). Bacterial composition was determined using 16S rRNA gene amplicon sequencing. The effects of ongoing factors on VM composition (utilising 291 monthly specimens) were assessed using generalised estimating equations population-averaged models, which accounted for repeated measures within individuals. Main outcome measures The relative abundance of vaginal bacterial taxa. Results Women who reported ongoing sex with a regular sexual partner (RSP) had a VM comprised of increased relative abundance of non-optimal BV-associated bacteria (Adjusted co-efficient [Adjusted co-eff] = 11.91, 95% CI 3.39to20.43, P = 0.006) and a decreased relative abundance of optimal, Lactobacillus species (Adjusted co-eff = -12.76, 95% CI -23.03 to -2.49, P = 0.015). A history of BV was also associated with a decreased relative abundance of Lactobacillus spp. (Adjusted co-eff = -12.35, 95% CI -22.68, P = 0.019). The relative abundance of Gardnerella, Atopobium and Sneathia spp. increased following sex with an RSP. Conclusions Sex with an untreated RSP after BV treatment was associated with a VM comprised of non-optimal BV-associated bacteria. BV treatment approaches may need to include partner treatment if they are to achieve a sustained optimal VM associated with improved health outcomes. Tweetable abstract Sex drives a return to a 'non-optimal' vaginal microbiota after antibiotics for bacterial vaginosis.

Background and objective To examine the microbial diversity associated with implants with or without peri-implantitis and to identify differences between the bacterial communities in these clinical conditions. Material and methods Twenty subjects were assigned to a Control group consisting of subjects with healthy implants and a Test group consisting of subjects with peri-implantitis sites, as well as a healthy implant site (n = 10/group). In the Test group, subgingival biofilm samples were taken from the deepest sites of the diseased implant. In both groups, samples were collected from one site around a healthy implant. DNA was extracted and the 16S rRNA gene was amplified and sequenced, and the phylotypes were identified by comparison with known 16S rRNA sequences. Results The phylogenetic identity of 1387 16S rRNA gene clones was determined. Healthy implants demonstrated higher proportions of Actinomyces, Atopobium, Gemella, Kingella and Rothia and lower levels of Campylobacter, Desulfobulbus, Dialister, Eubacterium, Filifactor, Mitsukella, Porphyromonas and Pseudoramibacter (Mann–Whitney U-test; P

Blood groups, finger prints, iris scans and DNA bar codes are several ways to distinguish or identify individual humans. According to Arumugam and colleagues (2011) we can now also be distinguished by the microbial communities in our faeces, our ‘enterotypes’. The human gut is one of the most densely populated ecosystems known, and although this ecosystem contains members of the three domains of life – bacteria, archaea and eucarya (Finegold et al., 1983) – it is dominated by bacteria. They are essential in digesting the food we eat and in keeping us healthy by stimulating our immune system and fighting off pathogenic bacteria. It is estimated that 1013–1014 microbes inhabit our gastrointestinal tract (GIT), with the greatest number residing in the distal gut, where they synthesize essential vitamins and process otherwise indigestible components of our diet such as plant polysaccharides (Backhed et al., 2005). Early studies used 16S ribosomal DNA (rDNA) analysis to type and enumerate the distal gut and faecal microbiota. More than 90% of the bacterial phylotypes present in the intestinal microbiota in healthy humans are members of only three bacterial divisions: the Bacteroidetes, the Firmicutes and the Actinobacteria (Zoetendal et al., 2006). Nevertheless, each healthy adult's gut appears to have a unique and relatively stable microbiota (Zoetendal et al., 1998; Turnbaugh et al., 2007), which is a reflection of the numerous different phylogenetic clusters among the Firmicutes, Clostridium clusters IV, IX and XIVa, including the predominant genera Clostridium, Eubacterium, Roseburia and Ruminococcus. Furthermore, the Actinobacteria that encompass mainly the genera Bifidobacterium and Atopobium also represent important members of the gut microbial community (Harmsen et al., 2002; Turroni et al., 2008). Notably, recent estimates of the diversity of the human gut microbial ecosystem indicate it may encompass more than 1000 species and a multitude of strains (Backhed et al., 2005; Blaut and Clavel, 2007; Rajilic‐Stojanovic et al., 2007). Microbiota composition studies in humans have discovered that aberrations in the microbiome composition is present in obese individuals (Ley et al., 2006; Turnbaugh et al., 2009) as well as in individuals with a variety of other diseases (Zoetendal et al., 2008). Since the largest part (∼80%) of gut microbes remains uncultured, metagenomics analysis has become fashionable in the past 5 years to estimate the types, relative abundance and genome content of microbes in various parts of the GIT. The first metagenomics analysis from just two faecal samples (Gill et al., 2006) led to early insight into enrichment of genes encoding specific metabolic pathways, including metabolism associated with glycans, amino acids and xenobiotics, but also methanogenesis and biosynthesis of vitamins and isoprenoids. However, this early study provided only a very fragmented view due to limitations in sample size, sequencing technology, number of bases sequenced and availability of suitable reference genomes of gut inhabitants.

Ecological and evolutionary forces shaping the normal and abnormal microflora of the genital econiche are discussed, in particular those related to bacterial vaginosis, which worldwide is the most common vaginal infection, with numerous obstetrical and gynecological complications, including acquisition and transmission of HIV and other sexually transmitted infections (STIs). Characterized by a heavy overgrowth of Gram-negative and Gram-positive anaerobes with no signs of inflammation, bacterial vaginosis has been regarded a microbiological and immunological enigma. Immune tolerance to both normal and abnormal vaginal microbiota, mainly derived from gut microflora, as a result of coevolution with humans might explain the absence of inflammation, supported by short-chain fatty acids, known to modulate immune responses, that are produced in large quantities by anaerobes. Recent studies have implicated the development of a vaginal biofilm with Gardnerella vaginalis and Atopobium vaginae as main players in the pathogenesis of bacterial vaginosis. Supporting this conclusion are data such as those demonstrating heavy growth of G. vaginalis and diversified anaerobes with numerous "clue cells" that are sloughing off from the biofilm. Gardnerella and Atopobium organisms attached to these clue cells can be demonstrated in the male genital econiche, likely reflecting a heterosexual transmission of the disorder.