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We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high-throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high-throughput-based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria.

Purpose: The aim of this study was to evaluate in the vagina of 60 pre-menopausal women the detection of orally administered multispecies probiotic formulations showing anti-microbial properties in test in vitro. Methods: A randomized, double-blind, three-arm parallel pilot study was carried out on 60 pre-menopausal women. Subjects were randomly divided in three groups (F_1, F_2, F_3). Each group received a daily oral administration of probiotic mixtures (for 14 days and at the day 21, 7 days after the wash-out) containing: Lactobacillus acidophilus and Lactobacillus reuteri (F_1), or Lactobacillus plantarum, Lactobacillus rhamnosus and Bifidobacterium animalis subsp. lactis (F_2), or placebo (F_3), respectively. Vaginal swabs were collected at four experimental times, at t0 and at t7, t14 and t21 days, and analyzed by qPCR. At the same time, the anti-microbial activity of the probiotic formulations was verified by assays in vitro against microorganisms as Escherichia coli and Candida albicans. Results: L. acidophilus and L. reuteri as well as L. plantarum, L. rhamnosus and B. lactis were significantly increased on 7 days in the groups administered with F_1 and F_2, respectively, compared to group F_3. A similar significant trend was observed on 21 days, 7 days after the wash-out. F_1 and F_2 showed coherent anti-microbial properties. Conclusion: Both probiotic formulations F_1 and F_2, chosen because of their anti-microbial activity against pathogens responsible for vaginal dysbiosis and infections, led to vaginal detection and enhancement of the amount of species of formulates when orally administered. This work provides the basis for further clinical investigations of the F_1 and F_2 capacity to prevent or treat uro-genital infections.

Background and Aim. The efficacy of supplementation treatment with two multispecies probiotic formulates on subjects diagnosed with IBS-C and the assessment of their gut microbiota were investigated. Methods. A randomized, double-blind, three-arm parallel group trial was carried out on 150 IBS-C subjects divided into three groups (F-1, F-2, and F-3). Each group received a daily oral administration of probiotic mixtures (for 60 days) F-1 or F-2 or placebo F-3, respectively. Fecal microbiological analyses were performed by species-specific qPCR to assess the different amount of probiotics. Results. The percentage of responders for each symptom was higher in the probiotic groups when compared to placebo group during the treatment period (t 60) and was maintained quite similar during the follow-up period (t 90). Fecal analysis demonstrated that probiotics of the formulations increased during the times of treatment only in fecal DNA from subjects treated with F-1 and F-2 and not with F-3, and the same level was maintained during the follow-up period. Conclusions. Multispecies probiotic supplementations are effective in IBS-C subjects and induce a different assessment in the composition of intestinal microbiota. This clinical study is registered with the clinical study registration number ISRCTN15032219.

In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.