[Show abstract][Hide abstract] ABSTRACT: The ability to inhibit the growth of Listeria cells and the presence of bacteriocin encoding genes was examined in 115 LAB strains isolated from Argentinean vacuum-packaged beef and different traditional fermented sausages. Lactobacillus (L) sakei, Lactobacillus (L) curvatus and Enterococcus (E) faecium showed a great inhibition of all Listeria strains evaluated while Pediococcus (P) acidilactici and Lactobacillus (L) plantarum demonstrated a limited or absent antilisterial activity. Both L. curvatus and L. sakei carried the sppA, sppQ and sapA structural genes, encoding for sakacin P, sakacin Q and curvacin A bacteriocins, respectively. Whilst L. curvatus exhibited a higher occurrence of these genes, L. sakei strains were more effective at inhibiting Listeria (L) strains, Listeria monocytogenes UC8159 and Listeria innocua 7 being the most sensitive to these bacteriocins. Among analyzed E. faecium strains, the wide distribution of entA, entB and entP genes accounted for the high antilisterial activity particularly observed against L. monocytogenes FBUNT. The structural gene plantEF was mostly present in Lactobacillus plantarum strains and no pedA gene was found in P. acidilactici evaluated strains. The antilisterial potential of L. sakei and E. faecium offers great possibilities for the meat industry as biopreservative cultures, although more studies are needed in order to conclude about this issue.
Food Control 01/2015; 47:53–59. · 2.82 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities.
To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 m a.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L− 1 for PCBs and up to 168 μg L− 1 for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.
Science of The Total Environment 11/2014; s 497–498:50–59. · 3.16 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: During a study to investigate the evolution of ampicillin resistance in Enterococcus faecium, we observed that a number of E. faecium strains, mainly from the recently described sub-clade A2, showed PBP5 sequences in between PBP5-S and PBP5-R. These hybrid PBP5-S/R patterns reveal a progression of amino acid changes from the S form to the R form of this protein; however, these changes do not strictly correlate with changes in ampicillin MICs.
Antimicrobial Agents and Chemotherapy 09/2014; · 4.45 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Peatlands are archives of extreme importance for the assessment of past ecological, environmental and climatic changes. The importance as natural archives is even greater in the case of ombrotrophic peat bogs, where the only inputs are atmospheric in origin. Here we integrated previously published physical and chemical results regarding the solid and liquid phase of peat with a biomolecular microbiological approach to assess the relationships between chemistry and microbial biodiversity along a Swiss bog profile corresponding to approximately 2,000 years of peat formation. The structure of bacterial and archaeal communities was assessed through a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach followed by sequencing of PCR-DGGE bands of interest. Both chemical and microbiological data showed a differentiation of properties along the peat profile, with three major zones identified. Both bacterial and archaeal profiles clustered according to the depth (i.e., age) of samples. Among bacteria, Acidobacteria were recovered primarily in the first layers of the profile, whereas methanogenic archaea were more commonly recovered in the deepest part of the core, corresponding to the occurring anoxic conditions. Finally, a number of sequences had low homologies with known species, especially in bacteria: this points to an almost unknown microbial community adapted to the extreme conditions of peat bogs, which are acidic, rich in dissolved organic C, and predominantly anoxic.
Biology and Fertility of Soils 07/2014; 50(5):815-826. · 3.40 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Matsoni, a traditional Georgian fermented milk, has variable quality and stability besides a short shelf-life (72-120 h at 6 °C) due to inadequate production and storage conditions. To individuate its typical traits as well as select and exploit autochthonous starter cultures to standardize its overall quality without altering its typicality, we carried out a thorough physico-chemical, sensorial and microbial characterization of traditional Matsoni. A polyphasic approach, including a culture-independent (PCR-DGGE) and two PCR culture-dependent methods, was employed to study the ecology of Matsoni. Overall, the microbial ecosystem of Matsoni resulted largely dominated by Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii subsp. bulgaricus. High loads of other lactic acid bacteria species, including Lb. helveticus, Lb. paracasei and Leuconostoc (Leuc.) lactis were found to occur as well. A selected autochthonous multiple strain culture (AMSC) composed of one Lb. bulgaricus, one Lb. paracasei and one S. thermophilus strain, applied for the pilot-scale production of traditional Matsoni, resulted the best in terms of enhanced shelf-life (one month), sensorial and nutritional quality without altering its overall typical quality. This AMSC is at disposal of SMEs who need to exploit and standardize the overall quality of this traditional fermented milk, preserving its typicality.
