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Summary 16S rDNA analysis revealed that Coriobacterium glomerans is a close phylogenetic neighbor of the genus Atopobium within the radiation of the actinomycetes line of descent where they form one of the deepest branching lineages. The relationship between members of the two genera is supported by the following, previously reported similarities: morphology, Gram-positive staining behaviour, anaerobic growth, production of acetate and L-lactic acid from glucose fermentation, and peptidoglycan of the A4 subgroup. Despite these similarities, Coriobacterium and Atopobium constitute separate genera as justified by significant differences in the primary structure of 16S rDNA and in the G+C content of ribosomal rDNA, as well as in the reported DNA base composition, and in end products from glucose fermentation.

Summary Comparative 16S rDNA studies of lactic acid bacteria and some of their phylogenetic relatives of the Clostridium/Bacillus subphylum of Gram-positive bacteria indicated that three misclassified Lactobacillus and Streptococcus species, described as members of the novel genus Atopobium , formed separate subline of descent within this subphylum. Inclusion of outside reference organisms such as members of the order Actinomycetales and a cyanobacterial species, serving as the root of Gram-positive bacteria, clearly showed Atopobium species to branch off within the actinomycetes line of descent. The importance of the use of an appropriate selection of reference organisms in phylogenetic studies is discussed.

Microbial colonization of the infant gut is essential for the development of the intestine and the immune system. The profile of intestinal microbiota in the full-term, vaginally delivered, breast-fed infant is considered as ideally healthy. However, in preterm infants this process is challenging, mainly because of organ immaturity, antibiotics use, and hospital stay. To assist in a proper microbiota development in these infants, a detailed knowledge of the colonization process, and the differences from that of full-term breast-fed infants, is needed. We assessed the establishment of the gut microbiota and its metabolic activity in preterm neonates (n = 21) during the first 3 months of life and compared it with that of vaginally delivered, exclusively breast-fed full-term infants (n = 20) using qualitative and quantitative culture-independent methods. Differences in the gut microbiota composition between both groups were observed. Preterm infants showed higher levels of facultative anaerobic microorganisms and reduced levels of strict anaerobes such as Bifidobacterium, Bacteroides, and Atopobium. Short-chain fatty acids concentrations were lower in preterm infants during the first days of life. Alterations occur in the process of microbiota establishment in preterm infants, indicating the need for intervention strategies to counteract them. © 2011 Federation of European Microbiological Societies., This work was funded by a CSIC (Spain) intramural project (Ref. 200870I049). S.A. was funded by a predoctoral JAE fellowship from CSIC, Spain. A.B. was the recipient of a postdoctoral fellowship from CONICET, Argentina.

In this study, we analyzed the diversity of vaginal microbiota in 9 bacterial vaginosis (BV) positive and 11 healthy women from the metropolitan area of Guangzhou in Southern China using full-length 16S rDNA. Our data confirmed that a shift in the abundance of bacterial species present in the vaginal environment comparing the BV and non-BV groups. Each sequence read was assigned to a genus or a species when possible. Principal component analysis was performed at genus levels. Most BV+ samples clustered together while there were two clusters among the BV- samples. Several bacteria have been found to be highly associated with BV, including Gardnerella, Atopobium, Megasphaera, Leptotrichia/Sneathia, and Prevotella. We found that the presence of any BV-associated organisms alone did not necessary cause BV. We identified several additional non-lactobacillus bacteria associated with BV, including a Coriobacteriaceae bacterium and a Ruminococcaceae bacterium. Our results showed that analysis of vaginal microbiota and the clustering of microbial profile could help identification of bacterial vaginosis and assessment of women's vaginal health. The presence or absence of certain bacterial species is not adequate for disease diagnosis; rather the prevalence of multiple organisms collectively should be used as markers for a microbial diagnosis of BV.

Although it is well established that early infant feeding has a major influence on the establishment of the gut microbiota, very little is understood about how the introduction of first solid food influences the colonization process. This study aimed to determine the impact of weaning on the faecal microbiota composition of infants from five European countries (Sweden, Scotland, Germany, Italy and Spain) which have different lifestyle characteristics and infant feeding practices. Faecal samples were collected from 605 infants approximately 4 weeks after the introduction of first solid foods and the results were compared with the same infants before weaning (6 weeks of age) to investigate the association with determining factors such as geographical origin, mode of delivery, previous feeding method and age of weaning. Samples were analysed by fluorescence in situ hybridization and flow cytometry using a panel of 10 rRNA targeted group- and species-specific oligonucleotide probes. The genus Bifidobacterium (36.5 % average proportion of total detectable bacteria), Clostridium coccoides group (14 %) and Bacteroides (13.6 %) were predominant after weaning. Similar to pre-weaning, northern European countries were associated with a higher proportion of bifidobacteria in the infant gut microbiota while higher levels of Bacteroides and lactobacilli characterized southern European countries. As before weaning, the initial feeding method influenced the Clostridium leptum group and Clostridium difficile+Clostridium perfringens species, and bifidobacteria still dominated the faeces of initially breast-fed infants. Formula-fed babies presented significantly higher proportions of Bacteroides and the C. coccoides group. The mode of birth influenced changes in the proportions of bacteroides and atopobium. Although there were significant differences in the mean weaning age between countries, this was not related to the populations of bifidobacteria or bacteroides. Thus, although the faecal microbiota of infants after first complementary foods was different to that before weaning commenced, many of the initial influences on microbiota composition were still evident.

