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4. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Author

Chng K. R., Li C., Bertrand D., Ng A. H. Q., Kwah J. S., Low H. M., Tong C., Natrajan M., Zhang M. H., Xu L., Ko K. K. K., Ho E. X. P., Av-Shalom T. V., Teo J. W. P., Khor C. C., Danko D., Bezdan D., Afshinnekoo E., Ahsanuddin S., Bhattacharya C., Butler D. J., De Filippis F., Hecht J., Kahles A., Karasikov M., Kyrpides N. C., Leung M. H. Y., Meleshko D., Mustafa H., Mutai B., Neches R. Y., Ng A., Nieto-Caballero M., Nikolayeva O., Nikolayeva T., Png E., Sanchez J. L., Shaaban H., Sierra M. A., Tong X., Young B., Alicea J., Bhattacharyya M., Blekhman R., Castro-Nallar E., Canas A. M., Chatziefthimiou A. D., Crawford R. W., Deng Y., Desnues C., Dias-Neto E., Donnellan D., Dybwad M., Elhaik E., Ercolini D., Frolova A., Graf A. B., Green D. C., Hajirasouliha I., Hernandez M., Iraola G., Jang S., Jones A., Kelly F. J., Knights K., Labaj P. P., Lee P. K. H., Shawn L., Ljungdahl P., Lyons A., Mason-Buck G., McGrath K., Mongodin E. F., Moraes M. O., Nagarajan N., Noushmehr H., Oliveira M., Ossowski S., Osuolale O. O., Ozcan O., Paez-Espino D., Rascovan N., Richard H., Ratsch G., Schriml L. M., Semmler T., Sezerman O. U., Shi L., Song L. H., Suzuki H., Court D. S., Thomas D., Tighe S. W., Udekwu K. I., Ugalde J. A., Valentine B., Vassilev D. I., Vayndorf E., Velavan T. P., Zambrano M. M., Zhu J., Zhu S., Mason C. E., Chen S. L., Ng O. T., Marimuthu K., Ang B., Genome Institute of Singapore (GIS), Singapore University of Technology and Design (SUTD), Singapore General Hospital, National University Hospital [Singapore] (NUH), Weill Cornell Medicine [Cornell University], Cornell University [New York], Nanyang Technological University [Singapour], Tan Tock Seng Hospital, Department of Computational and Systems Biology [Singapore], Funding for this work was provided by A*STAR (N.N.), and we are grateful for support from NMRC (NMRC CGAug16C005: O.T.N. and K.M.). C.E.M. acknowledges support from the WorldQuant Foundation, the Bill and Melinda Gates Foundation (OPP1151054) and the Alfred P. Sloan Foundation (G-2015-13964). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. We would like to thank J. Gilbert for insightful comments and feedback on this work., MetaSUB Consortium: David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Francesca De Filippis, Jochen Hecht, Andre Kahles, Mikhail Karasikov, Nikos C. Kyrpides, Marcus H. Y. Leung, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Xinzhao Tong, Ben Young, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Cañas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Mark Hernandez, Gregorio Iraola, Soojin Jang, Angela Jones, Frank J. Kelly, Kaymisha Knights, Paweł P. Łabaj, Patrick K. H. Lee, Levy Shawn, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F. Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan Özcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Lynn M. Schriml, Torsten Semmler, Osman U. Sezerman, Leming Shi, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Dominique Thomas, Scott W. Tighe, Klas I. Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar I. Vassilev, Elena Vayndorf, Thirumalaisamy P. Velavan, María M. Zambrano, Jifeng Zhu, Sibo Zhu & Christopher E. Mason, Weill Cornell Medicine [New York], Chng, K. R., Li, C., Bertrand, D., Ng, A. H. Q., Kwah, J. S., Low, H. M., Tong, C., Natrajan, M., Zhang, M. H., Xu, L., Ko, K. K. K., Ho, E. X. P., Av-Shalom, T. V., Teo, J. W. P., Khor, C. C., Danko, D., Bezdan, D., Afshinnekoo, E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., De Filippis, F., Hecht, J., Kahles, A., Karasikov, M., Kyrpides, N. C., Leung, M. H. Y., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nieto-Caballero, M., Nikolayeva, O., Nikolayeva, T., Png, E., Sanchez, J. L., Shaaban, H., Sierra, M. A., Tong, X., Young, B., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., Deng, Y., Desnues, C., Dias-Neto, E., Donnellan, D., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Graf, A. B., Green, D. C., Hajirasouliha, I., Hernandez, M., Iraola, G., Jang, S., Jones, A., Kelly, F. J., Knights, K., Labaj, P. P., Lee, P. K. H., Shawn, L., Ljungdahl, P., Lyons, A., Mason-Buck, G., Mcgrath, K., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O. O., Ozcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Ratsch, G., Schriml, L. M., Semmler, T., Sezerman, O. U., Shi, L., Song, L. H., Suzuki, H., Court, D. S., Thomas, D., Tighe, S. W., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E., Velavan, T. P., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Chen, S. L., Ng, O. T., Marimuthu, K., Ang, B., and Acibadem University Dspace