[Show abstract][Hide abstract] ABSTRACT: Red stripe is a bacterial disease of sugarcane causing important economic losses in Argentina that affects 30 % of the milling stems and consequently the juice quality. In this study, sugarcane leaves exhibiting red stripe symptoms were sampled in the 2008–09 growing season from 13 different sugarcane producing areas of Tucumán and Salta (northwest of Argentina). To achieve the identification and characterization of the causal agent of red stripe, bacterial isolation was performed. Species-specific PCR using Oaf1/Oar1 primers allowed the amplification of a fragment of 550 bp from approximately 50 % of the isolates; 16S rDNA sequences analysis displayed a similarity greater than 99 % with Acidovorax avenae subsp. avenae. By means of RAPD-PCR the presence of at least four different biotypes among the analyzed isolates was detected. Results of pathogenicity test allowed us to confirm A. avenae subsp. avenae as the pathogenic agent for red stripe. This study constitutes the first report on the identification and molecular characterization of this plant pathogen from the Argentina sugarcane production areas. The genetic diversity observed among A. avenae is an important factor to be considered to improve an accurate diagnosis and/or the selection of sugarcane tolerant clones.
European Journal of Plant Pathology 11/2013; 137(3). · 1.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Staphylococcus epidermidis strain UC7032 was isolated from ready-to-eat cured meat and is heteroresistant to glycopeptide antibiotics. The draft whole-genome analysis revealed that this strain shows common characteristics typical of strains that are involved in nosocomial infections.
[Show abstract][Hide abstract] ABSTRACT: Clostridium tyrobutyricum is considered the main agent of late-blowing defect in the production of hard cheese. Here, we described the draft genome sequences and annotation of C. tyrobutyricum strain UC7086, which was isolated from Grana Padano cheese with blowing defect, and C. tyrobutyricum DSM 2637 type strain in a comparative study.
[Show abstract][Hide abstract] ABSTRACT: a b s t r a c t Late blowing defect affects hard cheese production and Clostridium tyrobutyricum appears as the primary cause of this spoilage. Our aim was to develop a quantitative TaqMan real-time PCR method to detect this agent in different matrices along the whole agro-dairy chain, using specific primers targeting the phosphotransacetylase gene (pta). The optimised assay appeared to be sensitive and specific to quantify C. tyrobutyricum. Results demonstrated a 100% efficiency with low numbers of cells and spores (approx. 14 mL À1 or g À1) also detected in broth and in milk matrix artificially contaminated with C. tyrobutyricum. Combined with a DNA extraction method optimised to lyse both cells and spores, our method is suitable for silage and hay, faeces, milk and hard cheese samples without any enrichment. The molecular quantification by qPCR was found to be precise and could be used for the rapid determination of the presence of C. tyrobutyricum.
International Dairy Journal 06/2013; · 2.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Po river plain lowland springs comprise unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and had constant use ever since. Our aims were to identify the land use effects on the microbial communities of these soils, seek for associated diversity drivers and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high throughput sequencing of partial 16S rRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon (TOC) and pH were major diversity drivers for Bacteria, while pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights about potential roles of taxa in the organic carbon turnover. Verrucomicrobia, coincided with the higher values of the recalcitrant organic carbon while Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the less enzymatically active and relatively poorer in nutrients soils, may be explained to an extend by niche based theories like the resource heterogeneity hypothesis and Connell's intermediate disturbance hypothesis. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: The members of the genus Clostridium, including the spore-forming anaerobic bacteria, have a complex and strictly regulated life cycle, but very little is known about the genetic pathways involved in the different stages of their life cycle. Clostridium sporogenes, a Gram-positive bacterium usually involved in food spoilage and frequently isolated from late blowing cheese, is genetically indistinguishable from the proteolytic Clostridium botulinum. As the non-neurotoxic counterpart, it is often used as an exemplar for the toxic subtypes. In this work, we performed a microscopic study combined with a custom array-based analysis of the C. sporogenes cycle, from dormant spores to the early stationary phase. We identified a total of 211 transcripts in spores, validating the hypothesis that mRNAs are abundant in spores and the pattern of mRNA expression is strikingly different from that present in growing cells. The spore transcripts included genes responsible for different life-sustaining functions, suggesting there was transcript entrapment or basic poly-functional gene activation for future steps. In addition, 3 h after the beginning of the germination process, 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appeared to be more active in terms of gene transcription and protein synthesis than the spore, and genes coding for germination and sporulation factors seemed to be expressed at this point. These results suggest that spores are not silent entities, and a broader knowledge of the genetic pathways involved in the Clostridium life cycle could provide a better understanding of pathogenic clostridia types.
