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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
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7. 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

9. 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

17. 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

20. 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

21. 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

26. 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

27. 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

29. 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

34. Spoilage-related microbiota associated with chilled beef stored in air or vacuum pack

Author

Pennacchia, C., Ercolini, D., and Villani, F.

Subjects
*FOOD preservation, *FOOD spoilage, *BEEF, *MICROORGANISMS, *VACUUM technology, *ENTEROBACTERIACEAE, *LACTIC acid bacteria, *BACTERIAL growth, *DNA
Abstract

Abstract: In order to study the spoilage-related microbiota of beef at species level, a combination of culture-independent and culture-dependent methods was used to analyse nine different beef samples stored at 4°C in air or in vacuum pack. Plate counts on selective agars after 0, 7 and 20 days of storage showed that vacuum packaging reduced the viable counts of Brochothrix thermosphacta, Pseudomonas spp. and Enterobacteriaceae, whereas the growth of lactic acid bacteria (LAB) was unaffected. Storage in vacuum pack mainly affected viable counts and not necessarily the species diversity of microbial populations on meat. Such populations were studied by PCR-DGGE of DNA directly extracted from meat and from bulk cells from culture media, followed by sequencing of DGGE fragments. Pseudomonas spp., Carnobacterium divergens, B. thermosphacta, Rahnella spp. and Serratia grimesii, or close relatives were detected in the meat at time zero. The use of the culture-independent method highlighted the occurrence of species that were not detected by plating. Photobacterium spp. occurred in most meat samples stored in air or in vacuum pack, which indicates this organism probably has a role in spoilage. In contrast, culture-dependent analysis allowed detection of bacterial species that were not found in DNA extracted directly from meat. This was the case for several species of Serratia or Rhanella among the enterobacteria, and Leuconostoc spp. among the LAB. Besides advancing our knowledge of the species involved in the spoilage of vacuum-packaged meat, this study shows the benefits of combining culture-based and direct approaches to enhance understanding of populations of spoilage bacteria. [Copyright &y& Elsevier]

Published
2011
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35. Behaviour of Brochothrix thermosphacta in presence of other meat spoilage microbial groups

Author

Russo, F., Ercolini, D., Mauriello, G., and Villani, F.

Subjects
*FOOD storage, *MEAT, *ANIMAL products, *BEEF
Abstract

Abstract: The microbial flora of fresh meat stored aerobically at 5°C up to spoilage was enumerated and collected in order to have mixed spoilage bacterial groups to be used in competition tests against Brochothrix thermosphacta. The bacterial groups collected as bulk colonies were identified by PCR-DGGE followed by partial 16S rDNA sequencing. The predominant bacteria associated with the spoilage of the refrigerated beef were B. thermosphacta, Pseudomonas spp, Enterobacteriaceae and lactic acid bacteria (LAB). The interactions between B. thermosphacta and the other spoilage microbial groups were studied in vitro at 5°C. The results showed that a decrease of the growth of B. thermosphacta was evidenced in presence of LAB at 5°C while the bacterium is the dominant organism when inoculated with mixtures of Pseudomonas spp., LAB and Enterobacteriaceae. A better understanding of bacterial meat spoilage interactions may lead to improved quality of fresh meat stored in refrigerated conditions. [Copyright &y& Elsevier]

Published
2006
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36. Response of Escherichia coli O157:H7, Listeria monocytogenes, Salmonella Typhimurium, and Staphylococcus aureus to the Thermal Stress Occurring in Model Manufactures of Grana Padano Cheese.

Author

Ercolini, D., Fusco, V., Blaiotta, G., Sarghini, F., and Coppola, S.

Subjects
*FOOD pathogens, *RAW milk cheese, *THERMAL stresses, *ESCHERICHIA coli, *LISTERIA monocytogenes, *SALMONELLA typhimurium, *STAPHYLOCOCCUS aureus
Abstract

The purpose of this research was to investigate the effect of temperature in the technology of production of Grana cheese against Escherichia coli O157:H7, Listeria monocytogenes, Salmonella Typhimurium, and Staphylococcus aureus. According to the technology of production, the cheese curds are cooked at 55°C and then cooled at room temperature (25°C). A curd-cooling model was developed to estimate the temperature variation across the curd during cooling, and the thermal stress was applied to the pathogens according to the model in model-scale productions of Grana cheese artificially contaminated with approximately 104 cfu/mL of the selected pathogens. According to the numerical results, the initial temperature inside the cheese is kept at almost the initial value (above 50°C) for at least 4 h during cooling, whereas the crust of the curd cools rapidly to 30°C in the first hour. The best case was that of the core of the cheese where the high temperature was able to efficiently eliminate the contaminating pathogens. Moreover, the worst case was where the external ring of the curd in which a more rapid cooling allowed bacterial survival. Therefore, the thermal stress in the technology of production of Grana cheese can be only partially effective in the control of the selected pathogens. However, the whole technology of production includes other hurdles that can affect the survival of the pathogens and that need to be taken into account as a whole to evaluate the safety of Grana Padano cheese. [ABSTRACT FROM AUTHOR]

Published
2005
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37. Identification of Campania Citrus Limon L. by Random Amplified Polymorphic DNA Markers.

Author

Mariniello, L., Sommella, M. G., Cozzolino, A., Di Pierro, P., Ercolini, D., and Porta, R.

Subjects
CITRUS, GENETIC markers, GENETIC polymorphisms, CULTIVARS
Abstract

Genotypes of 10 lemon (Citrus limon L.) cultivars of the Campania region (Southern Italy) have been studied by using Random Amplified Polymorphic DNA (RAPD) markers with 44 arbitrary 10-mer primers. Some of the studied cultivars (Sorrento, Procida, Amalfi, and Gloria d’Amalfi) have been successfully distinguished by their band patterns using five out of the 44 selected primers, confirming that RAPD technology provides a useful tool to identify specific cultivars. [ABSTRACT FROM AUTHOR]

Published
2004
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38. PCR detection of staphylococcal enterotoxin genes inStaphylococcusspp. strains isolated from meat and dairy products. Evidence for new variants ofseG andseI inS. aureusAB-8802.

Author

Blaiotta, G., Ercolini, D., Pennacchia, C., Fusco, V., Casaburi, A., Pepe, O., and Villani, F.

Subjects
*STAPHYLOCOCCUS, *ENTEROTOXINS, *BACTERIAL toxins, *DAIRY products, *MEAT
Abstract

g. blaiotta, d. ercolini, c. pennacchia, v. fusco, a. casaburi, o. pepe and f. villani. 2004.Evaluation of the occurrence of most known staphylococcal enterotoxin (SE) genes,egc(enterotoxin gene cluster) and TSST1 (toxic shock syndrome toxin 1) gene in both coagulase-positive (CPS) and coagulase-negative (CNS) staphylococcal strains isolated from meat and dairy products.Specificity and reliability of the PCR detection methods used were ascertained by using nine reference strains ofStaphylococcus(S. aureus) harbouring SE genes (seA toseE;seG,seH,seI,seM, seJ,seN andseO) andegc(containing the following sequence of genes: seO,seM,seI,ϕ ent1,ϕ ent2,seN andseG). Of 109 wildStaphylococcusspp. strains analysed, only 11S. aureusstrains were SE and/or TSST1 PCR-positive. The last 11 strains also appeared to harbour theegc. Restriction endonuclease analysis of part of theegcof both reference and wild strains showed that different variants of theegcexist. Moreover, nucleotide sequences ofseG andseI indicate that theegcof the strain AB-8802 is characterized by the presence of variants of these enterotoxins (seGv andseIv).The occurrence of SE genes in CNS and other non-S. aureusspecies isolated from Napoli-type salami, raw water buffalo milk and natural whey cultures used for mozzarella cheese manufacturing is very rare.During this study it was shown that at least five differentegcmay exist inS. aureus. A thorough study ofegcpolymorphism should provide further insight into the phylogenetics of theegc. [ABSTRACT FROM AUTHOR]

Published
2004
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39. Selection of Lactobacillus strains from fermented sausages for their potential use as probiotics

Author

Pennacchia, C., Ercolini, D., Blaiotta, G., Pepe, O., Mauriello, G., and Villani, F.