Subjects
0301 basic medicine, Disease prevention, 030106 microbiology, Geographic Mapping, Drug resistance, Beds, Biology, Opportunistic Infections, Genome, General Biochemistry, Genetics and Molecular Biology, Article, Tertiary Care Centers, 03 medical and health sciences, Plasmid, Antibiotic resistance, Spatio-Temporal Analysis, Drug Resistance, Multiple, Bacterial, Drug Resistance, Bacterial, Patients' Rooms, Humans, Microbiome, Equipment and Supplies, Hospital, Genetics, Cross Infection, Infection Control, Singapore, Microbiota, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Resistome, Disinfection, 030104 developmental biology, Metagenomics, Biofilms, Equipment Contamination, Mobilome, Microbial genetics
Abstract

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections., Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Published
2020

12. Overlapping signatures in the gut microbiota dysbiosis in children with IgE- and non-IgE-mediated cow’s milk allergy

Author

De Filippis F., Laiola M., Nocerino R., Di Scala C., Cosenza L., Calignano A., De Caro C., Paparo L., Berni Canani R., Ercolini D., 7th International Human Microbiome Consortium Meeting 2018 Organising Committee, De Filippis, F., Laiola, M., Nocerino, R., Di Scala, C., Cosenza, L., Calignano, A., De Caro, C., Paparo, L., Berni Canani, R., and Ercolini, D.

Published
2018

14. Habitual diet selects distinct genetic and functional subtypes of intestinal Prevotella copri

Author

De Filippis F., PASOLLI, EDOARDO, Tett A., De Angelis M., Neviani E., Turroni S., Cocolin L., Gobbetti M., Segata N., Ercolini D., 7th International Human Microbiome Consortium Meeting 2018 Organising Committee, De Filippis, F., Pasolli, Edoardo, Tett, A., De Angelis, M., Neviani, E., Turroni, S., Cocolin, L., Gobbetti, M., Segata, N., and Ercolini, D.

Published
2018

22. Cystic fibrosis linked functional impairment and gut microbiota signatures: from omics data to clinical cue

Author

Vernocchi, P., Del Chierico, F., Russo, A., Majo, F., Valerio, M. C., Casadei, L., La Storia, A., Rizzo, C., Manetti, C., Paci, P., Montemitro, E., Ercolini, D., Marini, F., Fiscarelli, E., Dallapiccola, B., Miccheli, A., Lucidi, V., Putignani, L., DE FILIPPIS, FRANCESCA, European Society for Paediatric Gastroenterology, Hepatology and Nutrition, Vernocchi, P., Del Chierico, F., Russo, A., Majo, F., Valerio, M. C., Casadei, L., La Storia, A., DE FILIPPIS, Francesca, Rizzo, C., Manetti, C., Paci, P., Montemitro, E., Ercolini, D., Marini, F., Fiscarelli, E., Dallapiccola, B., Miccheli, A., Lucidi, V., and Putignani, L.

