Effects of the long-term storage of human fecal microbiota samples collected in RNAlater.

The adequate storage of fecal samples from clinical trials is crucial if analyses are to be performed later and in long-term studies. However, it is unknown whether the composition of the microbiota is preserved during long-term stool storage (>1 year). We therefore evaluated the influence of long-term storage on the microbiota composition of human stool samples collected in RNAlater and stored for approximately five years at -80 °C. We compared storage effects on stool samples from 24 subjects with the effects of technical variation due to different sequencing runs and biological variation (intra- and inter-subject), in another 101 subjects, based on alpha-diversity, beta-diversity and taxonomic composition. We also evaluated the impact of initial alpha-diversity and fecal microbiota composition on beta-diversity instability upon storage. Overall, long-term stool storage at -80 °C had only limited effects on the microbiota composition of human feces. The magnitude of changes in alpha- and beta- diversity and taxonomic composition after long-term storage was similar to inter-sequencing variation and smaller than biological variation (both intra- and inter-subject). The likelihood of fecal samples being affected by long-term storage correlated with the initial relative abundance of some genera and tend to be affected by initial taxonomic richness.

The health and life path of rare disease patients: results of the 2015 French barometer.

PURPOSE: A barometer has been set up to provide better knowledge about the daily situation of French rare disease (RD) patients, their families and relatives, in order to contribute to the elaboration of improvement measures. This report focuses on the care and life path of RD patients. PATIENTS AND METHODS: A preliminary survey was carried out with three patients, five parents and three RD experts to identify the main hurdles and disruptions in the life path of RD patients. It was used to design a larger survey comprising 60 questions as well as open fields allowing free expression. Respondents (448) comprised patients, parents of RD children and close relatives of patients. The Percentage of Maximum Deviation, Yates' correction for continuity and Fisher's test were employed to compare the responses between groups. RESULTS: Large disparities in the delays to obtain a diagnosis were identified (<1 year to >20 years), and longer delays were associated with negative perception of care conditions. While good interactions with education teams were reported (59% of respondents), the professional situation of both patients and parents was strongly and negatively impacted by the disease (51% did not work or stopped working). Three hundred respondents expressed various needs and psychological and personal issues were reported by 62% and 75% of respondents, respectively. Interestingly, the medical care path and daily life of RD patients were positively impacted by the follow-up in a specialized consultation, as reflected by changes in scores measured by our barometer (Fisher's test, p<0.05). CONCLUSION: Some of the main hurdles and sources of disruption in the life path of RD patients were identified, as well as some positive outcomes. These data could serve not only as a background for further studies, but also to better adapt the support to real needs and to improve the synergies between the many people involved in the life path of RD patients.

Clinical Practice Guidelines for Rare Diseases: The Orphanet Database.

Clinical practice guidelines (CPGs) for rare diseases (RDs) are scarce, may be difficult to identify through Internet searches and may vary in quality depending on the source and methodology used. In order to contribute to the improvement of the diagnosis, treatment and care of patients, Orphanet (www.orpha.net) has set up a procedure for the selection, quality evaluation and dissemination of CPGs, with the aim to provide easy access to relevant, accurate and specific recommendations for the management of RDs. This article provides an analysis of selected CPGs by medical domain coverage, prevalence of diseases, languages and type of producer, and addresses the variability in CPG quality and availability. CPGs are identified via bibliographic databases, websites of research networks, expert centres or medical societies. They are assessed according to quality criteria derived from the Appraisal of Guidelines, REsearch and Evaluation (AGREE II) Instrument. Only open access CPGs and documents for which permission from the copyright holders has been obtained are disseminated on the Orphanet website. From January 2012 to July 2015, 277 CPGs were disseminated, representing coverage of 1,122 groups of diseases, diseases or subtypes in the Orphanet database. No language restriction is applied, and so far 10 languages are represented, with a predominance of CPGs in English, French and German (92% of all CPGs). A large proportion of diseases with identified CPGs belong to rare oncologic, neurologic, hematologic diseases or developmental anomalies. The Orphanet project on CPG collection, evaluation and dissemination is a continuous process, with regular addition of new guidelines, and updates. CPGs meeting the quality criteria are integrated to the Orphanet database of rare diseases, together with other types of textual information and the appropriate services for patients, researchers and healthcare professionals in 40 countries.

Evolution of microbiological analytical methods for dairy industry needs.

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.

Tracking spore-forming bacteria in food: from natural biodiversity to selection by processes.