Subjects
*LACTOBACILLUS, *SAUSAGES, *BILE salts, *SALTS
Abstract

A rapid screening method was used to isolate potentially probiotic Lactobacillus strains from fermented sausages after enrichment in MRS broth at pH 2.5 followed by bile salt stressing (1% bile salts w/v). One hundred and fifty acid- and bile-resistant strains were selected, avoiding preliminary and time-consuming isolation steps. Strains were further characterized for survival at pH 2.5 for 3 h in phosphate-buffered saline and for growth in the presence of 0.3% bile salts with and without pre-exposure at low pH. Twenty-eight strains showed a survival >80% at pH 2.5 for 3 h; moreover, most of the strains were able to grow in the presence of 0.3% bile salts. Low pH and bile resistance was shown to be dependent on both the species, identified by phenotypic and molecular methods, and the strain tested.This is the first report on the direct selection of potentially probiotic lactobacilli from dry fermented sausages. Technologically interesting strains may be used in the future as probiotic starter cultures for novel fermented sausage manufacture. [Copyright &y& Elsevier]

Published
2004
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41. Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis

Author

Borriello Giorgia, Lucibelli Maria G, Pesciaroli Michele, Carullo Maria R, Graziani Caterina, Ammendola Serena, Battistoni Andrea, Ercolini Danilo, Pasquali Paolo, and Galiero Giorgio

Subjects
Salmonella, Virulence markers, Genetic characterization, Gastrointestinal ecology, Veterinary medicine, SF600-1100
Abstract

Abstract Background Salmonellosis in water buffalo (Bubalus bubalis) calves is a widespread disease characterized by severe gastrointestinal lesions, profuse diarrhea and severe dehydration, occasionally exhibiting a systemic course. Several Salmonella serovars seem to be able to infect water buffalo, but Salmonella isolates collected from this animal species have been poorly characterized. In the present study, the prevalence of Salmonella spp. in water buffalo calves affected by lethal gastroenteritis was assessed, and a polyphasic characterization of isolated strains of S. Typhimurium was performed. Results The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. (25%), characterized by different serovars, most frequently Typhimurium (21%), Muenster (11%), and Give (11%). The 13 S. Typhimurium isolates were all associated with enterocolitis characterized by severe damage of the intestine, and only sporadically isolated with another possible causative agent responsible for gastroenteritis, such as Cryptosporidium spp., Rotavirus or Clostridium perfringens. Other Salmonella isolates were mostly isolated from minor intestinal lesions, and often (78% of cases) isolated with other microorganisms, mainly toxinogenic Escherichia coli (35%), Cryptosporidium spp. (20%) and Rotavirus (10%). The S. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The isolates exhibited nine different phage types and 10 different genetic profiles. Three monophasic S. Typhimurium (B:4,12:i:-) isolates were also found and characterized, displaying three different phage types and three different virulotypes. The molecular characterization was extended to the 7 S. Muenster and 7 S. Give isolates collected, indicating the existence of different virulotypes also within these serovars. Three representative strains of S. Typhimurium were tested in vivo in a mouse model of mixed infection. The most pathogenic strain was characterized by a high number of virulence factors and the presence of the locus agfA, coding for a thin aggregative fimbria. Conclusions These results provide evidence that Salmonella is frequently associated with gastroenteritis in water buffalo calves, particularly S. Typhimurium. Moreover, the variety in the number and distribution of different virulence markers among the collected S. Typhimurium strains suggests that within this serovar there are different pathotypes potentially responsible for different clinical syndromes.

Published
2012
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42. Identification and characterization of human observational studies in nutritional epidemiology on gut microbiomics for joint data analysis

Author

Pinart, Mariona, Nimptsch, Katharina, Forslund, Sofia, Schlicht, Kristina, Gueimonde, Miguel, Brigidi, Patrizia, Turroni, Silvia, Ahrens, Wolfgang, Hebestreit, Antje, Wolters, Maike, Dötsch, Andreas, Nöthlings, Ute, Oluwagbemigun, Kolade, Cuadrat, Rafael, Schulze, Matthias, Standl, Marie, Schloter, Michael, De Angelis, Maria, Iozzo, Patricia, Guzzardi, Maria Angela, Vlaemynck, Geertrui, Penders, John, Jonkers, Daisy, Stemmer, Maya, Chiesa, Giulia, Cavalieri, Duccio, De Filippo, Carlotta, Ercolini, Danilo, De Filippis, Francesca, Ribet, David, Achamrah, Najate, Tavolacci, Marie-Pierre, Déchelotte, Pierre, Bouwman, Jildau, Laudes, Matthias, Pischon, Tobias, Pinart M., Nimptsch K., Forslund S.K., Schlicht K., Gueimonde M., Brigidi P., Turroni S., Ahrens W., Hebestreit A., Wolters M., Dotsch A., Nothlings U., Oluwagbemigun K., Cuadrat R.R.C., Schulze M.B., Standl M., Schloter M., De Angelis M., Iozzo P., Guzzardi M.A., Vlaemynck G., Penders J., Jonkers D.M.A.E., Stemmer M., Chiesa G., Cavalieri D., De Filippo C., Ercolini D., De Filippis F., Ribet D., Achamrah N., Tavolacci M.-P., Dechelotte P., Bouwman J., Laudes M., Pischon T., Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany, Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany, Host-Microbiome Factors in Cardiovascular Disease Lab, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany, German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany, Berlin Institute of Health (BIH), 10178 Berlin, Germany, Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany, Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain, Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain, Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany, Institute of Statistics, Bremen University, 28359 Bremen, Germany, Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany, Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany, Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany, Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany, German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany, Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany, Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy, Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy, Department Technology and Food, Flanders Research Institute for Agriculture, Fisheries and Food, 9090 Melle, Belgium, Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands, Department of Internal Medicine, Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva P.O. Box 653, Israel, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Florence, Italy, Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy, Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy, Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Normandie Université (NU)-Normandie Université (NU), Service de nutrition [CHU Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Normandie Université (NU), Centre d'Investigation Clinique [CHU Rouen] (CIC Rouen), Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands, Biobank Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany, Biobank Core Facility, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10178 Berlin, Germany, European Commission, Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Research Foundation - Flanders, Institut National de la Santé et de la Recherche Médicale (France), Federal Ministry of Education and Research (Germany), Federal Ministry of Food and Agriculture (Germany), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministero delle Politiche Agricole Alimentari e Forestali, National Institutes of Health (US), Ministero della Salute, Instituto de Salud Carlos III, Netherlands Organisation for Health Research and Development, Austrian Research Promotion Agency, Federal Ministry of Education, Science and Research (Austria), Ministry of Science, Technology and Space (Israel), Swedish Research Council for Sustainable Development, German Research Foundation, RS: CAPHRI - R4 - Health Inequities and Societal Participation, Med Microbiol, Infect Dis & Infect Prev, RS: NUTRIM - R2 - Liver and digestive health, Interne Geneeskunde, Pinart, M., Nimptsch, K., Forslund, S. K., Schlicht, K., Gueimonde, M., Brigidi, P., Turroni, S., Ahrens, W., Hebestreit, A., Wolters, M., Dotsch, A., Nothlings, U., Oluwagbemigun, K., Cuadrat, R. R. C., Schulze, M. B., Standl, M., Schloter, M., De Angelis, M., Iozzo, P., Guzzardi, M. A., Vlaemynck, G., Penders, J., Jonkers, D. M. A. E., Stemmer, M., Chiesa, G., Cavalieri, D., De Filippo, C., Ercolini, D., De Filippis, F., Ribet, D., Achamrah, N., Tavolacci, M. -P., Dechelotte, P., Bouwman, J., Laudes, M., Pischon, T., Humboldt-Universität zu Berlin, and CHU Rouen

Subjects
Nutritional Sciences, Metabolome, Metadata, Data sharing, Observational studies, Data integration, Dietary intake, Microbiome, Diet Surveys, Article, Eating, Nutritional Science, AGE, Humans, TX341-641, observational studies, Nutrition. Foods and food supply, Information Dissemination, Nutrition Survey, Nutrition Surveys, Observational studie, Gastrointestinal Microbiome, Diet Survey, Europe, Observational Studies as Topic, Cardiovascular and Metabolic Diseases, Data Integration, Data Sharing, Dietary Intake, Observational Studies, Technology Platforms, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Human
Abstract

In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease., This research was supported by the Joint Action “European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)”and the respective national/regional funding organisations: Fund for Scientific Research (FRS—FNRS, Belgium); Research Foundation—Flanders (FWO, Belgium); INSERM Institut National de la Santé et de la Recherche Médicale (France); Federal Ministry of Education and Research (BMBF, FKZ 01EA1906B, 01EA1906D); Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE, Germany, grant number 2819ERA10F); Ministry of Education, University and Research (MIUR), Ministry of agricultural, food and forestry policies (MiPAAF), National Institute of Health (ISS) on behalf of Ministry of Health (Italy); National Institute of Health Carlos III (Spain); The Netherlands Organisation for Health Research and Development (ZonMw, The Netherlands), Austrian Research Promotion Agency (FFG) on behalf of the Austrian Federal Ministry for Education, Science and Research (BMBWF), Ministry of Science and Technology (Israel), Formas (Sweden). This research was also supported by the German Research Foundation (DFG, KFO339: “food@”).

