Diversity of vaginal microbiome and metabolome during genital infections

We characterized the vaginal ecosystem during common infections of the female genital tract, as vulvovaginal candidiasis (VVC, n\u2009=\u200918) and Chlamydia trachomatis infection (CT, n\u2009=\u200920), recruiting healthy (HC, n\u2009=\u200921) and bacterial vaginosis-affected (BV, n\u2009=\u200920) women as references of eubiosis and dysbiosis. The profiles of the vaginal microbiome and metabolome were studied in 79 reproductive-aged women, by means of next generation sequencing and proton based-nuclear magnetic resonance spectroscopy. Lactobacillus genus was profoundly depleted in all the genital infections herein considered, and species-level analysis revealed that healthy vaginal microbiome was dominated by L. crispatus. In the shift from HC to CT, VVC, and BV, L. crispatus was progressively replaced by L. iners. CT infection and VVC, as well as BV condition, were mainly characterised by anaerobe genera, e.g. Gardnerella, Prevotella, Megasphaera, Roseburia and Atopobium. The changes in the bacterial communities occurring during the genital infections resulted in significant alterations in the vaginal metabolites composition, being the decrease of lactate a common marker of all the pathological conditions. In conclusion, according to the taxonomic and metabolomics analysis, we found that each of the four conditions is characterized by a peculiar vaginal microbiome/metabolome fingerprint

Proteobacteria Overgrowth and Butyrate-Producing Taxa Depletion in the Gut Microbiota of Glycogen Storage Disease Type 1 Patients

A life-long dietary intervention can affect the substrates' availability for gut fermentation in metabolic diseases such as the glycogen-storage diseases (GSD). Besides drug consumption, the main treatment of types GSD-Ia and Ib to prevent metabolic complications is a specific diet with definite nutrient intakes. In order to evaluate how deeply this dietary treatment affects gut bacteria, we compared the gut microbiota of nine GSD-I subjects and 12 healthy controls (HC) through 16S rRNA gene sequencing; we assessed their dietary intake and nutrients, their microbial short chain fatty acids (SCFAs) via gas chromatography and their hematic values. Both alpha-diversity and phylogenetic analysis revealed a significant biodiversity reduction in the GSD group compared to the HC group, and highlighted profound differences of their gut microbiota. GSD subjects were characterized by an increase in the relative abundance of Enterobacteriaceae and Veillonellaceae families, while the beneficial genera Faecalibacterium and Oscillospira were significantly reduced. SCFA quantification revealed a significant increase of fecal acetate and propionate in GSD subjects, but with a beneficial role probably reduced due to unbalanced bacterial interactions; nutritional values correlated to bacterial genera were significantly different between experimental groups, with nearly opposite cohort trends

Distribution of ermB, ermF, tet(W), and tet(M) resistance genes in the vaginal ecosystem of women during pregnancy and puerperium

The inhabitants of the vaginal ecosystem can harbor genetic determinants conferring antimicrobial resistance. However, detailed data about the distribution of resistance genes in the vaginal microbiome of pregnant women are still lacking. Therefore, we assessed the presence of macrolide (i.e., erm genes) and tetracycline (i.e., tet genes) resistance markers in the vaginal environment of Caucasian women at different gestational ages. Furthermore, the detection of resistance genes was related to the composition of the vaginal microbiota. A total of 228 vaginal samples, collected at different trimesters of pregnancy or during the puerperium, were tested for the presence of ermB, ermF, tet(W), and tet(M) by in-house end-point PCR assays. The composition of the vaginal microbiota was assessed through a microscopic evaluation (i.e., Nugent score) and by means of sequencing V3–V4 hypervariable regions of the bacterial 16 rRNA gene. Overall, the most detected resistance gene was tet(M) (76.7%), followed by ermB (55.2%). In 17% of women, mainly with a ‘normal’ vaginal microbiota, no resistance genes were found. Except for tet(W), a significant correlation between the positivity of resistance genes and a dysbiotic vaginal status (i.e., bacterial vaginosis (BV)) was noticed. Indeed, samples positive for at least one resistance determinant were characterized by a decrease in Lactobacillus spp. and an increase of BV-related genera (Prevotella, Gardnerella, Atopobium, Sneathia). A high predominance of vaginal Lactobacillus spp. (>85%) was associated with a lower risk of tet(W) gene detection, whereas the presence of Megasphaera (>1%) increased the risk of positivity for all analyzed genes. Different types of vaginal microbiota are associated with peculiar resistance profiles, being a lactobacilli-dominated ecosystem poor in or free of resistance genes. These data could open new perspectives for promoting maternal and neonatal health

Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows

Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups' prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7-10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health

Dietary treatment promotes gut microbial community changes in subjects affected by glycogenosis type 1

Background: The glycogen-storage diseases (GSDs) are caused by enzyme defects of glycogen degradation. These enzymes are mainly localized in the liver. Hepatomegaly and hypoglycemia are the principal abnormalities. The glycogen storage disease Ia and Ib are due to the defects of the glucose-6-phosphatase and glucose-6-phosphate translocase, respectively. The aim of dietary treatment is to prevent hypoglycemia and suppress secondary metabolic complications, by the intake of slow-release carbohydrates. Such a dietary intervention could affect the availability of substrates for microbial fermentation. In this study, we compared the gut microbiota composition and microbial metabolite production (i.e. short chain fatty acids -SCFAs-) of subjects with glycogenosis type 1 and healthy subjects, sex- and age-matched. Methods: Nine GSD1 subjects (6 males, age range 4-38 years old) and 12 healthy controls (CTR) were enrolled. We assessed dietary intake and performed gut microbiota analysis by next-generation sequencing using V3\u2013V4 hypervariable 16S rRNA genomic region. Fecal SCFAs were quantified by gas chromatography. Results: Alpha-diversity analysis revealed a significant reduction in microbial richness and evenness in the GSD group compared with CTR (PD whole tree, p = 0.03; observed species p = 0.02; Shannon, p = 0.002). Phylogenetic analysis highlighted a significant separation of gut microbiota according to both unweighted (p=0.004) and weighted Unifrac distances (p=0.01). In particular, GSD subjects were characterized by an increase in the relative abundance of Enterobacteriaceae (p=0.006) and Veillonellaceae (p=0.01), whereas CTR group was enriched in Ruminococcaceae (p=0.001). SCFAs quantification revealed an increase of fecal acetate and propionate in GSD subjects. Discussion: Despite GSD diet is enriched in resistant starch, usually considered good substrates for beneficial microbes, we found a dramatic increase in Proteobacteria. This phylum, and in particular Enterobacteriaceae, had been suggested to exert pro-inflammatory activity both locally, at the gastrointestinal mucosa, and systemically. Indeed, GSD subjects are at higher risk to develop chronic inflammatory bowel diseases. Whether our findings represent an effect of the disease itself, or a consequence of the diet is still unclear

Interplay between Genetic Disorders and Gut Microbial Community: Rubinstein-Taybi Syndrome as a Model