Sporeforming bacteria are ubiquitous in the environment and exhibit a wide range of diversity leading to their natural prevalence in foodstuff. The state of the art of sporeformer prevalence in ingredients and food was investigated using a multiparametric PCR-based tool that enables simultaneous detection and identification of various genera and species mostly encountered in food, i.e., Alicyclobacillus, Anoxybacillus flavithermus, Bacillus, B. cereus group, B. licheniformis, B. pumilus, B. sporothermodurans, B. subtilis, Brevibacillus laterosporus, Clostridium, Geobacillus stearothermophilus, Moorella and Paenibacillus species. In addition, 16S rDNA sequencing was used to extend identification to other possibly present contaminants. A total of 90 food products, with or without visible trace of spoilage were analysed, i.e., 30 egg-based products, 30 milk and dairy products and 30 canned food and ingredients. Results indicated that most samples contained one or several of the targeted genera and species. For all three tested food categories, 30 to 40% of products were contaminated with both Bacillus and Clostridium. The percentage of contaminations associated with Clostridium or Bacillus represented 100% in raw materials, 72% in dehydrated ingredients and 80% in processed foods. In the last two product types, additional thermophilic contaminants were identified (A. flavithermus, Geobacillus spp., Thermoanaerobacterium spp. and Moorella spp.). These results suggest that selection, and therefore the observed (re)-emergence of unexpected sporeforming contaminants in food might be favoured by the use of given food ingredients and food processing technologies.

Polyphasic approach for quantitative analysis of obligately heterofermentative Lactobacillus species in cheese.

Obligately heterofermentative lactobacilli (OHL) present in cheese during ripening can influence the flavour and texture of the final product. In order to better evaluate, follow and control this population, there is a current need for easy-to-use tools. In this study, a culture-dependent quantitative method (ABEV medium) was set up for direct and selective enumeration of total OHL from cheese, and a culture-independent method based on specific real time PCR (qPCR) assays was developed to target Lactobacillus fermentum and Lactobacillus parabuchneri individual species. These tools were applied for OHL quantification in manufactured Emmental and Tomme cheeses. The ABEV medium was well adapted for specific enumeration and isolation of OHL species present in milk-derived samples, even in the presence of background microbiota. qPCR assays showed 100% specificity and could accurately quantify the targeted species in various types of cheese. Culture-dependent and -independent techniques evaluated in manufactured cheese samples generated similar bacterial counts. The behaviour of L. fermentum and L. parabuchneri was characterized from milk samples to the end of ripening. In addition, PCR-TTGE was used to confirm the presence of inoculated species and to globally analyze the composition of naturally present species. This polyphasic approach illustrates the complementarity of the different methods.

Recent advances in quantitative PCR (qPCR) applications in food microbiology.

Molecular methods are being increasingly applied to detect, quantify and study microbial populations in food or during food processes. Among these methods, PCR-based techniques have been the subject of considerable focus and ISO guidelines have been established for the detection of food-borne pathogens. More particularly, real-time quantitative PCR (qPCR) is considered as a method of choice for the detection and quantification of microorganisms. One of its major advantages is to be faster than conventional culture-based methods. It is also highly sensitive, specific and enables simultaneous detection of different microorganisms. Application of reverse-transcription-qPCR (RT-qPCR) to study population dynamics and activities through quantification of gene expression in food, by contrast with the use of qPCR, is just beginning. Provided that appropriate controls are included in the analyses, qPCR and RT-qPCR appear to be highly accurate and reliable for quantification of genes and gene expression. This review addresses some important technical aspects to be considered when using these techniques. Recent applications of qPCR and RT-qPCR in food microbiology are given. Some interesting applications such as risk analysis or studying the influence of industrial processes on gene expression and microbial activity are reported.

A multiparametric PCR-based tool for fast detection and identification of spore-forming bacteria in food.

The presence of psychrotrophic or highly thermoresistant spore-forming bacteria in food and feedstuff responsible for food poisoning and spoilage raises major safety and economical issues. The aim of this study was to evaluate the performances of a ready-to-use PCR assay (alternative method) in comparison with the standard microbiological plating method regarding spore-forming bacteria detection in food samples. An overnight sample enrichment was selected to increase sporeformer diversity recovery, spore germination, bacterial growth and favour DNA extraction. A total of 180 sporeformer isolates representing 38 different species and 8 genera were tested in the PCR assays. Inclusivity and exclusivity results ensured specific detection and identification of the majority of targeted genera and species. Validation studies carried on artificially contaminated food samples showed detection of the inoculated contaminants in most cases, with increased detection limit for the alternative method which enabled detection with up 1 spore of B. cereus in 25 g food sample. Using naturally contaminated food samples, standard method comforted the alternative method. In a number of cases, the alternative method was able to identify species not detected with the standard method. In addition, identification and discrimination between the B. cereus group members was possible. Thus, associated to a key element, i.e., the enrichment step, the developed multiparametric PCR-based assays reported in this study provide a fast, sensitive and reliable detection and identification tool for mostly encountered spore-forming food contaminants.

