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Objectives The hospital environment has been implicated in the enrichment and exchange of pathogens and antibiotic resistance, but its potential in shaping the symbiotic microbial community of hospital staff is unclear. This study was designed to evaluate the alteration of the gut microbiome in medical workers compared to non-medical controls. Methods A prospective cross-sectional cohort study was conducted in the intensive care unit (ICU) and other departments of a centre in north-eastern China. Faecal samples of 175 healthy medical workers—short-term (1–3 months) workers (n = 80) and long-term (>1 year) workers (n = 95)—and 80 healthy non-medical controls were analysed using 16S rRNA amplicon sequencing. The hospital environmental samples (n = 9) were also analysed. Results The gut microbiomes of medical workers exhibited marked deviations in diversity and alteration in microbial composition and function. Short-term workers showed significantly higher abundances of taxa such as Lactobacillus, Butyrivibrio, Clostridiaceae, Clostridium, Ruminococcus, Dialister, Bifidobacterium, Odoribacter, and Desulfovibrio and lower abundances of Bacteroides and Blautia than the controls. Long-term workers showed higher abundances of taxa such as Dialister, Veillonella, Clostridiaceae, Clostridium, Bilophila, Desulfovibrio, Pseudomonas, and Akkermansia and lower abundances of Bacteroides and Coprococcus than the controls. The medical workers' department (ICU versus non-ICU) and position (resident doctor versus nursing staff) also impacted their gut microbiome. Compared with the non-ICU workers, workers in the ICU showed a significant increase in the abundances of Dialister, Enterobacteriaceae, Phascolarctobacterium, Pseudomonas, Veillonella, and Streptococcus and a marked depletion of Faecalibacterium, Blautia, and Coprococcus. In contrast with the nursing staff, the resident doctors showed a significant increase in Erysipelotrichaceae and Clostridium and a decrease in Bacteroides, Blautia, and Ruminococcus in the gut microbiome. Moreover, we found that the microbiota of hospital environments potentially correlated with the workers' gut microbiota. Conclusions Our findings demonstrated structural changes in the gut microbial community of medical workers.

The following specificcharacteristics of the composition of intestinal microbiota in patients with irritable bowel syndrome (IBS) were identified using a metagenomic analysis (16 S rRNA): 1) an increase in the representation of Actinobacteria, including Bifidobacterium spp., Firmicutes, including representatives of Streptococcaceae (Streptococcus), Lachnosperaceae (Dorea), Veillonellaceae (Dialister), Proteobacteria (Enterobacteriaceae and Desulfovibrionaceae families); 2) a decrease in the population of Bacteroidetes, including representatives of the families Prevotellacea (Prevotella spp.), Bacteroidaceae (Bacteroides spp.). Firmicutes belonging to the families Clostridiaceae and Ruminococcaceae (Fecalibacterium spp.). Flow cytometry in the study of the subpopulation composition of T regulatory (Treg) lymphocytes in patients with IBS revealed an increase in the number of CD45R0+CD62L+ central memory cells (CM), which can regulate the processes of maturation and differentiation of lymphocytes in lymphoid tissue. A decrease in the expression of exonucleases CD39 and CD73 was detected, which can have a significant effect on their activity. A reduction in effector memory cells (EM) Treg was observed. Changes in the expression level of exonucleases CD39 and CD73 were inversely correlated with the content of Proteobacteria and the representation of the genera Bifidobacterium spp. and Faecalibacterium spp. The content of СЫ Treg was directly correlated with the content of Dorea spp. The results may be indicative of impairment in the processes of Treg differentiation, which are closely related to changes in key components of intestinal microbiocenosis in IBS.

OBJECTIVE This study systematically aims to evaluate the salivary microbiome in patients with primary Sjogren's syndrome (pSS) using 16S rRNA sequencing approach. METHODS DNA isolation and 16S rRNA sequencing was performed on saliva of 37 pSS and 35 control (CC) samples on HiSeq 2500 platform. 16S rRNA sequence analysis was performed independently using two popular computational pipelines, QIIME and less operational taxonomic units scripts (LoTuS). RESULTS There were no significant changes in the alpha diversity between saliva of patients and controls. However, four genera including Bifidobacterium, Lactobacillus, Dialister and Leptotrichia were found to be differential between the two sets, and common between both QIIME and LoTuS analysis pipelines (Fold change of 2 and p

An obligately anaerobic, Gram-stain-negative, rod or coccobacilli organism was isolated from a faecal sample of a healthy Japanese woman. In the 16S rRNA gene sequence analysis, strain 5BBH33T showed the highest 16S rRNA gene sequence similarity to Dialister succinatiphilus YIT 11850T (95.9 %), Dialister propionicifaciens ADV 1053.03T (94.3 %), Dialister micraerophilus DSM 19965T (93.1 %), Dialister invisus DSM 15470T (92.5 %) and Dialister pneumosintes ATCC 33048T (91.4 %). The hsp60 gene sequence analysis also revealed strain 5BBH33T had relatively low hsp60 gene sequence similarities (74.4–85.3 %) to other Dialister species. Strain 5BBH33T showed 21.8–23.9 % in silico DNA–DNA hybridization values with other Dialister species. In addition, the average nucleotide identity values between strain 5BBH33T and other Dialister species ranged from 68.7–74.2 %, indicating that this strain should be considered as new species based on whole-genome relatedness. Strain 5BBH33T was asaccharolytic and largely unreactive for commercial kit. However, its growth was enhanced by adding 1 % (w/v) succinate to the medium; strain 5BBH33T was able to decarboxylate succinate to propionate. The strain 5BBH33T genome contained the enzymes involved in succinate utilization. These results improve our understanding of succinate-utilizing bacteria. On the basis of the collected data, strain 5BBH33T represents a novel species in the genus Dialister , for which the name Dialister hominis sp. nov. is proposed. The type strain of D. hominis is 5BBH33T (=JCM 33369T=DSM 109768T).

Non-alcoholic fatty liver disease (NAFLD) has been linked to altered gut microbiome, however, evidence from large population-based studies is limited. We compared gut microbiome profiles of 188 male and 233 female NAFLD cases with 571 male and 567 female controls from two longitudinal studies of urban Chinese adults. History of NAFLD was assessed during surveys administered in 2004–2017. Microbiota were assessed using 16S rRNA sequencing of stool samples collected in 2015–2018. Associations of NAFLD with microbiome diversity and composition were evaluated by generalized linear or logistic regression models. Compared with controls, male cases had lower microbial α-diversity, higher abundance of genera Dialister and Streptococcus and Bifidobacterium species, lower abundance of genus Phascolarctobacterium, and lower prevalence of taxa including order RF39 (all p &lt, 0.05). In contrast, female cases had higher α-diversity, higher abundance of genus Butyricimonas and a family of order Clostridiales, lower abundance of Dialister and Bifidobacterium species, and higher prevalence of RF39. Significant NAFLD–sex interactions were found for α-diversity and above taxa (all false discovery rate &lt, 0.1). In conclusion, we observed sex-specific gut microbiome features related to history of NAFLD. Further studies are needed to validate our findings and evaluate the health effects of NAFLD-related gut microbiota.