Introduction and aims The role bacteria play in the development and progression of Chronic Obstructive Pulmonary Disease (COPD) is unclear. We used culture-independent methods to describe differences and/or similarities in microbial communities in the lower airways of patients with COPD, healthy non-smokers and smokers. Methods Bronchial wash samples were collected from patients with COPD (GOLD 1–3; n = 18), healthy non-smokers (HV; n = 11) and healthy smokers (HS; n = 8). Samples were processed using the Illumina MiSeq platform. The Shannon-Wiener Index (SW) of diversity, lung obstruction (FEV 1 /FVC ratio) and ordination by Non-Metric Multidimensional Scaling (NMDS) on Bray-Curtis dissimilarity indices were analysed to evaluate how samples were related. Principal component analysis (PCA) was performed to assess the effect specific taxa had within each cohort. Characteristics of each cohort are shown in Table 1. Results There was no difference in taxa richness between cohorts (range: 69–71; p = 0.954). Diversity (SW Index) was significantly lower in COPD samples compared to samples from HV and HS (p = 0.009 and p = 0.033, respectively). There was no significant difference between HV and HS (p = 0.186). The FEV 1 /FVC ratio was significantly lower for COPD compared to HV (p = 9*10 –8 ) and HS (p = 2*10 –6 ), respectively. NMDS analysis showed that communities belonging to either of the healthy groups were more similar to each other than they were to samples belonging to the COPD group. PCA analysis showed that members of Streptococcus sp. and Haemophilus sp. had the largest effect on the variance explained in COPD. In HS, Haemophilus sp., Fusobaterium sp., Actinomyces sp., Prevotella sp. and Veillonella sp. had the largest effect on the variance explained, while in HV Neisseria sp., Porphyromonas sp., Actinomyces sp., Atopobium sp., Prevotella and Veillonella sp. had the largest effect on the variance explained. Conclusions The study demonstrates that microbial communities in the lower airways of patients with COPD are significantly different from that seen in healthy comparison groups. Patients with COPD had lower microbial diversity than either of the healthy comparison groups, higher relative abundance of members of Streptococcus sp. and lower relative abundance of a number of key anaerobes.

Background Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure and composition of vaginal microbial communities; most of the earlier studies focused on predominant vaginal bacteria in the process of BV. In the present study, the diversity and richness of vaginal microbiota in 50 BV positive and 50 healthy women from China were investigated using culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and barcoded 454 pyrosequencing methods, and validated by quantitative PCR. Results Our data demonstrated that there was a profound shift in the absolute and relative abundances of bacterial species present in the vagina when comparing populations associated with healthy and diseased conditions. In spite of significant interpersonal variations, the diversity of vaginal microbiota in the two groups could be clearly divided into two clusters. A total of 246,359 high quality pyrosequencing reads was obtained for evaluating bacterial diversity and 24,298 unique sequences represented all phylotypes. The most predominant phyla of bacteria identified in the vagina belonged to Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. The higher number of phylotypes in BV positive women over healthy is consistent with the results of previous studies and a large number of low-abundance taxa which were missed in previous studies were revealed. Although no single bacterium could be identified as a specific marker for healthy over diseased conditions, three phyla - Bacteroidetes, Actinobacteria and Fusobacteria, and eight genera including Gardnerella, Atopobium, Megasphaera, Eggerthella, Aerococcus, Leptotrichia/Sneathia, Prevotella and Papillibacter were strongly associated with BV (p < 0.05). These genera are potentially excellent markers and could be used as targets for clinical BV diagnosis by molecular approaches. Conclusions The data presented here have clearly profiled the overall structure of vaginal communities and clearly demonstrated that BV is associated with a dramatic increase in the taxonomic richness and diversity of vaginal microbiota. The study also provides the most comprehensive picture of the vaginal community structure and the bacterial ecosystem, and significantly contributes to the current understanding of the etiology of BV.

16S rRNA gene sequencing was performed on the species Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus in order to clarify their taxonomic position. Based on comparative sequence analyses these organisms represent a hitherto unknown line of descent within the lactic acid group of bacteria for which a new genus, Atopobium gen. nov., is proposed.

An analytical system based on rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) was established for the precise evaluation of human intestinal microbiota. Group- and species-specific primer sets for Clostridium perfringens , Lactobacillus spp. (six subgroups and three species), Enterococcus spp., and Staphylococcus spp. targeting 16S rRNA gene sequences were newly developed for the quantitative analysis of such subdominant populations in human intestines. They were used together with previously reported group-specific primer sets for Enterobacteriaceae , Pseudomonas spp., and six predominant bacterial groups (the Clostridium coccoides group, the Clostridium leptum subgroup, the Bacteroides fragilis group, Bifidobacterium spp., the Atopobium cluster, and Prevotella spp.) for the examination of fecal samples from 40 healthy adults by RT-qPCR with lower detection limits of 10 2 to 10 4 cells per g of feces. The RT-qPCR method gave data equivalent to those yielded by qPCR for predominant populations of more than 10 8 cells per g of feces and could quantify bacterial populations that were not detectable ( Staphylococcus and Pseudomonas ) or those only detected at lower incidences ( Prevotella , C. perfringens , Lactobacillus , and Enterococcus ) by qPCR or the culture method. The RT-qPCR analysis of Lactobacillus spp. at the subgroup level revealed that a subject has a mean of 4.6 subgroups, with an average count of log 10 (6.3 ± 1.5) cells per g of feces. These results suggest that RT-qPCR is effective for the accurate enumeration of human intestinal microbiota, especially the entire analysis of both predominant and subdominant populations.

This paper reports a case of sepsis associated with a previously unknown Atopobium species and highlights the role of 16S ribosomal subunit sequencing in the rapid identification of slow-growing or atypical organisms in the clinical laboratory.

Culture-based studies have shown that Streptococcus mutans and lactobacilli are associated with root caries (RC). The purpose of the present study was to assess the bacterial diversity of RC in elderly patients by use of culture-independent molecular techniques and to determine the associations of specific bacterial species or bacterial communities with healthy and carious roots. Plaque was collected from root surfaces of 10 control subjects with no RC and from 11 subjects with RC. The bacterial 16S rRNA genes from extracted DNA were PCR amplified, cloned, and sequenced to determine species identity. From a total of 3,544 clones, 245 predominant species or phylotypes were observed, representing eight bacterial phyla. The majority (54%) of the species detected have not yet been cultivated. Species of Selenomonas and Veillonella were common in all samples. The healthy microbiota included Fusobacterium nucleatum subsp. polymorphum , Leptotrichia spp., Selenomonas noxia , Streptococcus cristatus , and Kingella oralis . Lactobacilli were absent, S. mutans was present in one, and Actinomyces spp. were present in 50% of the controls. In contrast, the microbiota of the RC subjects was dominated by Actinomyces spp., lactobacilli, S. mutans , Enterococcus faecalis , Selenomonas sp. clone CS002, Atopobium and Olsenella spp., Prevotella multisaccharivorax , Pseudoramibacter alactolyticus , and Propionibacterium sp. strain FMA5. The bacterial profiles of RC showed considerable subject-to-subject variation, indicating that the microbial communities are more complex than previously presumed. The data suggest that putative etiological agents of RC include not only S. mutans , lactobacilli, and Actinomyces but also species of Atopobium , Olsenella , Pseudoramibacter , Propionibacterium , and Selenomonas .