Rubinstein-Taybi syndrome (RSTS) is a genetic disease affecting 1 out of 125,000 newborns characterized by intellectual disability, skeletal abnormalit the genes CREBBP, encoding for CBP protein, or EP300, encoding for p300 protein. As CBP and p300 are lysine acetyl-transferases, RSTS patients sho Pharmacological therapy with histone deacetylase inhibitors (HDACi) was shown to attenuate chromatin impairment improving the clinical phenotype in chain fatty acids, especially butyrate, display HDACi activity, the aim of this study was to assess the endogenous level of butyrate and the relative abu enrolled 23 RSTS patients and 16 healthy siblings (HC), as control group to minimize environmental factors having a well-recognized role on gut mic generation sequencing using V3-V4 hypervariable 16S rRNA genomic region. Fecal SCFAs were quantified by gas chromatography. Exogenous HDACi derived from RSTS patients was assessed by Alpha LISA technology. The biodiversity of gut communities (alpha-diversity) was similar for all the assesse difference among HC and RSTS subjects was highlighted in beta-diversity analyses, as Both unweighted and weighted Unifrac distances revealed a signi respectively). We found several significant differences in taxa relative abundance among the two groups across all phylogenetic levels. In particular, R Faecalibacterium and Roseburia. Fecal SCFA concentrations were similar except for butyrate that was found reduced in RSTS (p=0.07). LCLs treated acetylation compared to untreated cells.Despite sharing diet habits and the environment, RSTS gut microbiota is depleted in major butyrate-produc Deepening our knowledge of RSTS gut microbiota alterations could offer new hints to explore strategies aimed at restoring a normal microbial comm associated with RSTS, such as gastrointestinal discomfort

Quality of dietary carbohydrates affects gut microbial community of phenylketonuric subjects

Introduction - Low-phenylalanine diet, the cornerstone treatment for phenylketonuria (PKU), has been shown to increase glycemic index (GI) and glycemic load (GL), affecting the availability of substrates for microbial fermentation. Indeed, changes in the PKU gut microbiota and in microbial metabolites have been previously reported. Here we compared gut microbial communities of children with PKU and with mild hyperphenylalaninemia (MHP, unrestricted diet). Materials and Methods - Forty-two children (21 males/21 females, 4-18 years old) were enrolled in the study. We assessed dietary intake and performed gut microbiota analysis by next-generation sequencing using V3\u2013V4 hypervariable 16S rRNA genomic region. Results - While alpha-diversity analysis revealed no significant differences between PKU and MHP groups, phylogenetic analysis highlighted a significant separation of gut microbiota according to both unweighted (p=0.008) and weighted Unifrac distances (p=0.03). Major differences were seen within the Firmicutes phylum. Indeed, PKU children were depleted in Faecalibacterium spp. and enriched in Blautia spp. and Clostridium spp. We found a divergent response of members of the Firmicutes phylum with respect of daily glycemic index, higher in PKU children. F. prausnitzii, unclassified Ruminococcaceae and, to a lesser extent Roseburia spp. negatively correlated with GI, whereas other Lachnospiraceae (unclassified) were positively associated. Indicator species analysis suggested Faecalibacterium prausnitzii to be related to MHP status, whereas Ruminococcus bromii to be associated to PKU. Discussion and Conclusions - Despite PKU children have a higher vegetables and fiber intakes, considered good substrates for beneficial microbes, the quality of carbohydrates ingested seems to particularly affect F. prausnitzii abundance, a biomarker for a healthy status. Indeed, F. prausnitzii is one of the key species for butyrate production. It still remains to evaluate whether an improvement of current free-amino acid formulas could rebalance the microbial community

Impact of the ketogenic diet on human gut

Background The classic ketogenic diet (KD) is an normocaloric dietary protocol with a high intake of fats (85-90% of energy), which is used as a therapy for drug-resistant epilepsies and type 1 glucose transporter deficiency syndromes (GLUT1-DS). It is known that specific dietetic patterns can influence the composition of the intestinal microbiota; in particular, it was shown that KD is associated with various pro-inflammatory changes in the microbiota. Aim To verify the impact of KD on the intestinal microbiota, through the evaluation of: intestinal bacterial composition, markers of bacterial metabolism (short chain fatty acids, SCFA), toxicity of faecal water. Materials and Methods Faecal samples were collected in 12 patients with GLUT1-DS or drug-resistant epilepsy (KD) and in matched healthy subjects (CTR); additionally, in 7 patients samples were collected also before the dietary treatment. The bacterial composition was evaluated by analysis of Next Generation Sequencing and Real-Time PCR. SCFAs were measured by gas-chromatography. Toxicity of faecal water was assessed by Trypan Blue (cytotoxicity) and Comet Assay (genotoxicity). Results The microbiota composition of KD patients was significantly different than CTR, especially for a different Firmicutes /Bacteroidetes ratio. SCFA decreased significantly during a KD, as well as the level of genotoxicity of faecal water. Conclusions This study confirmed the impact of KD on the intestinal microbiota, highlighting the need for further research to avoid long-term adverse effects and optimize therapy