Improvement of an experimental colitis in rats by lactic acid bacteria producing superoxide dismutase.

The use of superoxide dismutases (SODs) in inflammatory diseases is hampered by their short circulatory half-life. To determine whether a bacterial supply of SOD into the colon might improve an experimental colitis, the effects of oral treatment with live recombinant lactic acid bacteria producing different amounts of SOD and those of colonic infusion of SOD were compared. Wistar rats were fitted with a catheter in the proximal colon through which TNBS was administered to induce colitis. Animals received a continuous intracolonic infusion of bovine SOD (40 U per rat per day) for 4 days after TNBS or were treated orally with live recombinant Lactococcus lactis or Lactobacillus plantarum strains (10 colony-forming units (CFU)/d), producing or not producing SOD, for 4 days before and after TNBS. SOD activity of bacterial extracts was 0, 26, 74, and 624 units/10 CFU for L. plantarum, L. lactis, L. lactis SOD, and L. plantarum SOD, respectively. Four days after TNBS, macroscopic and microscopic damage, myeloperoxidase (MPO) activity, and nitrotyrosine immunostaining were evaluated. TNBS induced macroscopic and microscopic damages, an increase in MPO activity, and intense immunostaining for nitrotyrosine. Macroscopic damage and MPO activity were reduced by bovine SOD. These parameters and microscopic damages also were reduced by L. lactis, L. lactis SOD, and L. plantarum SOD, but not by L. plantarum. Nitrotyrosine immunostaining was attenuated after treatment with the 4 bacterial strains. Although not all of the anti-inflammatory effects could be attributed directly to SOD, our results suggest that SOD-producing lactic acid bacteria open a novel approach in inflammatory bowel disease treatment.

Towards understanding molecular modes of probiotic action.

The possibility that certain microorganisms might be beneficial to human health is highlighted by the numerous consumer products containing probiotic bacteria. Probiotics are typically administered in food that, following entry into the gastro-intestinal tract, results in measurable health-promoting effects. Although there is a growing list of health benefits provided by the consumption of probiotics, their precise mechanisms of action remain largely unknown. Recent molecular- and genomics-based studies are starting to provide insight into the ways probiotic bacteria sense and adapt to the gastro-intestinal tract environment. Complementary approaches using host cell in vitro systems together with animal models and human volunteers are revealing specific intestinal cell responses to probiotics. These studies should ultimately disclose the molecular mechanisms and pinpoint the bacterial and host effector molecules and pathways by which probiotics are able to modulate human health.

Use of mouse models to evaluate the persistence, safety, and immune modulation capacities of lactic acid bacteria.

Recent clinical and experimental observations showed that specific probiotic microorganisms may provide therapeutic benefits in inflammatory bowel disease. However, a rigorous screening for new candidate probiotic strains with optimized therapeutic properties necessitates also determining possible adverse interactions with the host, particularly in individuals who are not healthy. We have evaluated the persistence of strains of lactic acid bacteria (LAB) in the digestive tracts of mice, their immunomodulation capacity, and their safety in healthy animals and in a colitis model. Following daily administration of 10(9) CFU of viable LAB orally, intragastrically, or intrarectally, the animals' feces were examined for bacterial excretion and cytokines were quantified in intestinal samples by quantitative reverse transcription-PCR. The level of bacterial translocation was assessed in healthy mice and in mice suffering from colitis induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS). Irrespective of the route of administration, the potential probiotic strain Lactobacillus plantarum NCIMB8826 was found to persist for up to 10 days in the digestive tracts of mice. This strain did not induce detrimental effects in healthy or in TNBS-treated animals, as was reflected by the absence of weight loss, intestinal inflammation, modification of cytokine levels in the ileum and colon (healthy mice), and bacterial dissemination (healthy and colitic animals). Moreover, the translocation of endogenous microflora to the mesenteric lymph nodes and spleen was greatly reduced in the TNBS-treated mice after administration of LAB. This property, together with the strain's persistence capacity and innocuousness renders L. plantarum NCIMB8826 an attractive candidate as a probiotic to be used in the prevention or treatment of chronic inflammation.