Published
2021
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43. Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans

Author

Danilo Ercolini, Raffaella Di Cagno, Andrea Osimani, Silvia Turroni, Francesca De Filippis, Camilla Lazzi, Stefano Tavoletti, Lucia Aquilanti, Vesna Milanović, Ilario Ferrocino, Francesca Clementi, Cristiana Garofalo, Nicoletta Pellegrini, Milanovic V., Aquilanti L., Tavoletti S., Garofalo C., Osimani A., De Filippis F., Ercolini D., Ferrocino I., Di Cagno R., Turroni S., Lazzi C., Pellegrini N., Clementi F., Milanovic, V., Aquilanti, L., Tavoletti, S., Garofalo, C., Osimani, A., De Filippis, F., Ercolini, D., Ferrocino, I., Di Cagno, R., Turroni, S., Lazzi, C., Pellegrini, N., and Clementi, F.

Subjects
Adult, DNA, Bacterial, Male, 0301 basic medicine, Saliva, Adolescent, lcsh:QH426-470, 030106 microbiology, Antibiotic resistance gene, Dietary habit, Article, Microbiology, Cohort Studies, Young Adult, 03 medical and health sciences, Antibiotic resistance, antibiotic resistance genes, stomatognathic system, human saliva, Genetics, medicine, Humans, Gene, dietary habits, Genetics (clinical), Vegans, Bacteria, biology, human salivary resistome, Drug Resistance, Microbial, Middle Aged, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Healthy Volunteers, Anti-Bacterial Agents, Diet, Resistome, lcsh:Genetics, 030104 developmental biology, Antibiotic resistance genes, Dietary habits, Human saliva, Human salivary resistome, Oral cavity, Vancomycin, Female, oral cavity, Omnivore, Nested polymerase chain reaction, Vegetarians, medicine.drug
Abstract

Food consumption allows the entrance of bacteria and their antibiotic resistance (AR) genes into the human oral cavity. To date, very few studies have examined the influence of diet on the composition of the salivary microbiota, and even fewer investigations have specifically aimed to assess the impact of different long-term diets on the salivary resistome. In this study, the saliva of 144 healthy omnivores, ovo-lacto-vegetarians, and vegans were screened by nested PCR for the occurrence of 12 genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and &beta, lactams. The tet(W), tet(M), and erm(B) genes occurred with the highest frequencies. Overall, no effect of diet on AR gene distribution was seen. Some differences emerged at the recruiting site level, such as the higher frequency of erm(C) in the saliva of the ovo-lacto-vegetarians and omnivores from Bologna and Turin, respectively, and the higher occurrence of tet(K) in the saliva of the omnivores from Bologna. A correlation of the intake of milk and cheese with the abundance of tet(K) and erm(C) genes was seen. Finally, when the occurrence of the 12 AR genes was evaluated along with geographical location, age, and sex as sources of variability, high similarity among the 144 volunteers was seen.

Published
2020

44. Altered gut microbiota and endocannabinoid system tone in vitamin D deficiency-mediated chronic pain

Author

Carmela Belardo, Livio Luongo, Serena Boccella, Fabiana Piscitelli, Dario Siniscalco, Sabatino Maione, Monica Iannotta, Francesca Guida, Danilo Ercolini, Ida Marabese, Flavia Ricciardi, Salvatore Paino, Francesca De Filippis, Vincenzo Di Marzo, Guida, F., Boccella, S., Belardo, C., Iannotta, M., Piscitelli, F., De Filippis, F., Paino, S., Ricciardi, F., Siniscalco, D., Marabese, I., Luongo, L., Ercolini, D., Di Marzo, V., Maione, S., Guida, F, Boccella, S, Belardo, C, Iannotta, M, Piscitelli, F, De Filippis, F, Paino, S, Ricciardi, F, Siniscalco, D, Marabese, I, Luongo, L, Ercolini, D, and Di Marzo, V

Subjects
0301 basic medicine, medicine.medical_specialty, Vitamin D deficiency, endocannabinoidome, Immunology, microbiome, Pain, Gut microbiota, Gut flora, digestive system, vitamin D deficiency, Mice, 03 medical and health sciences, Behavioral Neuroscience, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, medicine, Vitamin D and neurology, Animals, Endocannabinoid, Inflammation, Palmitoylethanolamide, biology, Endocrine and Autonomic Systems, Chronic pain, Akkermansia, medicine.disease, biology.organism_classification, Endocannabinoid system, Gastrointestinal Microbiome, 030104 developmental biology, Endocrinology, Nociception, chemistry, Chronic Pain, 030217 neurology & neurosurgery, Endocannabinoids
Abstract

Recent evidence points to the gut microbiota as a regulator of brain and behavior, although it remains to be determined if gut bacteria play a role in chronic pain. The endocannabinoid system is implicated in in- flammation and chronic pain processing at both the gut and central nervous system (CNS) levels. In the present study, we used low Vitamin D dietary intake in mice and evaluated possible changes in gut microbiota, pain processing and endocannabinoid system signaling. Vitamin D deficiency induced a lower microbial diversity characterized by an increase in Firmicutes and a decrease in Verrucomicrobia and Bacteroidetes. Concurrently, vitamin D deficient mice showed tactile allodynia associated with neuronal hyperexcitability and alterations of endocannabinoid system members (endogenous mediators and their receptors) at the spinal cord level. Changes in endocannabinoid (anandamide and 2-ara- chidonoylglycerol) levels were also observed in the duodenum and colon. Remarkably, the anti-inflammatory anandamide congener, palmitoylethanolamide, counteracted both the pain behaviour and spinal biochemical changes in vitamin D deficient mice, whilst increasing the levels of Akkermansia, Eubacterium and Enterobacteriaceae, as compared with vehicle-treated mice. Finally, induction of spared nerve injury in normal or vitamin D deficient mice was not accompanied by changes in gut microbiota composition. Our data suggest the existence of a link between Vitamin D deficiency – with related changes in gut bacterial composition – and altered nociception, possibly via molecular mechanisms involving the endocannabinoid and related mediator signaling systems.

Published
2020
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45. Diet influences the functions of the human intestinal microbiome

Author

De Angelis, Maria, Ferrocino, Ilario, Calabrese, Francesco Maria, De Filippis, Francesca, Cavallo, Noemi, Siragusa, Sonya, Rampelli, Simone, Di Cagno, Raffaella, Rantsiou, Kalliopi, Vannini, Lucia, Pellegrini, Nicoletta, Lazzi, Camilla, Turroni, Silvia, Lorusso, Nicola, Ventura, Mario, Chieppa, Marcello, Neviani, Erasmo, Brigidi, Patrizia, O’Toole, Paul W., Ercolini, Danilo, Gobbetti, Marco, Cocolin, Luca, De Angelis M., Ferrocino I., Calabrese F.M., De Filippis F., Cavallo N., Siragusa S., Rampelli S., Di Cagno R., Rantsiou K., Vannini L., Pellegrini N., Lazzi C., Turroni S., Lorusso N., Ventura M., Chieppa M., Neviani E., Brigidi P., O'Toole P.W., Ercolini D., Gobbetti M., Cocolin L., De Angelis, M., Ferrocino, I., Calabrese, F. M., De Filippis, F., Cavallo, N., Siragusa, S., Rampelli, S., Di Cagno, R., Rantsiou, K., Vannini, L., Pellegrini, N., Lazzi, C., Turroni, S., Lorusso, N., Ventura, M., Chieppa, M., Neviani, E., Brigidi, P., O'Toole, P. W., Ercolini, D., Gobbetti, M., Cocolin, L., De Angelis, Maria, Ferrocino, Ilario, Maria Calabrese, Francesco, De Filippis, Francesca, Cavallo, Noemi, Siragusa, Sonya, Rampelli, Simone, Di Cagno, Raffaella, Rantsiou, Kalliopi, Vannini, Lucia, Pellegrini, Nicoletta, Lazzi, Camilla, Turroni, Silvia, Lorusso, Nicola, Ventura, Mario, Chieppa, Marcello, Neviani, Erasmo, Brigidi, Patrizia, W O'Toole, Paul, Ercolini, Danilo, Gobbetti, Marco, and Cocolin, Luca