Here, we aim to understand the condition of the gut microbiome of Filipino adults in relation to their diet and metabolic status. Compared to rural Albay (n = 67), the gut microbiome of subjects living in urban Manila (n = 25) was more colonized by the order Clostridiales, which was negatively correlated with host carbohydrate consumption. Principal component analysis using the genus composition of the 92 total subjects indicated four microbiome types: one type driven by Prevotella, which was associated with high rice consumption and mainly consisted of healthy Albay subjects, one Clostridiales-driven group containing a number of type 2 diabetes mellitus (T2D) subjects from both Manila and Albay who showed lower butyrate levels in association with a decrease in Mediterraneibacter faecis, and the other two types showing dysbiosis-like microbiomes with Lactobacillus and Bifidobacterium overgrowth, with a high ratio of T2D and obese subjects. Multivariate logistic regression analysis suggested high dietary energy intake, and two Veillonellaeae genera, Dialister and Megasphaera, as T2D risk factors, while Prevotella and M. faecis as anti-T2D factors. In conclusion, low-carbohydrate diets restructured the Prevotella-driven gut microbiome, which may predispose Filipino people with high energy diet to T2D.

Modifiable lifestyle interventions may influence dental disease by shifting the composition of the oral microbiota. This study aimed to test whether lifestyle traits are associated with oral microbiota composition and function. Swedish volunteers, aged 16 to 79 years, completed a lifestyle traits questionnaire including lifestyle characteristics and oral health behaviours. Bacterial 16S rDNA amplicons were sequenced and classified into genera and species, using salivary DNA. Microbiota functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and the KO Database of Molecular Functions by ortholog annotation. Tests for association used partial least squares and linear regression analysis with correction for multiple testing. The main analysis included 401 participants and 229 common bacterial species (found in ≥10% of the participants). The overall microbiota composition was strongly associated with questions “do you think caries is a disease?” and “do you use floss or a toothpick?”. Enriched relative abundance of Actinomyces, Campylobacter, Dialister, Fusobacterium, Peptidophaga and Scardovia genera (all p &lt, 0.05 after adjustment for multiple testing), and functional profiles showing enrichment of carbohydrate related functions, were found in participants who answered “no” to these questions. Socio-demographic traits and other oral hygiene behaviours were also associated. Healthier oral microbiota composition and predicted functions are found in those with favourable oral health behaviours. Modifiable risk factors could be prioritized for possible interventions.

This study was aimed to evaluate the differences in the composition of gut microbiota, tryptophan metabolites and short-chain fatty acids in feces between volunteers who frequently ate chicken and who frequently ate pork. Twenty male chicken-eaters and 20 male pork-eaters of 18 and 30 years old were recruited to collect feces samples for analyses of gut microbiota composition, short-chain fatty acids and tryptophan metabolites. Chicken-eaters had more diverse gut microbiota and higher abundance of Prevotella 9, Dialister, Faecalibacterium, Megamonas, and Prevotella 2. However, pork-eaters had higher relative abundance of Bacteroides, Faecalibacterium, Roseburia, Dialister, and Ruminococcus 2. In addition, chicken-eaters had high contents of skatole and indole in feces than pork-eaters, as well as higher contents of total short chain fatty acids, in particular for acetic acid, propionic acid, and branched chain fatty acids. The Spearman’s correlation analysis revealed that the abundance of Prevotella 2 and Prevotella 9 was positively correlated with levels of fecal skatole, indole and short-chain fatty acids. Thus, intake of chicken diet may increase the risk of skatole- and indole-induced diseases by altering gut microbiota.

Gut microbiomes play important functional roles in human health and are also affected by many factors. However, few studies concentrate on gut microbiomes under exercise intervention. Additionally, antibiotic resistance genes (ARGs) carried by gut microbiomes may constantly pose a threat to human health. Here, ARGs and microbiomes of Chinese and Pakistanis participants were investigated using 16S rRNA gene sequencing and high-throughput quantitative PCR techniques. The exercise had no impact on gut microbiomes in the 12 individuals investigated during the observation period, while the different distribution of gut microbiomes was found in distinct nationalities. Overall, the dominant microbial phyla in the participants’ gut were Bacteroidota, Firmicutes and Proteobacteria. Some genera such as Prevotella and Dialister were more abundant in Pakistani participants and some other genera such as Bacteroides and Faecalibacterium were more abundant in Chinese participants. The microbial diversity in Chinese was higher than that in Pakistanis. Furthermore, microbial community structures were also different between Chinese and Pakistanis. For ARGs, the distribution of all detected ARGs is not distinct at each time point. Among these ARGs, floR was distributed differently in Chinese and Pakistani participants, and some ARGs such as tetQ and sul2 are positively correlated with several dominant microbiomes, particularly Bacteroidota and Firmicutes bacteria that did not fluctuate over time.

Background Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease. Results We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacterial and archaeal communities in Hu lambs. Thirty male Hu lambs were randomly assigned to two weaning-age groups: a group weaned at 30 days of age (W30) and a group weaned at 45 days of age (W45), with each group having five replicate pens. On the weaning day (day 30 for W30 and day 45 for W45) and at 5 days postweaning [day 35 for W30 (PW30) and day 50 for W45 (PW45)], one lamb from each replicate was randomly selected and sacrificed. Rumen contents were collected to examine the ruminal microbiota. Compared to W30, PW30 had a decreased relative abundance of Bacteroidetes. At genus level, the extended milk replacer feeding (W45 vs. W30) increased the relative abundance of Ruminococcus while decreased that of Prevotella and Dialister. Compared to W30, PW30 exhibited decreased relative abundances of Prevotella, Dialister and Bacteroides but an increased unclassified Coriobacteriaceae. No significant difference was noted in the detected archaeal taxa among the animals. The function “biosynthesis of secondary metabolites” was less predominant in PW30 than in W30, whereas the opposite held true for “metabolism of cofactors and vitamins.” Some bacterial genera were significantly correlated with rumen volatile fatty acid (VFA) concentration or other animal measures, including negative correlations between ruminal VFA concentration and unclassified Mogibacteriaceae and unclassified Veillonellaceae; positive correlations of ruminal papillae length with Fibrobacter and unclassified Lachnospiraceae, but negative correlations with Mitsuokella and Succiniclasticum; and negative correlations between plasma D-lactate concentration and Prevotella, unclassified Paraprevotellaceae, and Desulfovibrio. Our results revealed that the ruminal bacterial community underwent larger changes over time in lambs weaned at 30 days of age than in lambs weaned half a month later. Thus, extending milk replacer feeding to 45 days weaning was recommended from the perspective of the rumen microbial community in the Hu lamb industry.

The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL])., The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies. IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.

South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.