Atopobium vaginae, a fastidious, anaerobic, Gram-positive cocci-shaped bacterium that generates large quantities of lactic acid, is associated with bacterial vaginosis (BV). Published nucleic acid amplification tests for identifying A. vaginae are directed toward the 16S ribosomal DNA with suboptimal specificity and require isolation of the organism. Here, sequencing of an A. vaginae genomic library has led to the development of a highly specific and sensitive real-time PCR test for detection of A. vaginae directly from gynecological cervicovaginal swab samples. The real-time PCR did not cross-react with DNA extracted from other members of the Atopobium genus, species with closely related 16S ribosomal DNA, and a panel of 51 other human pathogens. The DNA extraction and PCR assembly were amenable to automation using Corbett Robotics X-tractor Gene and CAS-4200N liquid handling systems. The real-time PCR was used to analyze 96 cervicovaginal swab samples submitted to our clinical laboratory for detection of organisms associated with BV. Of those samples, 28 were positive for A. vaginae. Of the 28 positive samples, 23 were concomitant with Gardnerella vaginalis detection. These results suggest that further clinical study of the relationship of A. vaginae with G. vaginalis and the development of BV should be performed.

The use of non-culture gene amplification techniques has improved our understanding of the composition of the vaginal bacterial ecosystem. In most healthy women in the reproductive period the predominant vaginal bacteria are one or more of the following species of Lactobacillus: L. crispatus, L. iners and L. gasseri. However, in other apparently healthy women lactobacilli may be deficient or absent, being replaced by other lactic-acid-producing bacteria: Atopobium, Megasphaera and/or Leptotrichia species. Infection and/or proliferation of pathogenic bacteria in the vagina is suppressed by lactic acid production, bacteria-generated antimicrobial products, and the local activities of the innate and cell-mediated immune systems. Vaginal epithelial cells produce a range of compounds with antimicrobial activities. These cells also possess membrane-bound Toll-like receptors that recognize pathogen-associated molecular patterns. Recognition leads to pro-inflammatory cytokine production and antigen-specific immunity. Local production of IgG and IgA antibodies can also be initiated in the endocervix and vagina in response to infection.

Introduction Hormonal contraception (HC) has been associated with a reduced risk of bacterial vaginosis (BV). We conducted a prospective study to evaluate the relationship between vaginal microbiota and several HC methods. Methods During 2-years of follow-up, 108 women provided 2,662 mid-vaginal samples. Participants reported three HC methods [oral contraceptive pill (OCP), vaginal ring, implanon]. Controls not taking HC were also followed. Visits were scheduled at baseline, 2 weeks, 4 weeks, 3 months, 6 months, 12 months, 18 months, and 24 months. Additionally, participants self-collected mid-vaginal swabs twice-weekly in the two weeks before each visit. Vaginal microbiota composition was characterised on all samples by 16S rRNA gene analysis of the V3-V4 hypervariable regions. We identified four community state types (CSTs) which were dominated by Lactobacillus species. CST-IV-B was characterised by a low relative abundance of Lactobacillus spp. and higher proportions of BV-associated bacteria (Gardnerella and Atopobium). A multinomial model for dependence of proportions was used to evaluate the association between CST and HC. Jensen-Shannon distances between all pairs of samples were analysed to assess stability of the microbiota longitudinally. Results Women on OCPs had more stable bacterial communities than controls during the 2-year follow-up (p = 0.04). HC (overall) also tended toward greater stability (p = 0.10). The low- Lactobacillus CST-IV-B had an 83% lower probability among OCP users and a 55% lower probability among implanon users. CST-II (L. gasseri-dominated) was significantly higher in all HC types compared to controls. Additionally, OCP users were more likely to be CST-III-A ( L. iners -dominated) and CST-V (L. jensenni-dominated), while CST-III-A was also high among ring users. CST-I (L. crispatus-dominated) was associated with implanon. All reported findings were statistically significant (p Conclusion Women on HC experienced greater stability of the vaginal microbiota over time compared to controls. OCPs and the vaginal ring were protective against transition to a Lactobacillus -depleted state. Disclosure of interest statement The study was funded by the US National Institute of Allergy and Infectious Diseases (NIAID) R01-AI089878. No pharmaceutical grants were received in the development of this study.

The intestinal mucosa-associated microbiota could play important biological roles due to its close proximity with the animal host, but knowledge on its composition is still limited. The aim of this study was to characterize the microbial communities tightly associated with different parts (rumen, duodenum and colon) of the gastrointestinal tract (GIT) of healthy lambs and calves by using both cultural, and fluorescent in situ hybridization-flow cytometry (FCM-FISH) techniques. Lactic acid bacteria genera were one of the predominant bacteria detected in lambs and calves by both methodologies, possibly constituting an index of their healthy status. The levels of Lactobacillus were significantly higher (p < 0.05) in the rumen and duodenum of lambs, and in the rumen of calves. The levels of Bifidobacterium were significantly higher (p < 0.05) in the colon of both animal species and the rumen of lambs. Significant differences (p < 0.05) were found in counts of other microbial groups (yeast, Enterococcus, Propionibacterium, Bacteroides, Clostridium and Enterobacteriaceae) at diverse GI sections depending on the animal species. In general, microbial counts follow the same trends regardless the applied technique. The most remarkable differences were found in detection levels of Bacteroides and Clostridium, which tended to be significantly higher (p < 0.05) when analysed by FCM-FISH. This technique also allowed the detection of quantitatively important bacteria (sulphate-reducing bacteria, Atopobium and Coriobacterium), which are difficult to cultivate in selective medium. Therefore, FCM-FISH has been proven to be a sensitive high throughput approach that provides additional information to that obtained by traditional culture techniques about the complexity of the GI ecosystem of these animal species.

The microbial flora of the human vagina can affect the health of women, their fetuses, and newborns. Conventional cultivation methods fail to detect some fastidious vaginal bacteria, leading to an incomplete census. Recent advances in molecular biology have facilitated the detection and identification of bacteria without cultivation, and the advantages and limitations of this approach are described. Molecular studies of the vaginal flora have discovered many uncultivated bacterial species. For instance, several novel bacteria in the Clostridiales order are highly specific indicators of bacterial vaginosis, and bacteria related to Megasphaera, Leptotrichia, Atopobium, and Dialister species are commonly found in subjects with bacterial vaginosis. A more complete understanding of vaginal microbial populations resulting from the adoption of molecular tools may lead to better strategies to maintain healthy vaginal floras and will create opportunities to explore the role of novel bacteria in reproductive tract diseases.