Subjects
Tumor, Nitrogen, lcsh:R, lcsh:Medicine, Computational Biology, Article, Cell Line, Diet, Gastrointestinal Microbiome, Feces, Cell Line, Tumor, Humans, Metabolic Networks and Pathways, Metagenome, Metagenomics, lcsh:Q, Microbiome, lcsh:Science
Abstract

Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects of key dietary components on microbial functions and the way they modulate host–microbe interaction, we used for the first time a multi-omic approach that goes behind the mere gut phylogenetic composition and provides an overall picture of the functional repertoire in 27 fecal samples from omnivorous, vegan and vegetarian volunteers. Based on our data, vegan and vegetarian diets were associated to the highest abundance of microbial genes/proteins responsible for cell motility, carbohydrate- and protein-hydrolyzing enzymes, transport systems and the synthesis of essential amino acids and vitamins. A positive correlation was observed when intake of fiber and the relative fecal abundance of flagellin were compared. Microbial cells and flagellin extracted from fecal samples of 61 healthy donors modulated the viability of the human (HT29) colon carcinoma cells and the host response through the stimulation of the expression of Toll-like receptor 5, lectin RegIIIα and three interleukins (IL-8, IL-22 and IL-23). Our findings concretize a further and relevant milestone on how the diet may prevent/mitigate disease risk.

Published
2020

46. Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice

Author

Rosario Cuomo, Mariacristina Mazzitelli, Serena Boccella, Fabiana Piscitelli, Livio Luongo, Francesco Napolitano, F. De Filippis, Fabio Turco, V. Di Marzo, Sabatino Maione, Danilo De Gregorio, Fabio Arturo Iannotti, Monica Iannotta, Danilo Ercolini, Giovanni Sarnelli, Anna Furiano, V. de Novellis, Ilaria Palumbo, Francesca Guida, Alessandro Usiello, Guida, Francesca, Turco, F, Iannotta, M, Nulld, nullDe Gregorio, Palumbo, I, Sarnelli, G, Furiano, A, Napolitano, F, Boccella, S, Luongo, L, Mazzitelli, M, Usiello, A, Nullf, nullDe Filippi, Iannotti, Fa, Piscitelli, F, Ercolini, D, DE NOVELLIS, Vito, Nullv, nullDi Marzo, Cuomo, R, Maione, S., Guida, F, De Gregorio, D, Sarnelli, Giovanni, DE FILIPPIS, Francesca, Iannotti, F, De Novellis, V, Di Marzo, V, Guida, F., Turco, F., Iannotta, M., De Gregorio, D., Palumbo, I., Sarnelli, G., Furiano, A., Napolitano, F., Boccella, S., Luongo, L., Mazzitelli, M., Usiello, A., De Filippis, F., Iannotti, F. A., Piscitelli, F., Ercolini, D., de Novellis, V., Di Marzo, V., and Cuomo, R.

Subjects
Male, 0301 basic medicine, Immunology, Inflammation, Tropomyosin receptor kinase B, Gut flora, Hippocampal formation, Hippocampus, digestive system, Endocrine and Autonomic System, law.invention, 03 medical and health sciences, Behavioral Neuroscience, Probiotic, 0302 clinical medicine, Hippocampu, law, medicine, Animals, Social behavior, Intestinal Mucosa, Neurons, Endocannabinoidome, Behavior, Animal, biology, Endocrine and Autonomic Systems, Depression, Brain-Derived Neurotrophic Factor, Probiotics, Lachnospiraceae, medicine.disease, biology.organism_classification, Tail suspension test, Anti-Bacterial Agents, Gastrointestinal Microbiome, Intestines, Mice, Inbred C57BL, 030104 developmental biology, Dysbiosis, Microbiome, medicine.symptom, Neuroglia, 030217 neurology & neurosurgery, Endocannabinoids
Abstract

The microbiota-gut-brain axis (MGBA) regulates the reciprocal interaction between chronic inflammatory bowel and psychiatric disorders. This interaction involves multiple pathways that are highly debated. We examined the behavioural, biochemical and electrophysiological alterations, as well as gut microbiota composition in a model of antibiotic-induced experimental dysbiosis. Inflammation of the small intestine was also assessed. Mice were exposed to a mixture of antimicrobials for 2 weeks. Afterwards, they received Lactobacillus casei DG (LCDG) or a vehicle for up to 7 days via oral gavage. Perturbation of microbiota was accompanied by a general inflammatory state and alteration of some endocannabinoidome members in the gut. Behavioural changes, including increased immobility in the tail suspension test and reduced social recognition were observed, and were associated with altered BDNF/TrkB signalling, TRPV1 phosphorylation and neuronal firing in the hippocampus. Moreover, morphological rearrangements of non-neuronal cells in brain areas controlling emotional behaviour were detected. Subsequent probiotic administration, compared with vehicle, counteracted most of these gut inflammatory, behavioural, biochemical and functional alterations. Interestingly, levels of Lachnospiraceae were found to significantly correlate with the behavioural changes observed in dysbiotic mice. Our findings clarify some of the biomolecular and functional modifications leading to the development of affective disorders associated with gut microbiota alterations.

Published
2018
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47. Mediterranean diet consumption affects the endocannabinoid system in overweight and obese subjects: possible links with gut microbiome, insulin resistance and inflammation

Author

Nicolas Pons, Danilo Ercolini, Silvia Tagliamonte, Rosalia Ferracane, Marilena Vitale, Maria A Gallo, Paola Vitaglione, Victoria Meslier, Manolo Laiola, Tagliamonte, S., Laiola, M., Ferracane, R., Vitale, M., Gallo, M. A., Meslier, V., Pons, N., Ercolini, D., and Vitaglione, P.

Subjects
0301 basic medicine, medicine.medical_specialty, Medicine (miscellaneous), 030209 endocrinology & metabolism, Overweight, Diet, Mediterranean, 03 medical and health sciences, chemistry.chemical_compound, Oleoylethanolamide, 0302 clinical medicine, Insulin resistance, Internal medicine, Gut barrier, medicine, Humans, Microbiome, Obesity, Inflammation, Palmitoylethanolamide, Gut microbiome, Nutrition and Dietetics, biology, business.industry, Original Contribution, medicine.disease, biology.organism_classification, Cardiovascular disease risk, Gastrointestinal Microbiome, 030104 developmental biology, Endocrinology, chemistry, Homeostatic model assessment, medicine.symptom, Insulin Resistance, business, Akkermansia muciniphila, Endocannabinoids
Abstract

Purpose To investigate whether a Mediterranean diet (MD) affected the plasma concentrations of endocannabinoids (ECs), N-acylethanolamines (NAEs) and their specific ratios in subjects with lifestyle risk factors for metabolic diseases. To identify the relationship between circulating levels of these compounds and gut microbiome, insulin resistance and systemic inflammation. Methods A parallel 8-week randomised controlled trial was performed involving 82 overweight and obese subjects aged (mean ± SEM) 43 ± 1.4 years with a BMI of 31.1 ± 0.5 kg/m2, habitual Western diet (CT) and sedentary lifestyle. Subjects were randomised to consume an MD tailored to their habitual energy and macronutrient intake (n = 43) or to maintain their habitual diet (n = 39). Endocannabinoids and endocannabinoid-like molecules, metabolic and inflammatory markers and gut microbiome were monitored over the study period. Results The MD intervention lowered plasma arachidonoylethanolamide (AEA, p = 0.02), increased plasma oleoylethanolamide/palmitoylethanolamide (OEA/PEA, p = 0.009) and OEA/AEA (p = 0.006) and increased faecal Akkermansia muciniphila (p = 0.026) independent of body weight changes. OEA/PEA positively correlated with abundance of key microbial players in diet–gut–health interplay and MD adherence. Following an MD, individuals with low-plasma OEA/PEA at baseline decreased homeostatic model assessment of insulin resistance index (p = 0.01), while individuals with high-plasma OEA/PEA decreased serum high-sensitive C-reactive protein (p = 0.02). Conclusions We demonstrated that a switch from a CT to an isocaloric MD affects the endocannabinoid system and increases A. muciniphila abundance in the gut independently of body weight changes. Endocannabinoid tone and microbiome functionality at baseline drives an individualised response to an MD in ameliorating insulin sensitivity and inflammation. Clinical Trial Registry number and website NCT03071718; www.clinicaltrials.gov

Published
2021

49. Next-generation food research: Use of meta-omic approaches for characterizing microbial communities along the food chain

Author

Avelino Alvarez-Ordóñez, Paul D. Cotter, Danilo Ercolini, Min Yap, Orla O'Sullivan, Paul W. O'Toole, Yap, M., Ercolini, D., Alvarez-Ordonez, A., O'Toole, P. W., O'Sullivan, O., and Cotter, P. D.