[Show abstract][Hide abstract] ABSTRACT: Questo testo tratta, con competenze di diversa natura, le principali procedure per l'identificazione e la tipizzazione dei microrganismi negli alimenti, sia come target per indagini di tipo igienico-sanitario, sia per la ricerca di batteri di interesse tecnologico, ovvero associati a trasformazioni alimentari. Dopo un'esauriente introduzione sui diversi aspetti dell'ecofisiologia dei microrganismi negli alimenti e sulle tecniche di controllo dello sviluppo batterico, vengono prese in considerazione le diverse tipologie di generi alimentari, suddivisi in particolare tra prodotti fermentati e non fermentati. Accanto a questo filone più tradizionale, viene inoltre brevemente trattato quello più recente dei probiotici, alimenti con specifici batteri aggiunti per apportare benefici alla salute di chi li consuma.
Edited by Casa Editrice Ambrosiana, 09/2012; Giovanni Antonio Farris, Marco Gobbetti, Erasmo Neviani, Massimo Vincenzini., ISBN: 978-88-08-18246-3
[Show abstract][Hide abstract] ABSTRACT: The novel multi-million read generating sequencing technologies are very promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length screening ability, restricting studies in screening DNA stretches of single 16S rRNA gene hypervariable (V) regions. The aim of the present study was to assess the effects of properties of four consecutive V regions (V3-6) on commonly applied analytical methodologies in bacterial ecology studies. Using an in silico approach, the performance of each V region was compared with the complete 16S rRNA gene stretch. We assessed related properties of the soil derived bacterial sequence collection of the Ribosomal Database Project (RDP) database and concomitantly performed simulations based on published datasets. Results indicate that overall the most prominent V region for soil bacterial diversity studies was V3, even though it was outperformed in some of the tests. Despite its high performance during most tests, V4 was less conserved along flanking sites, thus reducing its ability for bacterial diversity coverage. V5 performed well in the non-redundant RDP database based analysis. However V5 did not resemble the full-length 16S rRNA gene sequence results as well as V3 and V4 did when the natural sequence frequency and occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regions of V6 provide the ability to amplify partial 16S rRNA gene sequences from very diverse owners, it was demonstrated that V6 was the least informative compared to the rest examined V regions. Our results indicate that environment specific database exploration and theoretical assessment of the experimental approach are strongly suggested in 16S rRNA gene based bacterial diversity studies.
PLoS ONE 08/2012; 7(8):e42671. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bacterial endospores are dormant structures produced by stressed bacterial cells. Due to their intrinsic resistance endospores are perfect vehicles for causing infection. A number of endospore producing bacteria can cause diseases including tetanus, anthrax and botulism; other spore forming species have been used in biotechnological applications such as probiotics and biocides. Modern molecular studies are providing new insights into the biochemical and biophysical characteristics of spore forming bacteria that may lead to promising new applications, detection methods and therapeutics.
In this book expert authors from around the world contribute comprehensive, up-to-date reviews on the current state of our knowledge of bacterial endospores. Topics covered include: gene regulation of sporulation, fruiting body development in Myxococcus xanthus, sporulation in Streptomyces, structure and composition of the bacterial spore, mechanisms of spore survival, germination of spores, spore peptidoglycan degradation, water and cations flux during sporulation and germination, the spore as an infectious agent, heterogeneity in spore populations, detection of bacterial spores, and the expression of recombinant proteins using spores.
An essential text for everyone involved in spore research, the expression of recombinant proteins and pathogen detection, this book is also recommended for all scientists that like to keep up with cutting-edge research in microbiology and biotechnology.
Edited by Ernesto Abel-Santos, 07/2012; Caister Academic Press., ISBN: 978-1-908230-00-3
[Show abstract][Hide abstract] ABSTRACT: The food chain is considered one of the main routes of antibiotic resistance diffusion between animal and human population. The resistance to antimicrobial agents among enterococci could be related to the efficient exchange of transferable genetic elements. In this study a sausage model was used to evaluate the persistence of antibiotic resistant enterococci during meat fermentation and to assess horizontal gene transfer among bacteria involved in meat fermentation. Enterococcus faecalis OG1rf harbouring either pCF10 or pAMβ1 plasmid was used as donor strain. The analysis of population dynamics during fermentation confirmed that the human isolate E. faecalis OG1rf was able to colonize the meat ecosystem with similar growth kinetics to that of food origin enterococci and to transfer the mobile genetic elements coding for tetracycline and erythromycin resistances. Transconjugant strains were detected after only two days of fermentation and increased their numbers during ripening even in the absence of selective antibiotic pressure. By means of culture-dependent and -independent molecular techniques, transconjugant strains carrying both tetracycline and erythromycin resistance genes were identified in enterococci, pediococci, lactobacilli and staphylococci groups. Our results suggest that the sausage model provides a suitable environment for horizontal transfer of conjugative plasmids and antibiotic resistance genes among food microbiota.