Most studies of the bacterial etiology of periodontitis have used either culture-based or targeted DNA approaches, and so it is likely that pathogens remain undiscovered. The purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. Samples from subjects with periodontitis and controls were analyzed using ribosomal 16S cloning and sequencing. Several genera, many of them uncultivated, were associated with periodontitis, the most numerous of which were gram positive, including Peptostreptococcus and Filifactor . The genera Megasphaera and Desulfobulbus were elevated in periodontitis, and the levels of several species or phylotypes of Campylobacter , Selenomonas , Deferribacteres , Dialister , Catonella , Tannerella , Streptococcus , Atopobium , Eubacterium , and Treponema were elevated in disease. Streptococcus and Veillonella spp. were found in high numbers in all samples and accounted for a significantly greater fraction of the microbial community in healthy subjects than in those with periodontitis. The microbial profile of periodontal health also included the less-abundant genera Campylobacter , Abiotrophia , Gemella , Capnocytophaga , and Neisseria . These newly identified candidates outnumbered Porphyromonas gingivalis and other species previously implicated as periodontopathogens, and it is not clear if newly identified and more numerous species may play a more important role in pathogenesis. Finally, more differences were found in the bacterial profile between subjects with periodontitis and healthy subjects than between deep and shallow sites within the same subject. This suggests that chronic periodontitis is the result of a global perturbation of the oral bacterial ecology rather than a disease-site specific microbial shift.

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species ofLactobacillusappeared to dominate the communities in four of the five women. However, the community of one woman was dominated byAtopobiumsp., whereas a second woman had appreciable numbers ofMegasphaerasp.,Atopobiumsp. andLeptotrichiasp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related toLactobacillus crispatus, whereas the second group of two women had clones ofLactobacillus inersthat were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.

Introduction Previous studies have shown that alterations of the bacterial microbiota in the lower female genital tract influence susceptibility to HIV infection and shedding. We assessed geographic differences in types of genital microbiota between HIV-infected and uninfected women from Rwanda and the United States. Methods Genera of lower genital tract bacterial microbiota were identified by high-throughput pyrosequencing of the 16S rRNA gene from 46 US women (36 HIV-infected, 10 HIV-uninfected) and 40 Rwandan women (18 HIV-infected, 22 HIV-uninfected) with similar proportions of low (0–3) Nugent scores. Species of Lactobacillus were identified by assembling sequences along with reference sequences into phylogenetic trees. Prevalence of genera and Lactobacillus species were compared using Fisher's exact tests. Results Overall the seven most prevalent genera were Lactobacillus (74%), Prevotella (56%), Gardnerella (55%), Atopobium (42%), Sneathia (37%), Megasphaera (30%), and Parvimonas (26%), observed at similar prevalences comparing Rwandan to US women, except for Megasphaera (20% vs. 39%, p = 0.06). Additionally, Rwandan women had higher frequencies of Mycoplasma (23% vs. 7%, p = 0.06) and Eggerthella (13% vs. 0%, p = 0.02), and lower frequencies of Lachnobacterium (8% vs. 35%, p

Objective Genital tract infection accounts for approximately 25-40% of all preterm births. We sought to assess the relationship between preterm birth and selected vaginal bacterial taxa associated with preterm birth either directly or through their association with bacterial vaginosis (BV). Study Design Vaginal fluid for Gram stain was collected between 17 and 22 weeks' gestation as part of a randomized trial of ultrasound-indicated cerclage for preterm birth prevention in women at high risk for recurrent spontaneous preterm birth. Bacterial deoxyribonucleic acid was extracted from the Gram stain slides and analyzed using quantitative polymerase chain reaction. Results Among the 499 participants, Mycoplasma was positively correlated with increased risk of preterm (risk ratio [RR], 1.83; 95% confidence interval [CI], 1.52–2.22) as was Mobiluncus (RR, 1.36; 95% CI, 1.07–1.73) and Atopobium (RR, 1.44; 95% CI, 1.1–1.87). However, there were strong interactions between the race/ethnic group and the presence of these and other individual taxa on risk of preterm birth. By contrast, bacterial vaginosis–associated bacteria (BVAB)-3 was consistently associated with a reduction in the risk of preterm birth for all racial/ethnic groups (0.55; 95% CI, 0.39–0.78). Conclusion BV is characterized by a reduction of Lactobacillus , and lactic acid–producing bacteria and the presence of Mobiluncus ; we found these factors and the presence of Mycoplasma to be associated with an increased risk of preterm birth. By contrast, the presence of a recently identified organism sufficient to cause BV, BVAB3, decreased the risk of preterm birth. These findings give insight into why treating BV has mixed impact on risk of preterm birth.

Microbiota have recently been shown to be associated with many disease conditions. However, the microbiota associated with tuberculosis (TB) infection, recurrence and treatment outcome have not been systematically characterized. Here, we used high throughput 16S RNA sequencing to analyze the sputum microbiota associated with Mycobacterium tuberculosis infection and also to identify the microorganisms associated with different outcomes of TB treatment. We recruited 25 new TB patients, 30 recurrent TB patients and 20 TB patients with treatment failure, as well as 20 healthy controls. Streptococcus, Gramulicatella and Pseudomonas were more abundant in TB patients while Prevotella, Leptotrichia, Treponema, Catonella and Coprococcus were less abundant in TB patients than in the healthy controls. We found reduced frequency and abundance of some genera such as Bulleidia and Atopobium in recurrent TB patients compared with those in new TB patients. In addition, the ratio of Pseudomonas / Mycobacterium in recurrent TB was higher than that in new TB while the ratio of Treponema / Mycobacterium in recurrent TB was lower than that in new TB, indicating that disruption of these bacteria may be a risk factor of TB recurrence. Furthermore, Pseudomonas was more abundant and more frequently present in treatment failure patients than in cured new patients, and the ratio of Pseudomonas / Mycobacterium in treatment failure was higher than that in new TB. Our data suggest that the presence of certain bacteria and the disorder of lung microbiota may be associated with not only onset of TB but also its recurrence and treatment failure. These findings indicate that lung microbiota may play a role in pathogenesis and treatment outcome of TB and may need to be taken into consideration for improved treatment and control of TB in the future.