Subjects
medicine.medical_specialty, Food Chain, meta-omic approache, Food industry, Food microbiome, media_common.quotation_subject, Food chain, medicine, Food Industry, Quality (business), Food research, Environmental planning, media_common, High-throughput sequencing, business.industry, Public health, Microbiota, digestive, oral, and skin physiology, high-throughput sequencing, Meta-omic approaches, food-processing environment, food microbiome, Fermentation, Business, Food-processing environment, Food quality, Food Science
Abstract

Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Published
2021

50. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Nadine Farhat, Tomoki Takeda, Astred Castro, Ken McGrath, Khaliun Sanchir, Iman Hajirasouliha, Eunice So, Laraib Zafar, Diana N. Nunes, Harun Mustafa, Amy Zhang, Priscilla Lisboa, Christian Schori, Marisano James, Jasna Chalangal, Sebastien Halary, Shahryar Rana, Yunmi Lee, Oli Schacher, Liliana Godoy, David A. Coil, Phanthira Pugdeethosal, Michelle D. Williams, German Marchandon, Angela Cantillo, Naoya Takahashi, Christopher Mozsary, Juana Gonzalez, Patrick K. H. Lee, Gerardo de Lamotte, Alessandro Robertiello, Steven Du, Fabienne Velter, Stefan G. Stark, Miguel Carbajo, Vincent Matthys, David A. Westfall, Julia Boeri, Irène Mauricette Mendy, Jonathan Cedillo, Francesco Oteri, Robert W. Crawford, Takayuki Ito, Tina Wunderlin, Maureen Muscat, David Paez-Espino, Carmen Urgiles, Aida Nesimi, Steffen Schaaf, Adan Ramirez-Rojas, Kunihiko Miyake, Christopher E. Mason, Anais Cardenas, Sharah Islam, Diego Benítez, Melissa Pool Pizzi, Kianna Ciaramella, Ciro Borrelli, Riham Islam, Dorottya Nagy-Szakal, Abd-Manaaf Bakere, Ait-hamlat Adel, Olha Lakhneko, Badamnyambuu Iderzorig, Ana Valeria Castro, Adam Phillips, Robert A. Petit, Flavia Corsi, Romain Conte, Krista Ryon, Soojin Jang, Joseph Benson, Fernanda de Souza Gomes Kehdy, Cindy Wang, Nicole Mathews, Jenn-Wei Chen, Rachel Paras, Paulina Pastuszek, Abigail Lyons, Paul Roldán, Muntaha Munia, Pierre Nicolas, Cassie L. Ettinger, Kyrylo Pyrshev, Katterinne N. Mendez, Eduardo Castro-Nallar, Valeriia Dotsenko, Michelle Tuz, Krizzy Mallari, Eileen Png, Yuya Sonohara, Tanja Miketic, Stéphane Delmas, Shu Zhang, Masaki Sato, Yuanting Zheng, Jifeng Zhu, Roland Häusler, Lucie Bittner, Savlatjon Rahmatulloev, Jonathan Foox, Bruno D'Alessandro, Alketa Plaku, Faisal Alquaddoomi, Yang Zhang, Kern Rei Chng, Juliana Lago, Allaeddine Chettouh, Tamera Henry, Houtan Noushmehr, Tranette Gregory, Sara Abdul Majid, Frank J. Kelly, Benjamin Pulatov, Laurie Casalot, Takema Kajita, Lennard Epping, Thais Fernanda Bartelli, Eftar Moniruzzaman, Renee Vivancos-Koopman, Thirumalaisamy P. Velavan, Tracy W. Liu, Yelyzaveta Tymoshenko, Alma Plaku, Nika Gurianova, Ambar Mendez, Anna Tomaselli, Sonia Dorado, Donato Giovannelli, Hira Choudhry, Synti Ng, Sheelta S. Kumar, Jennifer Q. Lu, Weijun Liang, Ellen Koag, Dennis Gankin, Maria João Amorim, Gwenola Simon, Kiyoshi Suganuma, Mikhail Karasikov, Christos A. Ouzounis, Madelyn May, Eran Elhaik, Stephan Ossowski, Kevin Bolzli, Matthew Arthur, Yuya Oto, Jananan Pathmanathan, Salah Mahmoud, Kou Takahashi, Brunna Marques, Kelly French, Felipe Sepúlveda, Shusei Yoshikawa, Paulo Thiago de Souza Santos, Andrew N. Gray, Juliana S Bernardes, Felipe Segato, Björn Brindefalk, George C. Yeh, Jhovana L. Velasco Flores, Jill Sullivan, Silva Baburyan, Denisse Flores, Russell Y. Neches, Sabrina Persaud, Rasheena Wright, Takumi Togashi, Verónica Antelo, Nao Kato, Skye Felice, Tatjana Mustac, Daisy Donnellan, Katerine Carrillo, Anna Litskevitch, Catalina García, Sota Ito, Naya Eady, Andrew Wan, Irene Meng, Sophie Guasco, Danilo Ercolini, Francesca De Filippis, Vincent Lemaire, Luice Fan, Lothar H. Wieler, Mariia Rybak, Jorge Sanchez, Jonathan S. Gootenberg, Itsuki Tomita, Maritza S Mosella, Laura Garcia, Natalka Makogon, Daisy Cheung, Hitler Francois Vasquez Arevalo, Freddy Asenjo, Gabriela P. Branco, Erika Cifuentes, Chloé Dequeker, Aspassia D. Chatziefthimiou, Alexis Terrero, Roy Meoded, Isabelle de Oliveira Moraes, Shaleni K. Singh, Orgil-Erdene Molomjamts, Karishma Miah, Laurent David, Wolfgang Haehr, Dao Phuong Giang, Romain Lannes, Prashanthi Ratnanandan, Ryota Yamanaka, Riccardo Vicedomini, Sadaf Ayaz, Oluwatosin M. Osuolale, Laura E. Vann, Gregory Chem, Andrea Gonzalez, Aszia Burrell, Ariel Chernomoretz, Sakura Ishizuka, Michelle Rivera, Avigdor Nosrati, Michelle B. Chen, Juliette Auvinet, Nils Ordioni, Tomoro Warashina, Guillaume Blanc, Tomislav Ivankovic, Christina Black, Lauren E. Hittle, David Hess-Homeier, Michael Kozhar, Hamood Suliman, Karobi Moitra, Saher Rahiel, Spyridon Gkotzis, Jenny Arevalo, Shaikh B. Iqbal, Beth Mutai, Mohammed Mohsin, Scott Tighe, Sylvie Collin, Yoshitaka Saito, Wayne Menary, Youping Deng, Lucy Lee, Esmeralda Jiminez, Ayuki Watanabe, Nikos C. Kyrpides, Natasha Mohan, Angelika Pupiec, Dedan Githae, Simone Cawthorne, Jonathan A. Eisen, Tomoki Iwashiro, Chiaki Homma, Thomas Saw Aung, Laura Molina, Marcus H. Y. Leung, Ophélie Da Silva, Yan Ling Wong, Hosna Noorzi, Mario Moreno, Alina Butova, Leming Shi, Brian W. Wong, Sarah S. Jackson, Moses Lin, Annabelle Meagher, Pujita Das, Catherine Burke, Mitsuki Ota, Maria Domenica Moccia, Nicolas Sprinsky, Catherine E. Pugh, David C. Green, Fazlina Fauzi, Erdenetsetseg Batdelger, Annie Geiger, Valeria Ventorino, Tolulope Oluwadare, Delisia Cuebas, Catalina Truong, Leonardo Posada, Michael Angelov, Tathiane M. Malta, Amanda Ng, Francesca Nadalin, Arya Hawkins-Zafarnia, Yuh Shiwa, Athena Mitsios, Milton Ozório Moraes, Manolo Laiola, Kalyn Ali, Jaden J.A. Hastings, Ikuto Saito, Maheen Shakil, Chisato Suzuki, Elena M. Vayndorf, Hubert Rehrauer, Ajay Menon, Kaitlan Russell, Aliyah Shari, Rebecca Smith, Gregorio Iraola, Max Priestman, Alan Briones, Silver A. Wolf, Camila Gonzalez-Poblete, Eleonora De Lazzari, Shirley Chiu, Michelle Ki, Irene Hoxie, Marianne Jaubert, Ayantu Jinfessa, Ryan J. King, Nghiem Xuan Hoan, Jalia Bynoe, Jacob Friedman, Aneisa Ramcharan, Pablo Fresia, Cristina Muñoz, Muhammad Afaq, Anyi Tang, Médine Benchouaia, Isabella Kuniko T. Takenaka, Anastasia Chasapi, Areeg Naeem, Hannah Benisty, Cecilia N. Cossio, Nathalie Hüsser, Mahfuza Sabina, Thais S. Sabedot, JoAnn Jacobs, Camila P. E. de Souza, Manuela Oliveira, Jean-Pierre Bouly, Mariko Usui, Wilson Miranda, Natalia Marciniak, Hiram Caballero, Samuel Weekes, Alexandra B. Graf, Emily Leong, Tatyana Nikolayeva, Dominique Thomas, Charlotte Greselle, Cecilia Salazar, Sreya Ray Chaudhuri, Kevin Becher, Sandra Roth, Ryusei Miura, Kari Oline Bøifot, Dimitri Manoir, Oliver Toth, Chandrima Bhattacharya, Manuel Perez, Isha Lamba, Takafumi Tsurumaki, Timothy D. Read, Anna-Lena M. Schinke, Ryan Sankar, Le Huu Song, Narasimha Rao Nedunuri, Emmanuel Dias-Neto, Ana Flávia Costa, Adiell Melamed, Christelle Desnues, Natalie R. Davidson, Aaron E. Darling, Hyung Jun Kim, Josephine Galipon, Jacqueline Orrego, Dimitar Vassilev, Michael Huber, Nur Hazlin Hazrin-Chong, Gaston H. Gonnet, Kaymisha Knights, Osman U. Sezerman, Dmitry Meleshko, Eunice Thambiraja, Jingcheng Yang, Aubin Fleiss, Gloria Nguyen, Katelyn Jackson, Nuria Aventin, Stephanie L. Hyland, Andrea Hässig, Catharine Aquino, Simona Lysakova, Israel O. Osuolale, Kasia Sluzek, Rania Siam, Alina Frolova, Samuel Hernandez, Yui Him Lo, Bazartseren Boldgiv, Ben Young, Maryna Korshevniuk, Majelia Ampadu, Yuk Man Tang, Amanda L. Muehlbauer, Sade Thomas, Gabriel Figueroa, Alexis Rivera, Lisbeth Pineda, Alexandra Dutan, Jennifer M. Tran, Chris K. Deng, Vedbar S. Khadka, Paola Florez de Sessions, Elizabeth