Object: Primary osteoporosis (PO) is the most common bone disease, which is characterized by decreased bone mass, damage of bone tissue microstructure, increased bone fragility, and is prone to fracture. Gut microbiome may be involved in bone metabolism of PO through gut–brain axis regulation of immune system and endocrine system, however, the specific mechanism is still unclear. The purpose of this study was to characterize the gut microbiome of patients with PO and its possible role in the occurrence and development of the disease.Methods: Fecal samples were collected from 48 PO patients and 48 healthy controls (HC). The composition of gut microbiome community was analyzed by 16s rDNA amplification sequencing, and the difference of gut microbiome composition between PO patients and HC individuals was compared. PICRUSt was also used to predict the biological function of gut microbiome in patients with PO, and to explore its possible role in the occurrence and development of this disease. The classification model is constructed by random forest algorithm so as to screen the key biomarkers.Result: The diversity of gut microorganisms in PO patients was significantly higher than that in HC group (p < 0.05) and there was significant difference in microbial composition in PO group. The abundance of Dialister (0.036 vs. 0.004, p < 0.001) and Faecalibacterium (0.331 vs. 0.132, p < 0.001) were significantly enriched which were the key flora related to PO. Although no significant correlation between bone mineral density and the richness of microbial communities are found, PICRUST results show that there are a wide range of potential pathways between gut microbiome and PO patients, including genetic information processing, metabolism, environmental information processing, cellular processes, human diseases, and organic systems. Notably, the discriminant model based on dominant microflora can effectively distinguish PO from HC (AUC = 93.56).Conclusions: The findings show that PO is related to the change of gut microbiome, especially the enriched Dialister and Faecalibacterium genera, which give new clues to understand the disease and provide markers for the diagnosis and new strategies for intervention treatment of the disease.

Background To date, the microbiota of the human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces penile anaerobic bacteria, that greater abundance of penile anaerobic bacteria is correlated with increased cytokine levels and greater risk of HIV infection, and that the penile microbiota is an important harbour for BV-associated bacteria. While circumcision has been shown to significantly reduce the risk of acquiring human papillomavirus (HPV) infection, the relationship of the penile microbiota with HPV is still unknown. In this study, we examined the penile microbiota of HPV-infected men as well as the impact of HIV status. Results The penile skin microbiota of 238 men from Cape Town (South Africa) were profiled using Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Corynebacterium and Prevotella were found to be the most abundant genera. Six distinct community state types (CSTs) were identified. CST-1, dominated by Corynebacterium, corresponded to less infections with high-risk HPV (HR-HPV) relative to CSTs 2–6. Men in CST-5 had greater relative abundances of Prevotella, Clostridiales, and Porphyromonas and a lower relative abundance of Corynebacterium. Moreover, they were significantly more likely to have HPV or HR-HPV infections than men in CST-1. Using a machine learning approach, we identified greater relative abundances of the anaerobic BV-associated bacteria (Prevotella, Peptinophilus, and Dialister) and lower relative abundance of Corynebacterium in HR-HPV-infected men compared to HR-HPV-uninfected men. No association was observed between HIV and CST, although the penile microbiota of HIV-infected men had greater relative abundances of Staphylococcus compared to HIV-uninfected men. Conclusions We found significant differences in the penile microbiota composition of men with and without HPV and HIV infections. HIV and HR-HPV infections were strongly associated with greater relative abundances of Staphylococcus and BV-associated bacterial taxa (notably Prevotella, Peptinophilus and Dialister), respectively. It is possible that these taxa could increase susceptibility to HIV and HR-HPV acquisition, in addition to creating conditions in which infections persist. Further longitudinal studies are required to establish causal relationships and to determine the extent of the effect.

Dysbiosis of gut microbiota during the progression of HBV-related liver disease is not well understood, as there are very few reports that discuss the featured bacterial taxa in different stages. The aim of this study was to reveal the featured bacterial species whose abundances are directly associated with HBV disease progression, that is, progression from healthy subjects to, chronic HBV infection, chronic hepatitis B to liver cirrhosis. Approximately 400 fecal samples were collected, and 97 samples were subjected to 16S rRNA gene sequencing after age and BMI matching. Compared with the healthy individuals, significant gut microbiota alterations were associated with the progression of liver disease. LEfSe results showed that the HBV infected patients had higher Fusobacteria, Veillonella, and Haemophilus abundance while the healthy individuals had higher levels of Prevotella and Phascolarctobacterium. Indicator analysis revealed that 57 OTUs changed as the disease progressed, and their combination produced an AUC value of 90% (95% CI: 86–94%) between the LC and non-LC groups. In addition, the abundances of OTU51 (Dialister succinatiphilus) and OTU50 (Alistipes onderdonkii) decreased as the disease progressed, and these results were further verified by qPCR. The LC patients had the higher bacterial network complexity, which was accompanied with a lower abundance of potential beneficial bacterial taxa, such as Dialister and Alistipes, while they had a higher abundance of pathogenic species within Actinobacteria. The compositional and network changes in the gut microbiota in varied CHB stages, suggest the potential contributions of gut microbiota in CHB disease progression.

Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual. Keywords: Culturomics, Dialister massiliensis sp. nov., Firmicutes, gut microbiota, taxonogenomics

It has been largely accepted that dietary changes have an effect on gut microbial composition. In this pilot study we hypothesised that Ramadan fasting, which can be considered as a type of time-restricted feeding may lead to changes in gut microbial composition and diversity. A total of 9 adult subjects were included in the study. Stool samples were collected before (baseline) and at the end of the Ramadan fasting (after 29 days). Following the construction of an 16S rRNA amplicon library, the V4 region was sequenced using the Illumina Miseq platform. Microbial community analysis was performed using the QIIME program. A total of 27,521 operational taxonomic units (OTUs) with a 97% similarity were determined in all of the samples. Microbial richness was significantly increased after Ramadan according to observed OTU results (P=0.016). No significant difference was found in terms of Shannon index or phylogenetic diversity metrics of alpha diversity. Microbial community structure was significantly different between baseline and after Ramadan samples according to unweighted UniFrac analysis (P=0.025). LEfSe analysis revealed that Butyricicoccus, Bacteroides, Faecalibacterium, Roseburia, Allobaculum, Eubacterium, Dialister and Erysipelotrichi were significantly enriched genera after the end of Ramadan fasting. According to random forest analysis, the bacterial species most affected by the Ramadan fasting was Butyricicoccus pullicaecorum. Despite this is a pilot study with a limited sample size; our results clearly revealed that Ramadan fasting, which represents an intermittent fasting regime, leads to compositional changes in the gut microbiota.

Individual bacteria and shifts in microbiome composition are associated with human disease, including cancer. To unravel the connections underlying oral bacterial dysbiosis and oral squamous cell carcinoma (OSCC), cancer lesion samples and anatomically matched normal samples were obtained from the same patients. We then profiled the bacteria within OSCC lesion surface samples at the species level using next-generation sequencing to comprehensively investigate bacterial community composition and functional genes in these samples. Significantly greater bacterial diversity was observed in the cancer samples than in the normal samples. Compared with previous studies, we identified many more taxa demonstrating remarkably different distributions between the groups. In particular, a group of periodontitis-correlated taxa, including Fusobacterium, Dialister, Peptostreptococcus, Filifactor, Peptococcus, Catonella and Parvimonas, was significantly enriched in OSCC samples. Additionally, several operational taxonomic units (OTUs) associated with Fusobacterium were highly involved in OSCC and demonstrated good diagnostic power. Our study revealed drastic changes in surface bacterial communities of OSCC. The findings enrich knowledge of the association between oral bacterial communities and oral cancer.