Published
2017

25. A communal catalogue reveals Earth's multiscale microbial diversity

Author

Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, JF, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, FQ, Campbell, AH, Caporaso, JG, Cardona, C, Carroll, JL, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwell, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, Ezenwa, V, Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, JF, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, FQ, Campbell, AH, Caporaso, JG, Cardona, C, Carroll, JL, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwell, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, and Ezenwa, V

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Published
2017

26. The metagenomics and metadesign of the subways and Urban biomes (MetaSUB) international consortium inaugural meeting report

Author

Afshinnekoo, E, Ahsanuddin, S, Ghedin, E, Read, T, Fraser, C, Dudley, J, Bowler, C, Mason, CE, Chernomoretz, A, Stolovitzky, G, Łabaj, PP, Graf, AB, Darling, A, Burke, C, Noushmehr, H, Dias-Neto, E, Guo, Y, Xie, Z, Lee, PKH, Shi, L, Ruiz-Perez, CA, Zambrano, MM, Siam, R, Ouf, A, Richard, H, Lafontaine, I, Wieler, LH, Semmler, T, Prithiviraj, B, Nedunuri, N, Mehr, S, Banihashemi, K, Lista, F, Anselmo, A, Suzuki, H, Kuroda, M, Yamashita, R, Sato, Y, Kaminuma, E, Aranda, CMA, Martinez, J, Dada, C, Dybwad, M, Oliveira, M, Schuster, S, Siwo, GH, Jang, S, Seo, SC, Hwang, SH, Ossowski, S, Bezdan, D, Chaker, S, Chatziefthimiou, AD, Udekwu, K, Liungdahl, P, Sezerman, U, Meydan, C, Elhaik, E, Gonnet, G, Schriml, LM, Mongodin, E, Huttenhower, C, Gilbert, J, Eisen, J, Hirschberg, D, Hernandez, M, McGrath, K, McGrath, L, Gray, A, Osuolale, O, Segata, N, Fillo, S, Iraola, G, Zhou, Y, Chang, Y, Li, Y, Zhend, Y, Hou, W, Ramirez, A, Cepeda, M, Desnues, C, Rascovan, N, Baron, C, Nagarajan, N, Ercolini, D, Menary, W, Tighe, S, Donia, M, Levy, S, Benito, J, Jones, A, Kasarskis, A, Maritz, J, Jorgensen, E, Neches, R, Livelli, T, Barnetche, JM, Pasolli, E, Greenfield, N, and Hasan, N

Subjects
Research Design, Databases, Genetic, Humans, Public Health, Metagenomics, City Planning, Ecosystem
Abstract

© 2016 The MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

Published
2016

27. Characterization of bacteriocin-coated antimicrobial polyethylene films by atomic force microscopy

Author

La Storia, A., Ercolini, D., Marinello, F., and Mauriello, G.

Subjects
Atomic force microscopy -- Usage, Business, Food/cooking/nutrition
Abstract

The atomic force microscopy (AFM) technique is employed for the characterization of the bacteriocin-coated polyethylene films, which are activated with the antimicrobial agents. The approach is found to be extremely useful in various applications, including food packaging and science.

Published
2008

28. 168 Loss of CFTR function drives the host-gut microbiota interaction: from omics data to clinical cue

Author

Vernocchi, P., primary, Del Chierico, F., additional, Russo, A., additional, Majo, F., additional, Valerio, M., additional, Casadei, L., additional, La Storia, A., additional, De Filippis, F., additional, Rizzo, C., additional, Manetti, C., additional, Paci, P., additional, Ercolini, D., additional, Marini, F., additional, Fiscarelli, E., additional, Dallapiccola, B., additional, Lucidi, V., additional, Miccheli, A., additional, and Putignani, L., additional

Published
2017
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29. FoodMicrobionet: a tool for the visualization and analysis of the structure of bacterial food microbial communities

Author

Parente, E., Cocolin, Luca Simone, De Filippis, F., Zotta, T., Ferrocino, Ilario, Neviani, E., De Angelis, M., Di Cagno, R., Cotter, P., Ercolini, D., 3rd International Conference on Microbial Diversity 2015 Organizing Committee, Parente, Eugenio, Cocolin, Luca, DE FILIPPIS, Francesca, Zotta, Teresa, Ferrocino, Ilario, Neviani, Erasmo, De Angelis, Maria, Di Cagno, Raffaella, Cotter, Paul D., and Ercolini, Danilo

Published
2015

32. Detection of endophytic bacteria in leaves of Vitis vinifera by using fluorescence in situ hybridization

Author

LO PICCOLO, Sandra, CONIGLIARO, Gaetano, TORTA, Livio, BURRUANO, Santa, MOSCHETTI, Giancarlo, ERCOLINI D, LO PICCOLO S, CONIGLIARO G, TORTA L, ERCOLINI D, BURRUANO S, and MOSCHETTI G

Subjects
fluorescence in situ hybridization, endophytic bacteria, Vitis vinifera
Abstract