Humphries, Hugues Richard, Hiba Naveed, Nora C. Toussaint, Mahshid Khavari, Maria del Mar Vivanco Ruiz, Antonin Thiébaut, Nicolás Rascovan, Marius Dybwad, Orhan Özcan, Lawrence Kwong, David Danko, Shaira Khan, Andrea Tassinari, Silvia Beurmann, Tsoi Ying Lai, Nanami Kubota, Tieliu Shi, Diana Chicas, Evan E. Afshin, Hirokazu Yano, Jonas Krebs, Mayuko Nakagawa, Hyun Jung Lee, Irene González Navarrete, Rachid Ounit, Lucia E. Alvarado-Arnez, Masaki Nasu, Allison Chan, Harilanto Andrianjakarivony, Jennifer Amachee, Mahdi Taye, Wan Chiew Ng, Kathryn O’Brien, Shino Ishikawa, Tristan Bitard-Feildel, Sora Takagi, Felix Hartkopf, Niamh B. O’Hara, Marcos A. S. Fonseca, Subhamitra Pakrashi, Amrit Kaur, Eva Hell, Patricia Vera-Wolf, Naimah Munim, Luiza Ferreira de Araújo, Mizuki Igarashi, Brianna Pompa-Hogan, Alessandra Carbone, Anne-Sophie Benoiston, Eric Helfrich, Michael A. Suarez-Villamil, Omar O. Abudayyeh, Natasha Abdullah, Jaime J. Fuentes, Juan Carlos Forero, Tetiana Yeskova, Denis Bertrand, Sambhawa Priya, Denisse Maldonado, Agier Nicolas, Ana Valeria B Castro, Starr Chatziefthimiou, André Kahles, Aaishah Francis, Fernanda Arredondo, Emilio Tarcitano, Irvind Buttar, Alex Alexiev, Jennifer Molinet, Sarah Shalaby, Itunu A. Oluwadare, Jason Sperry, Katrin Bakhl, Ana M. Cañas, Sofia Ahsanuddin, Miar Elaskandrany, Elodie Laine, Sven Bönigk, Johannes Werner, Stephen Eduard Boja Ruiz, Gargi Dayama, Paulina Buczansla, Brandon Valentine, Bharath Prithiviraj, Toni Bode, Stas Zubenko, Jake Cohen, Guilllaume Jospin, Zulena Saravi, Per O. Ljungdahl, Inderjit Kaur, Mauricio Moldes, Giuseppe KoLoMonaco, Denise Syndercombe Court, Sonia Bouchard, Sonia Losim, Sookwon Moon, Heba Shaaban, Suraj Patel, Sibo Zhu, Sarh Aly, Arif Asyraf Md Supie, LaShonda Dorsey, Juan Guerra, François Baudon, Rantimi A. Olawoyin, Alexia Bordigoni, Iqra Faiz, Mathilde Garcia, Gabriella Mason-Buck, María Gabriela Portilla, Niranjan Nagarajan, Fumie Takahara, Nancy Merino, Watson Andrew, Gina Kim, Yuma Sato, Hyenah Shim, Marie-Laure Jerier, Affifah Saadah Ahmad Kassim, Katerina Kuchin, Daniel Butler, Paweł P. Łabaj, Nadezhda Kobko-Litskevitch, Emmanuel F. Mongodin, Yuto Togashi, Paula Rodríguez, Pilar Lopez Hernandez, Xiaoqing Chen, Maria A. Sierra, Olga Nikolayeva, Manon Loubens, Colleen Conger, Hikaru Shirahata, Chenhao Li, Timothy Donahoe, Youngja Park, Lucia Elena Alvarado Arnez, Salama Chaker, Francisco Chavez, Alessandra Breschi, Jorge L. Sanchez, Kaung Myat San, Nayra Aguilar Rojas, Marcos Abraao, Kai Sasaki, Bryan Nazario, Olena Yemets, Klas I. Udekwu, Lynn M. Schriml, Anisia Peters, Aliaksei Holik, Mark Hernandez, Emile Faure, Malay Bhattacharyya, Josef W. Moser, Núria Andreu Somavilla, María Mercedes Zambrano, Kannan Rajendran, Gabriela E. Albuquerque, Tao Qing, Kazutoshi Tsuda, Ymke De Jong, Princess Osma, Mayra Arauco Livia, Javier Quilez Oliete, Carl Chrispin, Hyun Woo Joo, Ingrid Lafontaine, Nala An, Seisuke Sato, Felipe Segato Dezem, Andrew Maltez Thomas, Alexandre Desert, Xiao Wen Cai, O. Osuolale, Jun Wu, Coral Pardo-Esté, Courtney Robinson, Yuri Matsuzaki, Marina Nieto-Caballero, Cem Meydan, Ralph Schlapbach, Mark Menor, Sofia Castro, Rachel Kwong, Brittany Blyther, Olexandr Lykhenko, Jason R. Schriml, Christian Brion, Jenessa Orpilla, Juan A. Ugalde, Elsy Mankah Ngwa, Álvaro Aranguren, Lauren Mak, Matías Giménez, Ashanti Narce, Torsten Semmler, Stefan I. Tsonev, Abdollahi Nika, Katherine E. Dahlhausen, Monika Devi, Gunnar Rätsch, Oasima Muner, Carla Bello, Muhammad Al-Fath Amran, Anyelic Rosario, Melissa Ortega, Andrea Patrignani, Ante Peros, Elias McComb, Ryo Sato, Ireen Alam, Clara N. Dias, Soma Tanaka, Dayana Calderon, Ran Blekhman, Mathilde Mignotte, Alicia Boyd, Jochen Hecht, Thomas Neff, Xinzhao Tong, Josue Alicea, Kiara Olmeda, Sonia Marinovic, Carme Arnan, Kohei Ito, Samantha L. Goldman, Marianna S. Serpa, Renee Richer, Kaisei Sato, Jordana M. Silva, Akash Keluth Chavan, Sangwan Kim, Laís Pereira Ferreira, Sophie Vacant, Nowshin Sayara, Haruo Suzuki, Madeline Leahy, Juan C. Severyn, Sierra Vincent, Masaru Tomita, Maliha Mamun, Lucinda B. Davenport, Gabriella Oken, Dagmara Lewandowska, Gustavo Adolfo Malca Salas, Andrii Kuklin, Tyler Wong, Charlie Feigin, Eric Minwei Liu, Sonia L. Ghose, Daniela Bezdan, Antonietta La Storia, Juan P. Escalera-Antezana, Nuno Rufino de Sousa, Samuel M. Gerner, Weill Cornell Medicine [New York], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Genome Institute of Singapore (GIS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), AUTRES, Massachusetts Institute of Technology (MIT), Indian Statistical Institute [Kolkata], University of Minnesota System, Universidad Andrés Bello [Santiago] (UNAB), California State University [Sacramento], University of Naples Federico II, University of Hawaii, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Medical Genomics Group, University College of London [London] (UCL)-UCL Cancer Institute, Norwegian Defence Research Establishment (FFI), Lund University [Lund], Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, University of Vienna [Vienna], King‘s College London, University of Colorado [Boulder], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur Korea - Institut Pasteur de Corée, Fudan University [Shanghai], City University of Hong Kong [Hong Kong] (CUHK), Stockholm University, University of Maryland School of Medicine, University of Maryland System, Fundação Oswaldo Cruz (FIOCRUZ), University of São Paulo (USP), Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Barcelona Institute of Science and Technology (BIST), Elizade University, Acibadem Mehmet Ali Aydınlar University, Paléogénomique microbienne - Microbial paleogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Robert Koch Institute [Berlin] (RKI), East China Normal University [Shangaï] (ECNU), Cairo University, Vietnamese-German Center for Medical Research, Keio University, Université du Vermont, Universidad del Desarrollo, University of Sofia, University of Alaska [Fairbanks] (UAF), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Corporación Corpogen-Research Center, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Weill Cornell Medicine [Cornell University], Cornell University [New York], University of Naples Federico II = Università degli studi di Napoli Federico II, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Universidade de São Paulo = University of São Paulo (USP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Софийски университет = Sofia University, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Acibadem University Dspace, Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nikolayeva, O., Nikolayeva, T., Png, E., Ryon, K. A., Sanchez, J. L., Shaaban, H., Sierra, M. A., Thomas, D., Young, B., Abudayyeh, O. O., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., De Filippis, F., Deng, Y., Desnues, C., Dias-Neto, E., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Gankin, D., Gootenberg, J. S., Graf, A. B., Green, D. C., Hajirasouliha, I., Hastings, J. J. A., Hernandez, M., Iraola, G., Jang, S., Kahles, A., Kelly, F. J., Knights, K., Kyrpides, N. C., Labaj, P. P., Lee, P. K. H., Leung, M. H. Y., Ljungdahl, P. O., Mason-Buck, G., Mcgrath, K., Meydan, C., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Nieto-Caballero, M., 