Aims and Objectives: The oral microbial flora is highly complex and diverse with obligate anaerobic bacteria as the predominant component. Most of these are not yet cultivated/difficult to cultivate due to technical limitations. In this study, we aim to detect two novel oral bacterial species Dialister invisus and Olsenella uli by simplified and economical procedure of polymerase chain reaction (PCR) and study their association with primary and persistent endodontic infections. Material and Methods: The study involved 60 patients that included 30 patients of primary endodontic infections and 30 with persistent endodontic infections. The sample collection from the root canal was performed by universally accepted protocol by using sterile paper points. The deoxyribonucleic acid (DNA) extraction was done, followed by PCR with species specific primers. We made several changes to the protocol mentioned by original authors. We adopted a one-step protocol for amplification of bacterial DNA, omitting the 16SrDNA amplification step with universal primers. Results: It was seen that 7 (23.3 %) samples in primary endodontic infection group and 24 (80 %) samples in persistent endodontic infection group were positive for D. invisus. On the other hand, 11 (36.6 %) patients of primary endodontic infection showed positivity for O. uli in comparison to 9 (30 %) of persistent endodontic infection. Conclusion: The results from the present study showed efficient amplification of both O. uli and D. invisus in a single-step PCR. Hence, we conclude that the modified protocol used here with taq polymerase enzyme offers a faster and cheaper alternative to nested PCR without compromising the quality of amplification process.

Background: Microbial involvement in ankylosing spondylitis (AS) has been suggested; however, the relationship between gut microbiome and the disease phenotypes of AS remains to be established. This study was to characterize and investigate differences in the gut microbiome between AS patients and healthy controls (HCs), and to determine whether the gut microbiome profile associated with the disease phenotypes. Methods: 16S rRNA gene V4 region sequencing was performed on fecal DNA isolated from stool samples collected from 41 patients with AS [20 axial AS (axAS) and 21 peripheral AS (pAS)] and 19 HCs. QIIME based pipeline was used to process the raw sequence data. Alpha and beta diversities were assessed using QIIME, and comparisons of gut microbiome profile were performed using linear discriminant analysis (LDA) effect size (LEfSe) to examine differences between groups and subgroups. A gut microbiota-based model for predictive diagnosis of AS was constructed using random forest algorithm and its predictive value was assessed by receiver-operating characteristic analyses. Results: Our results showed that fecal microbial communities in patients with AS differ significantly from those in HCs, driven by a higher abundance of 7 genera ( Prevotella_9, Dialister, Comamonas, Collinsella, Streptococcus, Alloprevotella and Prevotella_2 ) and a lower abundance of 4 genera ( Eubacterium_ruminantium_ group, Ruminococcus_gnavus_group, Lachnospira and Bacteroides ). In addition, pAS patients were more enriched in Comamonas, Streptococcus and Collinsella, while axAS patients were more enriched in Prevotella_2 . An 8 genera-based model showed high accuracy for distinguishing AS patients from HCs with an area under the curve (AUC) up to 0.950. Conclusions: Our results revealed specific alterations in the gut microbiome in patients with different phenotypes of AS, and the classification model based on gut microbial features might provide a new direction for future clinical diagnosis. Lastly, discovery of the associated microbes of AS in the gut microbiome may help us to seek more treatments for this disease.

The relationship between gut microbial metabolism and mental health is one of the most intriguing and controversial topics in microbiome research. Bidirectional microbiota-gut-brain communication has mostly been explored in animal models, with human research lagging behind. Large-scale metagenomics studies could facilitate the translational process, but their interpretation is hampered by a lack of dedicated reference databases and tools to study the microbial neuroactive potential. Surveying a large microbiome population cohort (Flemish Gut Flora Project, n =1,054) with validation in independent data sets (n(total) =1,070), we studied how microbiome features correlate with host quality of life and depression. Butyrate-producing Faecalibacterium and Coprococcus bacteria were consistently associated with higher quality of life indicators. Together with Dialister, Coprococcus spp. were also depleted in depression, even after correcting for the confounding effects of antidepressants. Using a module-based analytical framework, we assembled a catalogue of neuroactive potential of sequenced gut prokaryotes. Gut-brain module analysis of faecal metagenomes identified the microbial synthesis potential of the dopamine metabolite 3,4-dihydroxyphenylacetic acid as correlating positively with mental quality of life and indicated a potential role of microbial gamma-aminobutyric acid production in depression. Our results provide population-scale evidence for microbiome links to mental health, while emphasizing confounder importance.

The high prevalence and serious long-term sequelae of Trichomonas vaginalis (TV) infection worldwide is of a particular concern; however, data regarding the differences in the composition of the vaginal microbiome in cases of single TV infection or mixed infections (i.e., presence of TV and bacterial vaginosis) are scarce. We employed metagenomic sequencing analyses to study gene expression in the vaginal microbiota of women with single TV infection and mixed infection. Women infected with only TV had significantly higher abundance of Mycoplasma, Prevotella, and Streptococcus compared to women without vaginal infection (control). Women infected with mixed infections had a significantly higher abundance of Mycoplasma, Prevotella, Streptococcus, Anaerococcus, Dialister, Peptostreptococcus, Peptoniphilus and a significantly lower abundance of Lactobacillus than TV alone. Mixed infections had a significantly higher abundance of Prevotella, Anaerococcus and Dialister. Our findings suggest that the bacterial community composition varies among healthy women, women with TV alone, and those with mixed infection, and we hypothesize that these bacterial vaginosis (BV)-associated bacterium may play a role in the pathogenesis and recurrence of TV. Probiotic pessaries may necessarily be the answer because shifting the vaginal microbiome and host responses is probably a complex undertaking.

Aim: To evaluate changes in the resident microbial population in the cranial vaginal mucosa induced by a progesterone‐releasing intravaginal device (PRID) compared to the vaginal microbiota of cows with reproductive disorders. Methods and Results: Vaginal discharge was evaluated by clinical examination and a Vaginitis Diagnosis Score was performed by exfoliative cytology. All samples classified as positive and some classified as negative by clinical evaluation were later diagnosed as positive for vaginitis by cytological analysis. Bacterial diversity profiles were performed by PCR‐DGGE and clustered according to the reproductive health status of the specimens, revealing a correspondence between the structures of the communities in the vagina and the clinical profile. Representative bands from each group were sequenced and identified as Ruminococcus sp., Dialister sp., Escherichia sp./Shigella sp., Virgibacillus sp., Campylobacter sp., Helcoccoccus sp., Staphylococcus sp., Bacillus sp., Actinopolymorpha sp., Exiguobacterium sp., Haemophilus sp./Histophilus sp., Aeribacillus sp., Porphyromonas sp., Lactobacillus sp. and Clostridium sp. Conclusion: Our results contribute to the knowledge of the vaginal microbiome in synchronized heifers showing positive or negative clinical vaginitis. Significance and Impact of the Study: This study contributes to the understanding of a dynamic vaginal colonization by bacterial consortiums during the synchronization with a widely used PRID protocol. Also, the results reveal the presence of well‐known metritis‐related pathogens as well as emerging uterine opportunistic pathogens. The provided information will allow to carry out further studies to elucidate functional roles of these native micro‐organisms in the bovine reproductive tract. Fil: Gonzalez Moreno, Candelaria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Agronomía y Zootecnia; Argentina Fil: Fontana, Cecilia Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Investigaciones Biológicas. Universidad Nacional de Tucumán. Instituto Superior de Investigaciones Biológicas; Argentina. Università Cattolica del Sacro Cuore; Italia Fil: Cocconcelli, P. S.. Università Cattolica del Sacro Cuore; Italia Fil: Callegari, M. L.. Università Cattolica del Sacro Cuore; Italia Fil: Otero, María Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Investigaciones Biológicas. Universidad Nacional de Tucumán. Instituto Superior de Investigaciones Biológicas; Argentina