To the Editor: The genus Atopobium (1) accommodates species formerly designated Lactobacillus minutus, L. rimae, and Streptococcus parvulus (2). Use of 16S rDNA sequence analysis showed these species to be closely related and to form a distinct line of descent within the lactic acid bacteria (3). Atopobium spp. usually have been recognized as part of the human gingival oral flora; some species, including A. rimae and A. parvulum, have been identified as agents of chronic periodontitis (4,5). A. rimae, formerly known as L. rimae (1), forms short, gram-positive, strictly anaerobic, elliptical bacteria with low G+C content (4). A. rimae produces large amounts of lactic acid and has been recovered previously from normal human gingival flora (4,5). Apart from periodontitis, it has not been implicated in other types of infection. We report an unusual case of A. rimae bacteremia. In May 2007, a 77-year-old woman with a history of right thoracotomy for pneumothorax 2 years earlier was hospitalized for inhalation pneumonia caused by paralysis of the right vocal cord. During hospitalization, septic shock and a fever of 38°C developed in the patient, complicated by acute respiratory failure and stroke. She was transferred to an intensive care unit with a PaO2/FiO2 >300 mm Hg, and a tracheotomy was performed. Three anaerobic blood specimens, drawn at entrance into the intensive care unit, yielded gram-positive cocci after 24-h incubation of the first bottle and gram-positive bacilli after 48-h incubation of the 2 other bottles. The gram-positive cocci were identified as Streptococcus gordonii using API STREP (bioMerieux, Marcy l’Etoile, France). The gram-positive bacilli were catalase negative and oxidase positive but remained unidentified with use of API ANA strip (bioMerieux). Minimum inhibitory concentrations of antibiotics were determined for the gram-positive bacilli using E-test assay (AB BIODISK, Solna, Sweden) on Columbia agar supplemented with 5% sheep blood. Minimum inhibitory concentrations were 0.064 μg/mL for penicillin G, 0.023 μg/mL for ampicillin, 0.012 μg/mL for amoxicillin–clavulanic acid, 0.032 μg/mL for imipenem, 90% ... In this case, phenotypic identification of gram-positive bacillus isolated from 2 blood cultures failed because the definite bacterial species A. rimae was not included in the API database used for the phenotypic identification. Final identification was achieved within 2 days by comparison of the almost complete 16S rDNA sequence with homologous sequences deposited in Genbank. This comparison yielded a 99% sequence similarity, regarded as criteria for accurate identification of bacterial organisms at the species level (8). In this patient, 2 A. rimae isolates were recovered from 2 different blood-culture bottles drawn 48 h apart, suggesting that A. rimae was not just a bypassing organism but indeed responsible for septicemia. In these specimens, S. gordonii was also isolated. Both species have been described as belonging to the oral flora, suggesting that these flora probably were the source for mixed septicemia in the patient. A. rimae was isolated as the patient was presenting with clinical features of septic shock, suggesting that A. rimae may have contributed to the shock. Antimicrobial drug treatment based on in vitro A. rimae susceptibility profile, along with reanimation measures, allowed for the patient’s recovery. This case report illustrates the usefulness of 16S rDNA sequencing for accurate identification of anaerobic organisms and suggests that A. rimae should be added to the list of organisms responsible for bacteremia in patients.

Background Although Sub-Saharan Africa is one of the most important areas in the world to study the complex relationships between the vaginal microbiome and reproductive health outcomes, data are limited. Methods Endocervical samples of 174 female sex workers in Kigali, Rwanda, were analysed cross-sectionally using a phylogenetic microarray specifically designed for the cervicovaginal microbiome. Women with sexually transmitted infections (STI) were purposefully oversampled. Two hundred fifty one probes were used for co-regularised spectral clustering analysis and 123 probes (specific at species or genus level) to describe the vaginal microbiome clusters. Demographic, behavioural, and clinical correlates of the clusters were also determined. Results The prevalence of HIV (36%) and other STIs (bacterial STI 46%, HPV 48%, and HSV-2 78%) in the analysis sample were high by design. Six distinct vaginal microbiome clusters were identified. Two clusters were dominated by Lactobacillus crispatus and L. iners, respectively, and were associated with a Nugent score of 0–3. Three clusters were dominated by Gardnerella vaginalis , Atopobium spp. and Prevotella spp in different compositions, and were associated with a Nugent score of 7–10. The sixth cluster, also dominated by anaerobic bacteria, was not associated with a particular Nugent score category. Women belonging to the L. crispatus cluster were significantly less likely to have bacterial (0% compared to 32–67%) and viral STIs (36% compared to 89–100%) than women in the other 5 clusters. Conclusion In this sample of African sex workers with a high prevalence of HIV and STIs, six vaginal microbiome clusters were identified. Sex workers with a vaginal microbiome dominated by L. crispatus (but not L. iners ) did not have bacterial STIs and were less likely to have viral STIs than women with other microbiome compositions. Longitudinal studies are needed to determine the temporal relationships between the vaginal microbiome and various STIs.

Background The vaginal microbiota can be clustered into six community state types (CSTs): 4 are dominated by Lactobacillus iners, L. crispatus, L. gasseri, L. jensenni , and 2 lack significant numbers of Lactobacillus spp. (termed CST IV-A and IV-B). CST IV-A is characterised by a diverse assemblage of strict anaerobes, while CST IV-B has higher proportions of the genera Atopobium, Gardnerella, among others. We sought to describe the relationship between vaginal microbiota and human papillomavirus (HPV) detection. Methods Thirty-two reproductive-age women self-collected mid-vaginal swabs twice-weekly for 16 weeks (n = 937 samples). Participants reported behaviours on daily diaries. Vaginal bacterial communities were characterised by pyrosequencing of barcoded 16S rRNA genes (V1-V2 region). Each swab was tested for 37 types of HPV DNA using the Roche HPV Linear Array genotyping test. The effects of CSTs on the rate of transition between HPV-negative and HPV-positive states were assessed using continuous-time Markov models. Additive mixed effects logistic regression and additive mixed effects Poisson models were used to model high risk HPV (hrHPV) and count of HPV types, respectively, with normalised menstrual cycle time. Results Participants had an average of 29 (range 25–33) samples tested for HPV, with point prevalence ranging from 58 to 77% and 16-week period prevalence of 84%. CST was significantly associated with changes in HPV status (p L. gasseri -dominated CSTs had the fastest HPV remission rate (HPV-positive to no detection) and CST IV-B had the slowest rate compared to L. crispatus -dominated CSTs (adjusted transition rate ratio (aTRR):7.58, 95% CI: 1.77–32.42 and aTRR:0.31, 95% CI: 0.09–1.05, respectively). Detection of hrHPV and count of different HPV types were highest in the middle of the menstrual cycle. Conclusion Vaginal microbiota dominated by L. gasseri were associated with increased clearance of detectable HPV. A mid-cycle increase in HPV detection suggests a role for sex hormones in modulating latent infection.