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., Shi, T., Siam, R., Song, L. H., Suzuki, H., Court, D. S., Tighe, S. W., Tong, X., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E. M., Velavan, T. P., Wu, J., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Abdullah, N., Abraao, M., Adel, A. -H., Afaq, M., Al-Quaddoomi, F. S., Alam, I., Albuquerque, G. E., Alexiev, A., Ali, K., Alvarado-Arnez, L. E., Aly, S., Amachee, J., Amorim, M. G., Ampadu, M., Amran, M. A. -F., An, N., Andrew, W., Andrianjakarivony, H., Angelov, M., Antelo, V., Aquino, C., Aranguren, A., Araujo, L. F., Vasquez Arevalo, H. F., Arevalo, J., Arnan, C., Alvarado Arnez, L. E., Arredondo, F., Arthur, M., Asenjo, F., Aung, T. S., Auvinet, J., Aventin, N., Ayaz, S., Baburyan, S., Bakere, A. -M., Bakhl, K., Bartelli, T. F., Batdelger, E., Baudon, F., Becher, K., Bello, C., Benchouaia, M., Benisty, H., Benoiston, A. -S., Benson, J., Benitez, D., Bernardes, J., Bertrand, D., Beurmann, S., Bitard-Feildel, T., Bittner, L., Black, C., Blanc, G., Blyther, B., Bode, T., Boeri, J., Boldgiv, B., Bolzli, K., Bordigoni, A., Borrelli, C., Bouchard, S., Bouly, J. -P., Boyd, A., Branco, G. P., Breschi, A., Brindefalk, B., Brion, C., Briones, A., Buczansla, P., Burke, C. M., Burrell, A., Butova, A., Buttar, I., Bynoe, J., Bonigk, S., Boifot, K. O., Caballero, H., Cai, X. W., Calderon, D., Cantillo, A., Carbajo, M., Carbone, A., Cardenas, A., Carrillo, K., Casalot, L., Castro, S., Castro, A. V., Castro, A., Castro, A. V. B., Cawthorne, S., Cedillo, J., Chaker, S., Chalangal, J., Chan, A., Chasapi, A. I., Chatziefthimiou, S., Chaudhuri, S. R., Chavan, A. K., Chavez, F., Chem, G., Chen, X., Chen, M., Chen, J. -W., Chernomoretz, A., Chettouh, A., Cheung, D., Chicas, D., Chiu, S., Choudhry, H., Chrispin, C., Ciaramella, K., Cifuentes, E., Cohen, J., Coil, D. A., Collin, S., Conger, C., Conte, R., Corsi, F., Cossio, C. N., Costa, A. F., Cuebas, D., D'Alessandro, B., Dahlhausen, K. E., Darling, A. E., Das, P., Davenport, L. B., David, L., Davidson, N. R., Dayama, G., Delmas, S., Deng, C. K., Dequeker, C., Desert, A., Devi, M., Dezem, F. S., Dias, C. N., Donahoe, T. R., Dorado, S., Dorsey, L., Dotsenko, V., Du, S., Dutan, A., Eady, N., Eisen, J. A., Elaskandrany, M., Epping, L., Escalera-Antezana, J. P., Ettinger, C. L., Faiz, I., Fan, L., Farhat, N., Faure, E., Fauzi, F., Feigin, C., Felice, S., Ferreira, L. P., Figueroa, G., Fleiss, A., Flores, D., Velasco Flores, J. L., Fonseca, M. A. S., Foox, J., Forero, J. C., Francis, A., French, K., Fresia, P., Friedman, J., Fuentes, J. J., Galipon, J., Garcia, M., Garcia, L., Garcia, C., Geiger, A., Gerner, S. M., Ghose, S. L., Giang, D. P., Gimenez, M., Giovannelli, D., Githae, D., Gkotzis, S., Godoy, L., Goldman, S., Gonnet, G. H., Gonzalez, J., Gonzalez, A., Gonzalez-Poblete, C., Gray, A., Gregory, T., Greselle, C., Guasco, S., Guerra, J., Gurianova, N., Haehr, W., Halary, S., Hartkopf, F., Hawkins-Zafarnia, A., Hazrin-Chong, N. H., Helfrich, E., Hell, E., Henry, T., Hernandez, S., Hernandez, P. L., Hess-Homeier, D., Hittle, L. E., Hoan, N. X., Holik, A., Homma, C., Hoxie, I., Huber, M., Humphries, E., Hyland, S., Hassig, A., Hausler, R., Husser, N., Petit, R. A., Iderzorig, B., Igarashi, M., Iqbal, S. B., Ishikawa, S., Ishizuka, S., Islam, S., Islam, R., Ito, K., Ito, S., Ito, T., Ivankovic, T., Iwashiro, T., Jackson, S., Jacobs, J., James, M., Jaubert, M., Jerier, M. -L., Jiminez, E., Jinfessa, A., De Jong, Y., Joo, H. W., Jospin, G., Kajita, T., Ahmad Kassim, A. S., Kato, N., Kaur, A., Kaur, I., de Souza Gomes Kehdy, F., Khadka, V. S., Khan, S., Khavari, M., Ki, M., Kim, G., Kim, H. J., Kim, S., King, R. J., Kolomonaco, G., Koag, E., Kobko-Litskevitch, N., Korshevniuk, M., Kozhar, M., Krebs, J., Kubota, N., Kuklin, A., Kumar, S. S., Kwong, R., Kwong, L., Lafontaine, I., Lago, J., Lai, T. Y., Laine, E., Laiola, M., Lakhneko, O., Lamba, I., de Lamotte, G., Lannes, R., De Lazzari, E., Leahy, M., Lee, H., Lee, Y., Lee, L., Lemaire, V., Leong, E., Lewandowska, D., Li, C., Liang, W., Lin, M., Lisboa, P., Litskevitch, A., Liu, E. M., Liu, T., Livia, M. A., Lo, Y. H., Losim, S., Loubens, M., Lu, J., Lykhenko, O., Lysakova, S., Mahmoud, S., Majid, S. A., Makogon, N., Maldonado, D., Mallari, K., Malta, T. M., Mamun, M., Manoir, D., Marchandon, G., Marciniak, N., Marinovic, S., Marques, B., Mathews, N., Matsuzaki, Y., Matthys, V., May, M., Mccomb, E., Meagher, A., Melamed, A., Menary, W., Mendez, K. N., Mendez, A., Mendy, I. M., Meng, I., Menon, A., Menor, M., Meoded, R., Merino, N., Miah, K., Mignotte, M., Miketic, T., Miranda, W., Mitsios, A., Miura, R., Miyake, K., Moccia, M. D., Mohan, N., Mohsin, M., Moitra, K., Moldes, M., Molina, L., Molinet, J., Molomjamts, O. -E., Moniruzzaman, E., Moon, S., de Oliveira Moraes, I., Moreno, M., Mosella, M. S., Moser, J. W., Mozsary, C., Muehlbauer, A. L., Muner, O., Munia, M., Munim, N., Muscat, M., Mustac, T., Munoz, C., Nadalin, F., Naeem, A., Nagy-Szakal, D., Nakagawa, M., Narce, A., Nasu, M., Navarrete, I. G., Naveed, H., Nazario, B., Nedunuri, N. R., Neff, T., Nesimi, A., Ng, W. C., Ng, S., Nguyen, G., Ngwa, E., Nicolas, A., Nicolas, P., Nika, A., Noorzi, H., Nosrati, A., Nunes, D. N., O'Brien, K., O'Hara, N. B., Oken, G., Olawoyin, R. A., Oliete, J. Q., Olmeda, K., Oluwadare, T., Oluwadare, I. A., Ordioni, N., Orpilla, J., Orrego, J., Ortega, M., Osma, P., Osuolale, I. O., Osuolale, O. M., Ota, M., Oteri, F., Oto, Y., Ounit, R., Ouzounis, C. A., Pakrashi, S., Paras, R., Pardo-Este, C., Park, Y. -J., Pastuszek, P., Patel, S., Pathmanathan, J., Patrignani, A., Perez, M., Peros, A., Persaud, S., Peters, A., Phillips, A., Pineda, L., Pizzi, M. P., Plaku, A., Pompa-Hogan, B., Portilla, M. G., Posada, L., Priestman, M., Prithiviraj, B., Priya, S., Pugdeethosal, P., Pugh, C. E., Pulatov, B., Pupiec, A., Pyrshev, K., Qing, T., Rahiel, S., Rahmatulloev, S., Rajendran, K., Ramcharan, A., Ramirez-Rojas, A., Rana, S., Ratnanandan, P., Read, T. D., Rehrauer, H., Richer, R., Rivera, A., Rivera, M., Robertiello, A., Robinson, C., Rodriguez, P., Rojas, N. A., Roldan, P., Rosario, A., Roth, S., Ruiz, M., Boja Ruiz, S. E., Russell, K., Rybak, M., Sabedot, T. S., Sabina, M., Saito, I., Saito, Y., Malca Salas, G. A., Salazar, C., San, K. M., Sanchez, J., Sanchir, K., Sankar, R., de Souza Santos, P. T., Saravi, Z., Sasaki, K., Sato, Y., Sato, M., Sato, S., Sato, R., Sato, K., Sayara, N., Schaaf, S., Schacher, O., Schinke, A. -L. M., Schlapbach, R., Schori, C., Schriml, J. R., Segato, F., Sepulveda, F., Serpa, M. S., De Sessions, P. F., Severyn, J. C., Shakil, M., Shalaby, S., Shari, A., Shim, H., Shirahata, H., Shiwa, Y., Da Silva, O., Silva, J. M., Simon, G., Singh, S. K., Sluzek, K., Smith, R., So, E., Andreu Somavilla, N., Sonohara, Y., Rufino de Sousa, N., Souza, C., Sperry, J., Sprinsky, N., Stark, S. G., La Storia, A., Suganuma, K., Suliman, H., Sullivan, J., Supie, A. A. M., Suzuki, C., Takagi, S., Takahara, F., Takahashi, N., Takahashi, K., Takeda, T., Takenaka, I. K., Tanaka, S., Tang, A., Man Tang, Y., Tarcitano, E., Tassinari, A., Taye, M., Terrero, A., Thambiraja, E., Thiebaut, A., Thomas, S., Thomas, A. M., Togashi, Y., Togashi, T., Tomaselli, A., Tomita, M., Tomita, I., Toth, O., Toussaint, N. C., Tran, J. M., Truong, C., Tsonev, S. I., Tsuda, K., Tsurumaki, T., Tuz, M., Tymoshenko, Y., Urgiles, C., Usui, M., Vacant, S., Vann, L. E., Velter, F., Ventorino, V., Vera-Wolf, P., Vicedomini, R., Suarez-Villamil, M. A., Vincent, S., Vivancos-Koopman, R., Wan, A., Wang, C., Warashina, T., Watanabe, A., Weekes, S., Werner, J., Westfall, D., Wieler, L. H., Williams, M., Wolf, S. A., Wong, B., Wong, Y. L., Wong, T., Wright, R., Wunderlin, T., Yamanaka, R., Yang, J., Yano, H., Yeh, G. C., Yemets, O., Yeskova, T., Yoshikawa, S., Zafar, L., Zhang, Y., Zhang, S., Zhang, A., Zheng, Y., and Zubenko, S.