Background Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P = 0.008). Principal coordinate analysis (PCoA) and Nonmetric multidimensional scaling (NMDS) revealed significant differences in gut microbial community structure between the normal weight group and the obese group. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that fifty-five species of bacteria were abundant in the fecal samples of the normal weight group and forty-five species of bacteria were abundant in the obese group. In regard to phyla, the gut microbiota in the obese group had lower proportions of Bacteroidetes (51.35%) compared to the normal weight group (55.48%) (P = 0.030). There was no statistical difference in Firmicutes between the two groups (P = 0.436), and the Firmicutes/Bacteroidetes between the two groups had no statistical difference (P = 0.983). At the genus level, Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Haemophilus were significantly more abundant in the obese group than in the normal weight group (P = 0.048, P = 0.018, P < 0.001, P = 0.040, and P = 0.003, respectively). The fecal microbiota of children in the obese group had lower proportions of Oscillospira and Dialister compared to the normal weight group (P = 0.002 and P = 0.002, respectively). Conclusions Our results showed a decrease in gut microbiota abundance and diversity as the BMI increased. Variations in the bacterial community structure were associated with obesity. Gut microbiota dysbiosis might play a crucial part in the development of obesity in Chinese children.

ObjectiveMethodsThis study aimed to examine the intestinal microbiota composition of school-aged children in association with (over)weight.The fecal microbiota composition of 295 children was analyzed using the Human Intestinal Tract Chip. Anthropometric outcomes (overweight [BMI85th percentile], age- and sex-standardized BMI and weight z scores) were measured at 6 to 7 years of age, and elastic net was used to select genus-like bacterial groups related to all anthropometric outcomes. Subsequently, multiple linear and logistic regression models were used to model associations between selected bacterial groups and anthropometric measures while controlling for confounders.ResultsConclusionsPrevotella melaninogenica, Prevotella oralis, Dialister, and uncultured Clostridiales II (UCII) accounted for 26.1% of the variation in microbiota composition. Several bacterial groups were inversely associated with the anthropometric outcomes: Sutterella wadsworthensis, Marvinbryantia formatexigens, Prevotella melanogenica, P oralis, Burkholderia, uncultured Clostridiales II, and Akkermansia, while Streptococcus bovis was positively associated with overweight. Microbial diversity and richness, and Bacteroidetes to Firmicutes ratio, were not significantly associated with any of the outcomes.In the largest population-based study on childhood gut microbiota and body weight so far, both new and previously identified bacterial groups were found to be associated with overweight. Further research should elucidate their role in energy metabolism.

Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium,Escherichia,Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program.

Intra-oral halitosis (IOH) is an unpleasant odor emanating from the oral cavity. It is thought that the microbiota of the dorsal tongue coating plays a crucial role in this condition. The aim of the study was to investigate the composition of the tongue microbiome in subjects with and without IOH. A total of 26 subjects, 16 IOH patients and 10 healthy subjects were recruited based on their organoleptic score and volatile sulfur compound (VSC) measurements. The composition of the tongue microbiome was studied using the 16s amplicon sequencing of the V3-V4 hyper variable region with an Illumina MiSeq. The sequenced data were analyzed using QIIME, and the sequences obtained were distributed across 7 phyla, 27 genera and 825 operational taxonomic units (OTUs). At a higher taxon level, TM7 was associated with IOH patients whereas Gemellaceae was significantly abundant in the healthy subjects. At OTU level, we found several significant OTUs that differentiated the IOH patients from the controls. These included Aggregatibacter (OTUid 4335776), Aggregatibacter segnis (A. segnis), Campylobacter, Capnocytophaga, Clostridiales, Dialister, Leptotrichia, Parvimonas, Peptostreptococcus, Peptococcus, Prevotella, Selenomonas, SR1, Tannerella, TM7-3 and Treponema in the IOH group. In the control group, Aggregatibacter (OTUid 4363066), Haemophilus, Haemophilus parainfluenza (H. parainfluenza), Moryella, Oribacterium, Prevotella, several Streptococcus, Rothia dentocariosa (R. dentocariosa) and OTU from Gemellaceae were significantly abundant. Based on our observation, it was concluded that the bacterial qualitative composition of the IOH and the control group was almost the same, except for the few above-mentioned bacterial species and genera.

The gut microbiota has a crucial effect on human health and physiology. Hypothyroid Hashimoto's thyroiditis (HT) is an autoimmune disorder manifested with environmental and genetic factors. However, it is hypothesized that intestinal microbes might play a vital role in the pathogenesis of HT. The aim of current was to investigate and characterize the gut microbial composition of HT patients both quantitatively and qualitatively. The fecal samples from 29 HT patients and 12 healthy individuals were collected. The PCR-DGGE targeted V3 site of 16S rRNA gene and real time PCR for Bifidobacterium Lactobacillus, Bacteroides vulgatus and Clostridium leptum were performed. Pyrosequencing of 16S rRNA gene with V4 location was performed on 20 randomly selected samples. The comparative analysis of diversity and richness indices revealed diversification of gut microbiota in HT as compared to control. The statistical data elucidate the alterations in phyla of HT patients which was also affirmed at the family level. We observed the declined abundance of Prevotella_9 and Dialister, while elevated genera of the diseased group included Escherichia-Shigella and Parasutterella. The alteration in gut microbial configuration was also monitored at the species level, which showed an increased abundance of E. coli in HT. Therefore, the current study is in agreement with the hypothesis that HT patients have intestinal microbial dysbiosis. The taxa statistics at species-level along with each gut microbial community were modified in HT. Thus, the current study may offer the new insights into the treatment of HT patients, disease pathway, and mechanism.

Aim This study was aimed at detecting, identifying, quantifying and comparing the bacteria present in the placental tissues of women with pre-eclampsia with that of normotensive pregnant women. Material and Methods Placental tissue samples were collected from 55 primiparous women with pre-eclampsia (cases) and 55 matched primiparous normotensive pregnant women (controls) at the time of delivery by cesarean section. Genotyping was carried out in two stages. First the samples were screened for the presence of bacteria by polymerase chain reaction (PCR) for the 16S rRNA gene. Next, the samples that were PCR-positive for the 16S rRNA gene were screened by next-generation sequencing on an Illumina MiSeq platform. Results Seven (12.7%) placental tissue samples from women with pre-eclampsia were PCR-positive. All the placental samples from control women were negative (P = 0.006). The complete microbiome of the seven samples was revealed through next-generation sequencing. The organisms that were present included Bacillus cereus, Listeria, Salmonella, Escherichia (all of which are usually associated with gastrointestinal infection); Klebsiella pneumonia and Anoxybacillus (both of which are usually associated with respiratory tract infections); and Variovorax, Prevotella, Porphyromonas, and Dialister (all of which are usually associated with periodontitis). Conclusions This study confirms the presence of bacteria in the placental tissues of a subset of women with pre-eclampsia and supports the role of bacteria in the multifactorial cause of pre-eclampsia.