Background Gut microbiota have long been thought to contribute to inflammatory disease, and some have considered the bacterial flora as one of the environmental factors causing rhumatoid arthritis (RA). Recently, two gnotobiotic experiments have shown that only one indigenous microflora is critical for the development of arthritis.Wu, et al. have demonstrated that Segmented Filamentous Bacteria induce the differentiation of Th17 cells and cause arthritis in K/BxN mice. Furthermore, Abdollahi-Roodsaz et al. showed the induction of arthritis in IL-1 receptor antagonist-knockout mice by oral administration of Lactobacillus sp. under germ-free condition. In humans, gut microbiota might regulate the host immune systems. Some changes of bacterial flora may cause autoimmune arthritis.On the other hand, new culture-independent genomic analysis techniques of the human microbiome have advanced and make us possible to clarify and quantify in-cultured commensal bacteria. Objectives To explore the differences of fecal microbiota between RA patients and healthy volunteers, employing the newly developed the Yakult Intestinal Flora-SCAN (YIF-SCAN®), based on reverse transcription–quantitative PCR (RT-qPCR) using specific primers that target bacterial rRNA molecules. Methods Fecal samples were collected from 37 RA patients and 59 healthy volunteers in NHO Osaka Minami Medical Center between January and November, 2011. YIF-SCAN® was performed to quantify the bacterial count with 16S or 23S rRNA-targeted group-specific primers. Results Clinical characteristics of both groups are shown in Table 1. There were no statistically significant difference in the bacterial counts and the prevalence of obligate anaerobic bactrerial groups ( Clostridium coccoides group, C. leptum subgroup, Bacteroides fragilis group, Bifidobacterium , Atopobium cluster, Prevotella ) and C. difficile, C. perfringens between RA and healthy volunteers. Interestingly, Table 2 showed that in facultative anaerobic groups, total bacterial population levels of Lactobacillus (especially L. gasseri, L. reuteri, L. plantarum, L. fermentum subgroup ) and Enterococcus were significantly higher in RA. The prevalence of L. reuteri, L. ruminis, L. fermentum subgroup was significantly higher in RA. Conclusions We obviously found the differences of fecal microbiota between RA patients and healthy volunteers. Clinical significance of these observations is still unknown.For further understanding of these results, samples of RA patients who have been treated with biologics for 6 months and attained clinical remission are being re-examined for analysis. References H-J Wu et al., Immunity 32: 815-827, (2010) S. Abdollahi-Roodsaz et al., J Clin Invest 118: 205-216, (2008) J. U. Scher et al., Nat. Rev. Rheumatol. 7: 569-578, (2011) Disclosure of Interest None Declared

Methods Children with eczema at 2 years old (n=26) and their matched (for gender, mode of delivery and feeding in first 6 months) healthy controls (n=26) were selected from the placebo group of a cohort of at-risk infants participating in an randomized double-blind placebo controlled trial on the protective effects of supplemental probiotics (first 6 months) on eczema and allergies. Children with eczema were subclassified into atopic eczema (n=12) and non-atopic eczema (n=14). Molecular evaluation of fecal microbiota were conducted using Fluorescence In Situ Hybridization-Flow Cytometry (FISH-FC) for fecal samples collected at 3 days, 1, 3, and 12 months. Probes were selected to target Eubacterium rectale-Clostridium coccoides group (Erec482), Clostridium leptum subgroup (Clep866 and the corresponding competitor probes), Bacteroides-Prevotella group (Bac303), Bifidobacterium genus (Bif164), Atopobium group (Ato291), LactobacilliEnterococci group (Lab158), Enterobacteriaceae family (Enter1432) and Clostridium perfringens (Cperf191). Linear mixed model was used to evaluate the longitudinal differences (i.e. 4 time points) of bacterial targets while adjusting for gender, mode of delivery, feeding up to 6 months, and allergic rhinitis and wheezing within the eczema group at 2 years of age. Results Longitudinal analyses over four time points showed that higher relative abundance of Enterobacteriaceae [coefficient (B): 1.104, 95% confidence interval (CI):0.175-2.033, adj p=0.022] in children with eczema by 2 years of age. Similar observations were made when eczema group was subanalyzed into non-atopic and atopic eczema, where higher relative abundance of Enterobacteriaceae [B:1.357, 95%CI; 0.382-2.332, adj p=0.008] and [B:1.165, 95%CI; 0.221-2.109, adj p=0.019] were observed respectively as compared to healthy controls. Relative abundance of Clostridium perfringens were also higher when subanalyzed for non-atopic [B:0.572, 95%CI; 0.0009-1.144, adj p=0.050] and atopic eczema [B:0.000451, 95%CI: 0.0001-0.0007, adj p=0.012] compared to healthy controls.

Background The vaginal microbiota of healthy women consists of a wide variety of anaerobic and aerobic bacterial genera and species dominated by the genus Lactobacillus. The activity of lactobacilli helps to maintain the natural healthy balance of the vaginal microbiota. This role is particularly important during pregnancy because vaginal dismicrobism is one of the most important mechanisms for preterm birth and perinatal complications. In the present study, we characterized the impact of a dietary supplementation with the probiotic VSL#3, a mixture of Lactobacillus, Bifidobacterium and Streptococcus strains, on the vaginal microbiota and immunological profiles of healthy women during late pregnancy. Results An association between the oral intake of the probiotic VSL#3 and changes in the composition of the vaginal microbiota of pregnant women was revealed by PCR-DGGE population profiling. Despite no significant changes were found in the amounts of the principal vaginal bacterial populations in women administered with VSL#3, qPCR results suggested a potential role of the probiotic product in counteracting the decrease of Bifidobacterium and the increase of Atopobium, that occurred in control women during late pregnancy. The modulation of the vaginal microbiota was associated with significant changes in some vaginal cytokines. In particular, the decrease of the anti-inflammatory cytokines IL-4 and IL-10 was observed only in control women but not in women supplemented with VSL#3. In addition, the probiotic consumption induced the decrease of the pro-inflammatory chemokine Eotaxin, suggesting a potential anti-inflammatory effect on the vaginal immunity. Conclusion Dietary supplementation with the probiotic VSL#3 during the last trimester of pregnancy was associated to a modulation of the vaginal microbiota and cytokine secretion, with potential implications in preventing preterm birth. Trial registration ClinicalTrials.gov NCT01367470