[Show abstract][Hide abstract] ABSTRACT: Litter soil cover constitutes an important micro-ecosystem in sustainable viticulture having a key role in nutrient cycling and serving as a habitat of complex microbial communities. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are known to regulate nitrification in soil while little is known regarding their function and diversity in litter. We investigated the effects of two fungicides, penconazole and cyprodinil, commonly used in vineyards, on the function and diversity of total and active AOB and AOA in a microcosm study. Functional changes measured via potential nitrification and structural changes assessed via denaturating gradient gel electrophoresis (DGGE) at the DNA and RNA levels were contrasted with pesticide dissipation in the litter layer. The latter was inversely correlated with potential nitrification, which was temporarily inhibited at the initial sampling dates (0 to 21 days) when nearly 100 % of the applied pesticide amounts was still present in the litter. Fungicides induced changes in AOB and AOA communities with RNA-DGGE analysis showing a higher sensitivity. AOA were more responsive to pesticide application compared to AOB. Potential nitrification was less sensitive to the fungicides and was restored faster than structural changes, which persisted. These results support the theory of microbial redundancy for nitrification in a stressed litter environment.
[Show abstract][Hide abstract] ABSTRACT: EFSA is requested to assess the safety of a broad range of biological agents (including microorganisms and viruses) in the context of notifications for market authorisation as sources of food and feed additives, enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed by EFSA for its own use to provide a generic risk assessment approach applicable across EFSA's scientific Panels, for biological agents notified for intentional use in the whole food chain. The safety of unambiguously defined biological agents at the highest taxonomic unit that is appropriate for the purpose for which an application is intended and the completeness of the body of knowledge are assessed. Identified safety concerns for a taxonomic unit are where sensible reflected as 'qualifications' when a recommendation for the QPS list is given. The list of QPS recommended biological agents is reviewed and updated annually. Therefore, the only valid list is the one in the most recent scientific opinion. The 2011 update reviews microorganisms previously assessed including bacteria, yeasts, filamentous fungi and viruses used for plant protection purposes and confirms the previous recommendations. The anamorph yeast form Phaffia rhodozyma of Xanthophyllomyces dendrorhous was included on the QPS list and to the qualification for yeasts 'absence of resistance to antimycotics used for medical treatment of yeast infections', the sentence was added that 'in the case of Saccharomyces cerevisiae this qualification applies for yeast strains able to grow above 37 °C'. The body of knowledge of filamentous fungi and enterococci was updated and their ineligibility for the QPS list confirmed.
[Show abstract][Hide abstract] ABSTRACT: Six strains of non-starter lactic acid bacteria (NSLAB) were used to extend the shelf-life of the fresh cheese Tosèla manufactured with pasteurised cows' milk. The acidification kinetics of three Lactobacillus paracasei, one Lactobacillus rhamnosus and two Streptococcus macedonicus were studied in synthetic milk medium. Lb. paracasei NdP78 and NdP88 and S. macedonicus NdP1 and PB14-1 showed an interesting acidifying capacity and were further characterised for growth in UHT milk and production of antimicrobial compounds. Lb. paracasei NdP78 and S. macedonicus NdP1 grew more than 2 log cycles in 6 h. Lb. paracasei NdP78 was also found to produce a bacteriocin-like inhibitory substance (BLIS) active against Listeria monocytogenes. The four NSLAB strains (singly or in combination) were used to produce experimental pilot-scale cheeses which were compared by a panel. The cheese manufactured with the mixed culture Lb. paracasei NdP78 - S. macedonicus NdP1 was the most appreciated for its sensory properties. The cheeses produced at factory-scale showed higher concentrations of lactobacilli (7.90 log CFU/g) and streptococci (6.10 log CFU/g), but a lower development of coliforms (3.10 log CFU/g) and staphylococci (2.78 log CFU/g) than control cheese (4.86, 4.89, 4.93 and 5.00 log CFU/g of lactobacilli, streptococci, coliforms and staphylococci, respectively) processed without NSLAB addition. The food pathogens Salmonella spp. and Listeria monocytogenes were never detected. The dominance of the species inoculated was demonstrated by denaturing gradient gel electrophoresis (DGGE), whereas strain recognition was evaluated by randomly amplified polymorphic DNA (RAPD)-PCR. From the results obtained, Lb. paracasei NdP78 and S. macedonicus NdP1 were able to persist during the storage of Tosèla cheese and their combination influenced positively the sensory characteristics and shelf-life of the final product.