This study examined the fecal bacterial diversity of 15-week-old pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Pyogenic liver abscess (PLA) is a severe disease with considerable mortality and is often polymicrobial. Understanding the pathogens that cause PLA is the basis for PLA treatment. Here, we profiled the bacterial composition in PLA fluid by pyrosequencing the 16S ribosomal RNA (rRNA) gene based on next-generation sequencing (NGS) technology to identify etiological agents of PLA and to provide information of their 16S rRNA sequences for application to DNA-based techniques in the hospital. Twenty patients with PLA who underwent percutaneous catheter drainage, abscess culture, and blood culture for isolates were included. Genomic DNAs from abscess fluids were subjected to polymerase chain reaction and pyrosequencing of the 16S rRNA gene with a 454 GS Junior System. The abscess and blood cultures were positive in nine (45%) and four (20%) patients, respectively. Pyrosequencing of 16S rRNA gene showed that 90% of the PLA fluid samples contained single or multiple genera of known bacteria such as Klebsiella, Fusobacterium, Streptococcus, Bacteroides, Prevotella, Peptostreptococcus, unassigned Enterobacteriaceae, and Dialister. Klebsiella was predominantly found in the PLA fluid samples. All samples that carried unassigned bacteria had 26.8% reads on average. We demonstrated that the occurrence of PLA was associated with eight known bacterial genera as well as unassigned bacteria and that 16S rRNA gene sequencing was more useful than conventional culture methods for accurate identification of bacterial pathogens from PLA.

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

Background Systemic lupus erythematosus (SLE) in patients from Spain is associated with intestinal dysbiosis. This study explores whether the alteration of the gut microbiome in SLE patients from China is consistent with the intestinal dysbiosis of SLE patients from Spain. Results The depletion of Firmicutes and the enrichment of Bacteroidetes in SLE patients from China were consistent with the SLE patients from Spain. Furthermore, we found that nine genera of gut microbiota were SLE-related microorganisms in Chinese subjects. Genera Rhodococcus, Eggerthella, Klebsiella, Prevotella, Eubacterium, Flavonifractor and Incertae sedis were significantly enriched, while genera Dialister and Pseudobutyrivibrio were significantly depleted in SLE patients. Receiver operating characteristic analysis indicated that the nine genera have the potential to distinguish SLE patients from healthy controls. Conclusions Comparing the dysbiosis of the gut microbiome among SLE patients from China or Spain, may indicate that the gut microbiome profiles of SLE patients are more influenced by disease than ethnicity.

// Rafael Guerrero-Preston 1, 2 , Filipa Godoy-Vitorino 3 , Anne Jedlicka 4 , Arnold Rodriguez-Hilario 3 , Herminio Gonzalez 3 , Jessica Bondy 1 , Fahcina Lawson 1 , Oluwasina Folawiyo 1 , Christina Michailidi 1 , Amanda Dziedzic 4 , Rajagowthamee Thangavel 5 , Tal Hadar 1 , Maartje G. Noordhuis 1, 6 , William Westra 7 , Wayne Koch 1 , David Sidransky 1 1 Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA 2 Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico 3 Natural Sciences Department, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico 4 Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA 5 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA 6 Department of Otorhinolaryngology-Head and Neck Surgery, University of Groningen, University Medical Center, Groningen, The Netherlands 7 Department of Pathology-Surgical Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA Correspondence to: Rafael Guerrero-Preston, email: rguerre3@jhmi.edu David Sidransky, email: dsidrans@jhmi.edu Keywords: microbiome, 16s rRNA, oral cancer, oropharyngeal cancer, human papilloma virus (HPV) Received: February 23, 2016 Accepted: May 16, 2016 Published: May 30, 2016 ABSTRACT Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection. The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella , with lower numbers of Citrobacter and Neisseraceae genus Kingella . HNSCC patients had a significant loss in richness and diversity of microbiota species (p

Human intestinal flora comprises thousands of bacterial species. Growth and composition of intestinal microbiota is dependent on various parameters, including immune mechanisms, dietary factors and intestinal motility. Patients with spinal cord injury (SCI) frequently display neurogenic bowel dysfunction due to the absence of central nervous system control over the gastrointestinal system. Considering the bowel dysfunction and altered colonic transit time in patients with SCI, we hypothesized the presence of a significant change in the composition of their gut microbiome. The objective of this study was to characterize the gut microbiota in adult SCI patients with different types of bowel dysfunction. We tested our hypothesis on 30 SCI patients (15 upper motor neuron [UMN] bowel syndrome, 15 lower motor neuron [LMN] bowel syndrome) and 10 healthy controls using the 16S rRNA sequencing. Gut microbial patterns were sampled from feces. Independent of study groups, gut microbiota of the participants were dominated by Blautia, Bifidobacterium, Faecalibacterium and Ruminococcus. When we compared all study groups, Roseburia, Pseudobutyrivibrio, Dialister, Marvinbryantia and Megamonas appeared as the genera that were statistically different between groups. In comparison to the healthy group, total bacterial counts of Pseudobutyrivibrio, Dialister and Megamonas genera were significantly lower in UMN bowel dysfunction group. The total bacterial count of Marvinbryantia genus was significantly lower in UMN bowel dysfunction group when compared to the LMN group. Total bacterial counts of Roseburia, Pseudobutyrivibrio and Megamonas genera were significantly lower in LMN bowel dysfunction group when compared to healthy groups. Our results demonstrate for the first time that butyrate-producing members are specifically reduced in SCI patients when compared to healthy subjects. The results of this study would be of interest since to our knowledge, microbiome-associated studies targeting SCI patients are non-existent and the results might help explain possible implications of gut microbiome in SCI. Copyright © 2016 Gungor et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Seventy-four strains representing the four species of the genusDialisterwere isolated from various clinical samples.Dialister pneumosintesandDialister micraerophiluswere the two mainly encountered species. Fifty-five isolates were tested against 14 antimicrobial agents. Decreased susceptibilities to piperacillin, metronidazole, macrolides, fluoroquinolones, and rifampin were demonstrated. The clinical impact of these decreased susceptibilities remains to be investigated but should prompt microbiologists to perform antimicrobial susceptibility testing for clinically importantDialisterspp.

INTRODUCTION: This study was conducted to evaluate the microbiomes of endodontic- periodontal lesions (EPL) before and after chemomechanical preparation (CMP). METHODS: Clinical samples were taken from 15 root canals (RC) with necrotic pulp tissues and from their associated periodontal pockets (PP, n=15) of teeth with EPL before and after CMP. The Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) protocol and viable culture were used to analyze samples from RC and PP. The Mann-Whitney test and Benjamini-Hochberg corrections were performed to correlate the clinical and radiographic findings with microbial findings (p

Although gut microbiota has been studied relatively extensively in the context of allergic diseases, there have been several contradictions between these studies. By applying high-throughput sequencing, we aimed to analyze the differences in gut microbiota between atopic and healthy children at 5 and 12 years of age. 51 stool samples were collected from 14 atopic and 15 healthy children and analyzed with 454 pyrosequencing of the 16S rRNA gene. At the ages of 5 and 12 years, Bacteroides, Prevotella, and Dialister dominated gut microbiota in both atopic and healthy groups of children. Children in the atopic group had lower abundance and prevalence of Akkermansia in gut microbiota than their healthy counterparts. Thus, the composition of gut microbiota does not seem to be significantly different between atopic and healthy children, but lower abundance and prevalence of Akkermansia indicate that this bacterium may accompany or play a role in IgE-mediated atopic diseases.