Background Bacterial vaginosis (BV) is the most common vaginal infection/disorder. BV is characterised by imbalance in the normal vaginal microbiota with a shift towards higher bacterial diversity and increased pH. The aim of the present study was to describe the differences in vaginal microbiota composition in women suffering from BV compared to healthy women, using massive parallel 454 pyrosequencing. Methods 163 vaginal samples were collected from women diagnosed with characteristic BV (n=73), women with intermediate BV (n=11), and from healthy women on their regular check-ups (n=79). DNA from the samples was isolated and the bacterial compositions as well as the relative abundance of these bacteria were analysed using 454 pyrosequencing, with GS Titanium amplicons kit (Roche Inc.), of the hypervariable region V4 on the 16S rRNA gene. Finally, 17 different species-specific PCRs were used to verify the species of bacteria found in the 454 pyrosequencing. Results Extensive imbalance of the vaginal microbiota of women with BV compared to healthy controls was revealed. The dominating taxons of the 73 BV cases were Gardnerella, Atopobium, Prevotella, Lactobacillus, Megasphera and Sneathia, while most of the 79 healthy controls had a microbiota totally dominated by Lactobacillus with the BV associated taxons hardly detectable. Furthermore, the 11 patients with intermediate BV predominantly had a mix of the BV associated taxon Gardnerella as well as Lactobacillus. A few of the healthy controls seemed to have a microbiota changing towards the intermediate microflora. Gardnerella may be the first bacteria to establish in the transition from healthy vaginal flora towards a BV associated flora. Conclusions A clear difference in the composition of the vaginal microbiota between individuals suffering from BV and healthy controls was identified. The present findings are important steps towards the determination of valid potential bacterial markers for BV, are shedding light upon why some women develop BV, as well as show how the microbiota is involved in the development of BV. Knowledge of the composition of the vaginal microbiota is crucial in the development of a BV diagnostic tool and for elucidating appropriate treatment for use in clinical practice.

Background Bacterial vaginosis (BV) is a disturbance of the vaginal microflora. BV can cause discharge complaints and lead to pelvic inflammatory disease, ectopic pregnancy and premature birth. We evaluated a combination of PCR assay's and whole bacterial community analysis with the standard diagnostic algorithm to validate a molecular assay for the determination of BV. Methods 160 women with vaginal discharge complaints were included. 80 women were classified as BV and 80 as non-BV according to Amsel criteria. Gram stains from vaginal smears were made for Nugent scoring. Vaginal swabs were tested with PCR assays for Gardnerella vaginalis , Atopobium vaginae , BV associated bacterium type 2 (BVAB2) and Megaspheara type 1 (MS1). Whole bacterial community analysis was performed by fluorescent Terminal Restriction Fragment Length polymorphism (TRFLP) of 16S-rDNA. TRFLP patterns and predictive fragments of a number of BV associated bacteria were analysed with Bionumerics software (Applied Maths, Belgium). Results Compared to Amsel criteria, the highest sensitivity of 100% was achieved with a duplex PCR for G. vaginalis and/or A vaginae and the highest specificity of 86% was found with a singleplex BVAB2 specific PCR. Best overall performance was shown using a duplex real time PCR for BVAB2 and/or MS1 with a sensitivity of 90% and a specificity of 78% with respect to Amsel criteria. Using Nugent criteria as a standard, this duplex PCR has a sensitivity of 84% and specificity of 86%. From TRFLP results, the presence of predictive fragments of Prevotella, Aerococcus, Megaspheara, Mycoplasma, Peptostreptococcus, Leptotrichia, Eggerthella, Gardnerella, Atopobium and Dialister was most associated with BV positive samples. Cluster analysis of microbial profiles revealed clear differences between BV and non-BV and indicated possible intermediate or transition stages. Conclusions A combination of bacterial species are involved in BV. For molecular diagnostics a duplex PCR of Gardnerella en/of Atopobium can be used for initial screening confirmed by a BVAB2 specific PCR. A more effective alternative is a real time duplex PCR targeting BVAB2 and/or MS1. Microbial profiling supports most targets used in the PCR assays. Cluster analysis of microbial profiles can be used to interpret discordant validation results and possibly for diagnosis.

Coeliac disease (CD) is the most common immune-mediated enteropathy characterized by chronic inflammation of the small intestinal mucosa. The ingestion of gluten is responsible for the symptoms of CD, but other environmental factors are also thought to play a role in this disorder. In this study, the composition of the duodenal microbiota of coeliac children with active disease, symptom-free CD patients on a gluten-free diet and control children was determined. Bacteriological analyses of duodenal biopsy specimens were carried out by fluorescent in situ hybridization coupled with flow cytometry. The proportions of total bacteria and Gram-negative bacteria were significantly higher in CD patients with active disease than in symptom-free CD patients and controls. Bacteroides and Escherichia coli groups were significantly more abundant in CD patients with active disease than in controls, whilst these bacterial deviations were normalized in symptom-free CD patients. The ratio of Lactobacillus–Bifidobacterium to Bacteroides–E. coli was significantly reduced in coeliac patients with either active or inactive disease compared with controls. The differences in Atopobium, Eubacterium rectale–Clostridium coccoides, Clostridium histolyticum, Clostridium lituseburense, sulphate-reducing bacteria and Faecalibacterium prausnitzii populations among the three groups of children were less relevant. Overall, the higher incidence of Gram-negative and potentially pro-inflammatory bacteria in the duodenal microbiota of coeliac children was linked to the symptomatic presentation of the disease and could favour the pathological process of the disorder.