Subjects
Urban Population, Drug Resistance, Sequence assembly, Microbiologia, microbiome, global health, computer.software_genre, Medical and Health Sciences, shotgun sequencing, BGC, 0302 clinical medicine, Databases, Genetic, 11. Sustainability, Global health, AMR, 11 Medical and Health Sciences, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, built environment, metagenome, antimicrobial resistance, NGS, de novo assembly, biology, Shotgun sequencing, Microbiota, built Environment, Bacterial, Biodiversity, Biological Sciences, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infection, Biotechnology, Geospatial analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, General Biochemistry, Genetics and Molecular Biology, Databases, 03 medical and health sciences, Antibiotic resistance, Genetic, Drug Resistance, Bacterial, International MetaSUB Consortium, Genetics, Humans, Microbiome, 030304 developmental biology, Human Genome, 06 Biological Sciences, 15. Life on land, biology.organism_classification, Resistènica als medicaments antiinfecciosos, SAÚDE PÚBLICA, Genòmica, 13. Climate action, Evolutionary biology, Metagenomics, Antimicrobial Resistance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, 030217 neurology & neurosurgery, Archaea, Developmental Biology
Abstract

Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities., Graphical abstract, Highlights • Cities possess a consistent “core” set of non-human microbes • Urban microbiomes echo important features of cities and city-life • Antimicrobial resistance genes are widespread in cities • Cities contain many novel bacterial and viral species, This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.

Published
2021
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