Background: Bacterial Vaginosis (BV) is the common vaginal infection in women and it has been linked to enhanced risks for pre-term birth, pelvic inflammatory disease and sexually transmitted diseases. BV is caused by a disorder of vaginal microbiota which changes from the normal lactobacillus dominated community to a more diverse community of non-lactobacillus bacteria. Several previous reports analyzed the overall vaginal microbial communities of volunteers from limited sampling area and they suggested a possible link between the vaginal microbial contents and the ethnicity of women. Here, we analyzed the diversity of vaginal microbiota in 10 subjects associated with BV (BV+) and 10 subjects without BV (BV-) from the metropolitan area of Herbing in Northern China using full-length 16S rDNA. Results: The vaginal bacterial communities detected in subjects with BV were much more taxon rich and diverse than those without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per 10 subjects with BV was nearly three times greater than 10 subjects without BV by 29.4 ± 9.3 versus 11.7 ± 7.8 (Mean ±SD). Our data confirmed that there is a shift in the abundance of bacterial species present in the vaginal environment when BV and non-BV groups were compared. 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 BV- samples. Several bacteria have been found to be associated with BV, including Gardnerella, Atopobium, Peptoniphilus, Leptotrichia/Sneathia, Prevotella, Parvimonas and Dialister, Based on result of classification, four possible novel phylotype microorganisms were found. Conclusions: The data presented here on the composition and richness of the vaginal microbial ecosystem in BV and health state will provide the depth insight in the etiology of BV.

Members of the Dialister genus are asaccharolytic obligately anaerobic gram-negative coccobacilli that are culture-difficult or remain uncultivated. Their participation in endodontic infections has been only consistently demonstrated after advent of molecular biology approaches. This study was undertaken to characterize Dialister species in samples from primary endodontic infections using a devised 16S rRNA gene-based group-specific heminested PCR assay followed by sequencing of PCR products. Genomic DNA was isolated directly from clinical samples and used as template for PCR. Amplicons from positive specimens were sequenced and phylogenetically analyzed to determine species identity. Ten of 21 clinical samples yielded sequences with the highest percent similarities to oral Dialister species/phylotypes. Seven sequences were from Dialister invisus, and the other three sequences belonged to Dialister pneumosintes, Dialister oral clone BS095 and Dialister sp. clone IS013B24. Findings demonstrated that different Dialister species can take part in the microbiota associated with apical periodontitis lesions.

The primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. Our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-cultivated species of the oral cavity. Tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjects with halitosis, defined as an organoleptic score of 2 or more and volatile sulfur compound levels greater than 200 ppb. 16S rRNA genes from DNA isolated from tongue dorsum scrapings were amplified by PCR with universally conserved bacterial primers and cloned into Escherichia coli . Typically, 50 to 100 clones were analyzed from each subject. Fifty-one strains isolated from the tongue dorsa of healthy subjects were also analyzed. Partial sequences of approximately 500 bases of cloned inserts from the 16S rRNA genes of isolates were compared with sequences of known species or phylotypes to determine species identity or closest relatives. Nearly complete sequences of about 1,500 bases were obtained for potentially novel species or phylotypes. In an analysis of approximately 750 clones, 92 different bacterial species were identified. About half of the clones were identified as phylotypes, of which 29 were novel to the tongue microbiota. Fifty-one of the 92 species or phylotypes were detected in more than one subject. Those species most associated with healthy subjects were Streptococcus salivarius , Rothia mucilaginosa , and an uncharacterized species of Eubacterium (strain FTB41). Streptococcus salivarius was the predominant species in healthy subjects, as it represented 12 to 40% of the total clones analyzed from each healthy subject. Overall, the predominant microbiota on the tongue dorsa of healthy subjects was different from that on the tongue dorsa of subjects with halitosis. Those species most associated with halitosis were Atopobium parvulum , a phylotype (clone BS095) of Dialister , Eubacterium sulci , a phylotype (clone DR034) of the uncultivated phylum TM7, Solobacterium moorei , and a phylotype (clone BW009) of Streptococcus . On the basis of our ongoing efforts to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species that colonize the oral cavity, there are now over 600 species.

Cultural studies have indicated that a subset of the oral microflora is responsible for endodontic infections. Approximately 50% of oral bacteria are unculturable, so it is likely that currently unknown bacteria are present in such infections. In this study, cultural and molecular analyses were performed on the microflora in aspirate samples collected from 5 infected root canals. 16S rDNA sequences from 261 isolates and 624 clones were identified by comparison with database sequences. Sixty-five taxa were identified, of which 26 were found by the molecular method alone. A mean of 20.2 taxa was found in each sample. A new species of Dialister was the only organism present in all 5 samples. Twenty-seven novel taxa were detected, 18 of which belonged to the phylum Firmicutes and 8 to Bacteroidetes. Culture-independent, molecular analysis has revealed a more diverse microflora associated with endodontic infections than that revealed by cultural methods alone.

An animal feeding trial was conducted on 18 seven‐day‐old Holstein dairy bull calves weighing 42 ± 3 kg each. Calves were randomly assigned into three groups (n = 6 each). The dietary treatments were as follows: (1) milk and starter for the control group (MS), (2) supplementation of oat hay from week 2 on the basis of milk and starter (MSO2), and (3) supplementation of oat hay from week 6 on the basis of milk and starter (MSO6). All animals were fed starter and oat hay ad libitum. The major phyla in the different groups of rumen fluid included Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Euryarchaeota. The major genera were identified, and major genera proportions in the three groups were as follows: Methanobrevibacter (Euryarchaeota), 2.1%, 1.7%, and 2.1%; Olsenella (Actinobacteria), 23.9%, 17.7%, and 12.8%; Prevotella (Bacteroidetes), 10.5%, 16.5%, and 19.2%; Dialister (Firmicutes), 3.3%, 4.1%, and 2.8%; Succiniclasticum (Firmicutes), 3.8%, 4.7%, and 9.2%; and Sharpea (Firmicutes), 0.4%, 2.5%, and 0.2%, respectively. There were no significant differences in the various phyla among the three groups (p > .05). The results showed that calves hay supplementation time did not affect the diversity of the rumen microbiota in the suckling calves. However, the hay supplementation altered the proportion of the various microbial populations, supplementation of oat hay from week 2 on the basis of milk and starter could improve calves rumen pH.

Background To understand differences in the gut microbiota between elderly people of urbanized town communities (UTC) and longevity village communities (LVC), we analyzed fecal microbiota collected from individuals living in 2 UTC (Seoul and Chuncheon) and 3 LVC (Gurye, Damyang, and Soonchang) selected on the basis of indices for superlongevity (the ratio of centenarians to the total population) and longevity (the ratio of those aged 85 years or greater to those aged 65 years or greater) in South Korea by 454 pyrosequencing. Results Taxonomy-based analysis showed that The relative abundance of Firmicutes, Tenericutes, and Actinobacteria was significantly lower in LVC than in UTC. Due to an increase of Firmicutes and a reduction of Bacteroidetes, the ratio of Firmicutes to Bacteroidetes in the gut microbiota was greater in UTC adults than in UTC children or LVC adults. The population levels of Bacteroides, Prevotella, and Lachnospira were significantly higher in LVC than in UTC, but the levels of Dialister, Subdoligranulum, Megamonas, EF401882_g, and AM275436_g were lower in LVC than in UTC. Although most of the species detected in LVC were detected in UTC, some Bacteroides spp. and Faecalibacterium spp. were detected only in LVC. Among Bacteroides spp., ACWH_s, EF403317_s, and EF403722_s were detected in children and LVC samples only but FJ363527_s, 4P000677_s, and 4P000015_s were detected in UTC samples. EF402172_s and EF404388_s, members of Faecalibacterium spp., which are known to have anti-inflammatory properties, were detected in LVC and children only (>3.9% of total sequence). In addition, the fecal lipopolysaccharides (LPS) content was significantly higher in UTC than in LVC. Conclusions These findings suggest that maintaining gut microbiota, including Faecalibacterium spp. EF402172_s and EF404388_s, as well as low LPS levels may play an important role in preserving residents’ health in LVC. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0386-8) contains supplementary material, which is available to authorized users.