Backgrounds and AimsAPECED is a rare autoimmune disease caused by mutations in the Autoimmune Regulator gene. A significant proportion of patients also have gastrointestinal symptoms, including malabsorption, chronic diarrhea, and obstipation. The pathological background of the gastrointestinal symptoms remains incompletely understood and involves multiple factors, with autoimmunity being the most common underlying cause. Patients with APECED have increased immune responses against gut commensals. Our objective was to evaluate whether the intestinal microbiota composition, predicted functions or fungal abundance differ between Finnish patients with APECED and healthy controls, and whether these associate to the patients’ clinical phenotype and gastrointestinal symptoms.MethodsDNA was isolated from fecal samples from 15 patients with APECED (median age 46.4 years) together with 15 samples from body mass index matched healthy controls. DNA samples were subjected to analysis of the gut microbiota using 16S rRNA gene amplicon sequencing, imputed metagenomics using the PICRUSt2 algorithm, and quantitative PCR for fungi. Extensive correlations of the microbiota with patient characteristics were determined.ResultsAnalysis of gut microbiota indicated that both alpha- and beta-diversity were altered in patients with APECED compared to healthy controls. The fraction of Faecalibacterium was reduced in patients with APECED while that of Atopobium spp. and several gram-negative genera previously implicated in biofilm formation, e.g. Veillonella, Prevotella, Megasphaera and Heamophilus, were increased in parallel to lipopolysaccharide (LPS) synthesis in imputed metagenomics. The differences in gut microbiota were linked to patient characteristics, especially the presence of anti-Saccharomyces cerevisiae antibodies (ASCA) and severity of gastrointestinal symptoms.ConclusionsGut microbiota of patients with APECED is altered and enriched with predominantly gram-negative bacterial taxa that may promote biofilm formation and lead to increased exposure to LPS in the patients. The most pronounced alterations in the microbiota were associated with more severe gastrointestinal symptoms.

Background Bacterial vaginosis (BV) is a common condition that is associated with preterm birth and acquisition of complex communities of vaginal bacteria that include several fastidious species. Treatment of BV in pregnancy has mixed effects on the risk of preterm delivery, which some hypothesize is due to variable antibiotic efficacy for the fastidious bacteria. Both oral and intravaginal metronidazole can be used to treat bacterial vaginosis in pregnancy, but little is known about the impact of different routes of antibiotic administration on concentrations of fastidious vaginal bacteria. Methods This was a sub-study of a larger randomized trial of oral versus vaginal metronidazole for treatment of BV in pregnancy. Fifty-three women were evaluated, including 30 women who received oral metronidazole and 23 who received intravaginal metronidazole. Bacterial taxon-specific quantitative PCR assays were used to measure concentrations of bacterial vaginosis associated bacterium (BVAB) 1, 2, and 3, Gardnerella vaginalis, Atopobium species, Leptotrichia/Sneathia species, Megasphaera species, and Lactobacillus crispatus before and after antibiotic treatment. Results Concentrations of Leptotrichia and Sneathia spp. and the fastidious Clostridia-like bacterium designated BVAB1 decreased significantly with oral (p = .002, p = .02) but not vaginal therapy (p = .141, p = .126). The fastidious bacterium BVAB3 did not significantly decrease with either treatment. Concentrations of Atopobium spp., reportedly resistant to metronidazole in vitro, dropped significantly with oral (p = .002) and vaginal (p = .001) treatment. There was no significant difference in the magnitude of change in bacterial concentrations between oral and vaginal treatment arms for any of the bacterial species. Lactobacillus crispatus concentrations did not change. Conclusion Both oral and vaginal metronidazole therapy in pregnant women result in a significant decrease in concentrations of most BV-associated anaerobic bacteria, with the exception that Leptotrichia, Sneathia and BVAB1 do not significantly decrease with vaginal metronidazole therapy. These data suggest that the route of antibiotic administration has a minor impact on bacterial eradication in pregnant women with BV. Trail Registration This trial is registered with ClinicalTrials.gov, number NCT00153517

Chronic tonsillitis (CT) and tonsillar hypertrophy (TH) are common tonsillar diseases that are related to infection and inflammation. Little is known about tonsillar microbiota and its role in CT and TH. This study aims to identify palatine tonsillar microbiota both on the surface and in the core tissues of CT and TH patients. In total, 22 palatine tonsils were removed and collected from CT and TH patients who underwent surgery. The surface and core microbiota in the tonsils of CT and TH patients were compared using 16S rRNA gene sequencing of V3-V4 regions. Differential tonsillar microbiotas were found in the CT versus TH patients and surface versus core tissues. Further, a higher relative abundance of bacterial genera, including Haemophilus, Streptococcus, Neisseria, Capnocytophaga, Kingella, Moraxella, and Lachnospiraceae [G-2] in patients with TH and Dialister, Parvimonas, Bacteroidales [G-2], Aggregatibacter, and Atopobium in patients with CT, was observed. Of these, the differential genera of Dialister, Parvimonas, and Neisseria served as key factors in the tonsillar microbiota network. Notably, four representable tonsillar microbial types were identified, with one, consisting of a higher abundance of Haemophilus and Neisseria, exclusively detected in the TH patients. This study analyzed the different tonsillar microbiota from the surface and core tissues of CT and TH patients. Several bacteria and various microbial types related to CT and TH were identified, along with potential bacterial networks and related immune pathways.IMPORTANCE The human microbiota has been shown to be functionally connected to infectious and inflammation-related diseases. So far, only limited studies had been performed on tonsillar microbiota, although tonsils play an essential role in the human immune defense system and encountered numerous microorganisms. Our work presented different tonsillar microbiota from surface and core tissues of chronic tonsillitis (CT) and tonsillar hypertrophy (TH) patients. Notably, one tonsillar microbiota type, which contains a higher abundance of Haemophilus and Neisseria, was only detected in the TH patients. Furthermore, certain bacteria, such as Haemophilus, Neisseria, Dialister, and Parvimonas, may serve as microbial biomarkers to discriminate CT patients from TH patients. These data provide important microbiota data in the tonsillar research area and are highly useful for researchers both in the oral microbiome field and clinical field.

Bacterial vaginosis is a synergistic polymicrobial syndrome characterized by depletion of Lactobacillus spp., especially those that produce hydrogen peroxide, and an intense increase in the quantity of commensal vaginal anaerobic bacteria to 100- to 1000-fold above normal levels. While the bacterial spectrum of these organisms has long been known to include Gardnerella vaginalis, Prevotella spp., anaerobic Gram-positive cocci, Mobiluncus spp. and Mycoplasma hominis, innovative use of molecular diagnostics has identified novel species apparently associated with this syndrome, including Atopobium vaginalis. Effecting resolution of bacterial vaginosis is important, in particular for the 8 to 23% of women afflicted with symptomatic disease during their reproductive years. Bacterial vaginosis has been consistently associated with numerous adverse sequelae related to the upper genital tract, including pelvic inflammatory disease and postsurgical infection in the setting of invasive gynecologic procedures, and may increase women's risk of acquiring HIV infection. Pregnant women with bacterial vaginosis experience a higher rate of preterm delivery and low-birth-weight infants. While antibiotics with activity against anaerobes--typically, metronidazole and clindamycin applied vaginally or taken orally--are the mainstays of therapy, bacterial vaginosis frequently recurs. For these reasons, innovative approaches to therapy are urgently required.