Previous investigation on five cultivars of healthy Sicilian grapevine allowed the isolation of endophytic bacteria belonging to Bacillus genus from different organs (bud, leaf, stalk and shoot). The aim of this work was to use fluorescence in situ hybridization (FISH) experiments in healthy and damaged leaf tissues of Vitis vinifera to visualize and localize bacteria associated with plant materials. The leaves were cleared to minimize the autofluorescence of the plant fragments. The use of fluorescently labelled bacterial probe Eub338 in FISH experiments on discoloured grapevine leaf disks allowed the estimation of the spatial distribution of different bacterial colonies. At the same time, one cleared disk each foliar sample was minced on Plate Count Agar to detect cultivable endophytic bacteria. The combined microscopic approach showed a differential location of microbial colonies within the leaf tissues examined. Particularly, the bacterial colonies were found in the veins, cells, hairs, intercellular spaces and more in the cut edges of leaf disk. Several bacterial species were isolated from leaf tissue. The high presence of microbial colonies in leaf tissue suggests a potential use of these endophytic bacteria as plant growth promoting and sources of resistance against pathogenic agents, such as fungi. Further studies are required to understand the role of bacterial endophytes in plant-microbe inter- actions. Besides, the DGGE (Denaturing Gradient Gel Electrophoresis) analysis from foliar disks will be carried out to detect uncultivable endophytic bacterial populations.

Published
2008

35. Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber

Author

Vitaglione, P., Mennella, I., Ferracane, R., Rivellese, A.A., Giacco, R., Ercolini, D., Gibbons, S.M., la Storia, A., Gilbert, A.J., Jonnalagadda, S., Thielecke, F., Gallo, M.A., Scalfi, L., Fogliano, V., Vitaglione, P., Mennella, I., Ferracane, R., Rivellese, A.A., Giacco, R., Ercolini, D., Gibbons, S.M., la Storia, A., Gilbert, A.J., Jonnalagadda, S., Thielecke, F., Gallo, M.A., Scalfi, L., and Fogliano, V.

Abstract

Background: Epidemiology associates whole-grain (WG) consumption with several health benefits. Mounting evidence suggests that WG wheat polyphenols play a role in mechanisms underlying health benefits. Objective: The objective was to assess circulating concentration, excretion, and the physiologic role of WG wheat polyphenols in subjects with suboptimal dietary and lifestyle behaviors. Design: A placebo-controlled, parallel-group randomized trial with 80 healthy overweight/obese subjects with low intake of fruits and vegetables and sedentary lifestyle was performed. Participants replaced precise portions of refined wheat (RW) with a fixed amount of selected WG wheat or RW products for 8 wk. At baseline and every 4 wk, blood, urine, feces, and anthropometric and body composition measures were collected. Profiles of phenolic acids in biological samples, plasma markers of metabolic disease and inflammation, and fecal microbiota composition were assessed. Results: WG consumption for 4–8 wk determined a 4-fold increase of serum dihydroferulic acid (DHFA) and a 2-fold increase of fecal ferulic acid (FA) compared with RW consumption (no changes). Similarly, urinary FA at 8 wk doubled the baseline concentration only in WG subjects. Concomitant reduction of plasma tumor necrosis factor-a (TNF-a) after 8 wk and increased interleukin (IL)-10 only after 4 wk with WG compared with RW (P = 0.04) were observed. No significant change in plasma metabolic disease markers over the study period was observed, but a trend toward lower plasma plasminogen activator inhibitor 1 with higher excretion of FA and DHFA in the WG group was found. Fecal FA was associated with baseline low Bifidobacteriales and Bacteroidetes abundances, whereas after WG consumption, it correlated with increased Bacteroidetes and Firmicutes but reduced Clostridium. TNF-a reduction correlated with increased Bacteroides and Lactobacillus. No effect of dietary interventions on anthropometry and body composition was fou

Published
2015

37. Diversity of Staphylococcus strains based on partial kat (catalase) gene sequences and designs of a PCR-RFLP assay for identification and differentiation of coagulase positive species (S. aureus, S. delphini, S. hyicus, S. intermedius, S. pseudintermedius)

Author

Blaiotta G., Fusco V., Ercolini D., Pepe O., and Coppola S.