Background The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut microbiota, it is important to replicate studies in overlooked populations. Thus, we describe here, for the first time, the gut microbiota of Colombian adults via the pyrosequencing of the 16S ribosomal DNA (rDNA), comparing it with results obtained in Americans, Europeans, Japanese and South Koreans, and testing the generality of previous observations concerning changes in Firmicutes and Bacteroidetes with increasing body mass index (BMI). Results We found that the composition of the gut microbiota of Colombians was significantly different from that of Americans, Europeans and Asians. The geographic origin of the population explained more variance in the composition of this bacterial community than BMI or gender. Concerning changes in Firmicutes and Bacteroidetes with obesity, in Colombians we found a tendency in Firmicutes to diminish with increasing BMI, whereas no change was observed in Bacteroidetes. A similar result was found in Americans. A more detailed inspection of the Colombian dataset revealed that five fiber-degrading bacteria, including Akkermansia, Dialister, Oscillospira, Ruminococcaceae and Clostridiales, became less abundant in obese subjects. Conclusion We contributed data from unstudied Colombians that showed that the geographic origin of the studied population had a greater impact on the composition of the gut microbiota than BMI or gender. Any strategy aiming to modulate or control obesity via manipulation of this bacterial community should consider this effect. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0311-6) contains supplementary material, which is available to authorized users.

Objective The aim of this study was to determine whether oral supplementation with l -glutamine (GLN) modifies the gut microbiota composition in overweight and obese adults. Methods Thirty-three overweight and obese adults, ages between 23 and 59 y and body mass index between 25.03 and 47.12 kg/m2, were randomly assigned to receive either oral supplementation with 30 g of l -alanine (ALA group control) or 30 g of GLN (GLN group) daily for 14 d. We analyzed the gut microbiota composition with new-generation sequencing techniques and bioinformatics analysis. Results After 14 d of supplementation, adults in the GLN group exhibited statistically significant differences in the Firmicutes and Actinobacteria phyla compared with those in the ALA group. The ratio of Firmicutes to Bacteroidetes, a good biomarker for obesity, decreased in the GLN group from 0.85 to 0.57, whereas it increased from 0.91 to 1.12 in the ALA group. At the genus level, Dialister, Dorea, Pseudobutyrivibrio, and Veillonella, belonging to the Firmicutes phylum, had statistically significant reduction. Conclusion Oral supplementation with GLN, for a short time, altered the composition of the gut microbiota in overweight and obese humans reducing the Firmicutes to Bacteroidetes ratio, which resembled weight loss programs already seen in the literature.

Previous studies of oral microbiota by culture-dependent or targeted DNA approaches demonstrated that hyposalivation, a reduction in salivary secretions, might increase the amount of certain oral pathogens. However, the relationship between hyposalivation and the balance of oral microbiota, especially uncultivable bacteria, remains still unclear. The aim of this study was to elucidate the relationship between hyposalivation and oral microbiota by analyzing terminal restriction fragment length polymorphism (T-RFLP) of 16S rDNA. The 61 subjects were divided into two groups, hyposalivation group and normo-salivation group. The microbiota of tongue-coating samples was analyzed by T-RFLP. The amount of saliva, the number of Candida albicans, and also the dental status including plaque index, gingival index, bleeding on probing, probing pocket depth and decayed, missing, and filled teeth (DMFT) were assessed. Regarding the dental status, none of the evaluated factors were significantly different between the groups except the number of DMFT. According to the T-RFLP profiles, the patterns of microbiota in the tongue coating were classified into two groups, Clusters I and II. Cluster I is made up 76 % of subjects with hyposalivation, while Cluster II is made up 61 % of subjects with normo-salivation (p

A relatively wide range of bacteria have been isolated from root canals using standard culture techniques. However, only 50% of the bacteria in the oral cavity are cultivable (S. S. Socransky et al., Arch. Oral Biol. 8:278–280, 1963); hence, bacterial diversity in endodontic infections is underestimated. This study used a PCR-based 16S rRNA gene assay, followed by cloning and sequencing of 16S rRNA amplicons from a small subset of samples to assess the diversity of bacteria present in infected root canals. A total of 41 clinical samples from 15 de novo and 26 refractory cases of endodontic infections were assessed. Of these samples, 44% were positive by culture and 68% were positive by PCR. Eight samples were selected for further analysis. Of these, the two de novo cases yielded sequences related to those of the genera Enterococcus, Lactobacillus, Propionibacterium , and Streptococcus and two clones were related to previously uncultivated bacteria, while the sinus-associated, de novo case yielded sequences related to those of the genera Lactobacillus, Pantoea, Prevotella , and Selenomonas . The five refractory cases produced clones which were related to the genera Capnocytophaga, Cytophaga, Dialister, Eubacterium, Fusobacterium, Gemella, Mogibacterium, Peptostreptococcus, Prevotella, Propionibacterium, Selenomonas, Solobacterium, Streptococcus , and Veillonella and two clones representing previously uncultivated bacteria. The phylogenetic positions of several clones associated with the Clostridiaceae and Sporomusa subgroups of the Firmicutes grouping are also shown. This study demonstrates that molecular techniques can detect the presence of bacteria in endodontic infections when culture techniques yield a negative result and can be used to identify a wider range of endodontic-infection-related bacteria including the presence of previously unidentified or unculturable bacteria.

There is mounting evidence for a possible role for Campylobacter concisus in Crohn’s disease (CD). However, the pathogenic potential of C. concisus remains disputed due to its presence in healthy subjects. It is documented that genetic diversity exists within this species, with some strains possessing putative virulence determinants such as exotoxin 9/DnaI that may enable them to persist intracellularly in host cells. In order to clarify this, we employed real-time PCR to determine C. concisus and exotoxin 9 levels within faecal samples of CD patients and healthy controls, and correlated these levels with abundances of microbial taxa identified in a subset of subjects. Both C. concisus and exotoxin 9 levels were found to be higher in CD patients than healthy controls, suggesting not only that CD patients had a greater abundance of C. concisus but also that their strains were likely to be more virulent. Moreover, C. concisus levels correlated with the exotoxin 9 levels in CD patients but not in healthy controls, indicating that healthy controls were colonized by non-virulent C. concisus strains. Correlations with the intestinal microbiota found C. concisus levels to correlate with Eubacterium, Subdoligranulum and Blautia, while exotoxin 9 levels correlated with Dialister, Oscillospira, Lachnospira and Prevotella. This suggests that either the composition of the intestinal microbial flora has the ability to influence levels of both virulent and non-virulent C. concisus strains, or infection with C. concisus may modulate the levels of specific bacterial taxa within the gastrointestinal tract.