Proteobacteria Overgrowth and Butyrate-Producing Taxa Depletion in the Gut Microbiota of Glycogen Storage Disease Type 1 Patients

A life-long dietary intervention can affect the substrates’ availability for gut fermentation in metabolic diseases such as the glycogen-storage diseases (GSD). Besides drug consumption, the main treatment of types GSD-Ia and Ib to prevent metabolic complications is a specific diet with definite nutrient intakes. In order to evaluate how deeply this dietary treatment affects gut bacteria, we compared the gut microbiota of nine GSD-I subjects and 12 healthy controls (HC) through 16S rRNA gene sequencing; we assessed their dietary intake and nutrients, their microbial short chain fatty acids (SCFAs) via gas chromatography and their hematic values. Both alpha-diversity and phylogenetic analysis revealed a significant biodiversity reduction in the GSD group compared to the HC group, and highlighted profound differences of their gut microbiota. GSD subjects were characterized by an increase in the relative abundance of Enterobacteriaceae and Veillonellaceae families, while the beneficial genera Faecalibacterium and Oscillospira were significantly reduced. SCFA quantification revealed a significant increase of fecal acetate and propionate in GSD subjects, but with a beneficial role probably reduced due to unbalanced bacterial interactions; nutritional values correlated to bacterial genera were significantly different between experimental groups, with nearly opposite cohort trends

Pharyngeal microbiome alterations during Neisseria gonorrhoeae infection

Pharyngeal gonorrhoea is a common sexually transmitted infection among \u2018men having sex with other men\u2019 (MSM). Neisseria gonorrhoeae (NG) pharyngeal infections are usually characterized by the absence of symptoms, acting as an important reservoir for their further spread. To the best of our knowledge, no information about the composition of the pharyngeal microbiome during an ongoing NG infection is currently available. Therefore, in this study, we characterized the pharyngeal bacterial community profiles associated with NG infection in a well-selected cohort of HIV-negative MSM reporting unsafe oral intercourse. A total of 70 pharyngeal swabs were considered, comparing non-infected subjects (n = 45) versus patients with pharyngeal gonorrhoea (n = 25) whose microbiota composition was analyzed from pharyngeal swabs through sequencing of hypervariable V3-V4 regions of the 16S rRNA gene. The pharyngeal microbiome of all subjects was dominated by Prevotellaceae, Veillonellaceae and Streptococcaceae families. Patients with pharyngeal gonorrhoea harboured a pharyngeal microbiome quite similar to negative subjects. Nevertheless, when looking to less-represented bacterial species (relative abundance approximately 1% or less), an imbalance between aerobe and anaerobe microorganisms was observed in NG-infected patients. In particular, the pharyngeal microbiome of NG-positive individuals was richer in several anaerobes (e.g. Treponema, Parvimonas, Peptococcus, Catonella, Filifactor) and poorer in various aerobe genera (i.e. Pseudomonas, Escherichia), compared to non-infected controls. No significant differences were noticed in the distribution of commensal Neisseria species of the oropharynx between NG-positive and negative subjects. Metabolic variations induced by changes in the microbiome abundance were assessed by a functional prediction of the bacterial metabolic pathways: a more abundant involvement of D-glutamine and D-glutamate metabolism, carbohydrate metabolism, as well as a greater activation of the energy metabolism was observed in patients with pharyngeal gonorrhoea compared to non-infected individuals. Information about the bacterial composition of the pharyngeal microbiome in case of gonorrhoea could shed light on the pathogenesis of the infection and open new perspectives for the prevention and control of this condition