Abstract

A set of degenerate PCR primers was designed and used to amplify and sequence about 75% of the catalase (kat) gene from each of 49 staphylococcal strains. In some strains of Staphylococcus xylosus, S. saprophyticus, and S. equorum, two catalase genes, katA and katB, were found. A phylogenetic tree was generated and showed diversities among 66 partial (about 900-bp) staphylococcal kat nucleotide sequences (including 17 sequences found in GenBank) representing 26 different species. The topology of this tree showed a distribution of staphylococcal species similar, but not identical, to those reported previously based on 16S rRNA, hsp60, sodA, rpoB, tuf, and gap genes. The kat gene sequences were less conserved than those of 16S rRNA, rpoB, hsp60, and tuf genes and slightly more conserved than those of the gap gene. Therefore, kat gene sequence analysis may provide an additional marker for inferring phylogenetic relationships of staphylococci. Moreover, the discrete nucleotide polymorphism revealed in this gene could be exploited for rapid, low-cost identification of staphylococcal species through PCR-restriction fragment length polymorphism (RFLP) analysis. In this study, a PCR-RFLP assay performed by using only the TaqI restriction enzyme was successfully developed for rapid unequivocal identification/differentiation, at species and subspecies levels, of coagulase-positive staphylococci (CPS). The assay was validated by testing the DNA from 100 staphylococcal strains, including reference and wild CPS strains isolated from different environments. This reliable, rapid, and low-cost approach (requiring about 6 h from DNA isolation to the achievement of results and

Published
2010

40. Lactobacillus Strain Diversity Based on Partial hsp60 Gene Sequences and Design of PCR-Restriction Fragment Length Polymorphism Assays for Species Identification and Differentiation

Author

Blaiotta G., Fusco V., Ercolini D., Aponte M., Pepe O., and Villani F.

Subjects
fungi, food and beverages
Abstract

A phylogenetic tree showing diversities among 116 partial (499-bp) Lactobacillus hsp60 (groEL, encoding a 60-kDa heat shock protein) nucleotide sequences was obtained and compared to those previously described for 16S rRNA and tuf gene sequences. The topology of the tree produced in this study showed a Lactobacillus species distribution similar, but not identical, to those previously reported. However, according to the most recent systematic studies, a clear differentiation of 43 single-species clusters was detected/identified among the sequences analyzed. The slightly higher variability of the hsp60 nucleotide sequences than of the 16S rRNA sequences offers better opportunities to design or develop molecular assays allowing identification and differentiation of either distant or very closely related Lactobacillus species. Therefore, our results suggest that hsp60 can be considered an excellent molecular marker for inferring the taxonomy and phylogeny of members of the genus Lactobacillus and that the chosen primers can be used in a simple PCR procedure allowing the direct sequencing of the hsp60 fragments. Moreover, in this study we performed a computer-aided restriction endonuclease analysis of all 499-bp hsp60 partial sequences and we showed that the PCR-restriction fragment length polymorphism (RFLP) patterns obtainable by using both endonucleases AluI and TacI (in separate reactions) can allow identification and differentiation of all 43 Lactobacillus species considered, with the exception of the pair L. plantarum/L. pentosus. However, the latter species can be differentiated by further analysis with Sau3AI or MseI. The hsp60 PCR-RFLP approach was efficiently applied to identify and to differentiate a total of 110 wild Lactobacillus strains (including closely related species, such as L. casei and L. rhamnosus or L. plantarum and L. pentosus) isolated from cheese and dry-fermented sausages.

Published
2008

42. Evaluation of PCR-DGGE analysis for molecular typing of cheeses

Author

Ercolini, D., Giuseppe BLAIOTTA, Moschetti, G., Coppola, S., Ercolini, Danilo, Blaiotta, Giuseppe, G., Moschetti, and Coppola, Salvatore

Abstract

Molecular typing of several cheeses was achieved by PCR-DGGE analysis of microbial DNA directly extracted from the dairy samples. Cheese-specific fingerprints were obtained analyzing the variable V3 region of 16S rDNA, the profiles showed to be repeatable and reliable after repeated analysis of the same sample. Statistical analysis of molecular data showed relevant differences among cheeses highlighting the potential of the PCR-DGGE fingerprinting for the discrimination of dairy products. The variability of the fingerprints obtained by different samples of the same type of cheese definitely compromises the use of the technique to develop class-specific profiles to be used for cheeses classification, allowing just to detect the degree of complexity of the microbiota.

Published
2002

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