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Prof. Annamaria Bevivino
Head of Agrifood Sustainability, Quality and Safety Laboratory, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center,

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Research Keywords & Expertise

0 Soil Microbiome
0 Cystic Fibrosis pathogens
0 Opportunistic pathogens
0 microbial ecology and diversity
0 Plant-microbe and microbe-microbe interactions

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Opportunistic pathogens
Soil Microbiome
Microbial consortia for biotechnological application

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Short Biography

Annamaria Bevivino is the Head of the ENEA Laboratory for AgriFood Sustainability, Quality and Safety, Biotechnologies and Agriculture Division, Department for Sustainability, Rome (ITALY) and Professor of AgroFood Microbiology, Master's Degree in Food Science and Human Nutrition, University Campus Bio-Medico di Roma. In 1997, she obtained her degree in Biological Science at “La Sapienza” University of Rome with the mark of 110/110 cum laude. Her research activity focuses on the investigation of i) food, soil, plant and human microbiome, ii) soil and rhizosphere plant-growth promoting bacteria, iii) polymicrobial and plant-microbe interactions. She is author of more than 50 peer-reviewed publications and 180 communications at national and international conferences. She is a member of several scientific societies, She is a member of several scientific societies; i.e., SIMGBM (Italian Society of General Microbiology and Microbial Biotechnology), Federation of European Microbiological societies (FEMS), Italian Society of Cystic Fibrosis (SIFC), European Cystic Fibrosis Society (ECFS), SIMTREA (Italian Society of Agro-Food and Environmental Microbiology). She is academic editor for PlosOne and Frontiers in Microbiology and member of the Scientific Committee of the Microbial Resource Research Infrastructure – MIRRI-IT. Actually, she is WP leader of H2020 SIMBA project https://simbaproject.eu. Google scholar– Citations 2897; H index= 30; i-10-index: 41.

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Project

Project Goal: SIMBA aims at providing a holistic and innovative approach to the development of microbial solutions to increase food and nutrition security. SIMBA focuses in particular on the identification of viable land and aquatic microbiomes that can assist in the sustainability of European agro- and aquaculture.

Starting Date:01 November 2018

Current Stage: Identification of microbial consortia and analysis of the efficacy of microbiome application in field

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Project

Project Goal: To investigate the overall gene functions harbored by the resident microbial populations and their relation to patient’s lung disease status. Additionally, to analyze the dynamics of the lung microbiome will be studied also in wild type and CF mice, in the naïve status and after chronic infection with Pseudomonas aeruginosa, with the aim to explore the possibility to therapeutically manipulate lung microbiome communities.

Starting Date:01 August 2017

Current Stage: Analysis of gut-lung microbiome in CF mice

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Journal article
Published: 19 February 2021 in Microorganisms
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A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.

ACS Style

Silvia Tabacchioni; Stefania Passato; Patrizia Ambrosino; LiRen Huang; Marina Caldara; Cristina Cantale; Jonas Hett; Antonella Del Fiore; Alessia Fiore; Andreas Schlüter; Alexander Sczyrba; Elena Maestri; Nelson Marmiroli; Daniel Neuhoff; Joseph Nesme; Søren Sørensen; Giuseppe Aprea; Chiara Nobili; Ombretta Presenti; Giusto Giovannetti; Caterina Giovannetti; Anne Pihlanto; Andrea Brunori; Annamaria Bevivino. Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms 2021, 9, 426 .

AMA Style

Silvia Tabacchioni, Stefania Passato, Patrizia Ambrosino, LiRen Huang, Marina Caldara, Cristina Cantale, Jonas Hett, Antonella Del Fiore, Alessia Fiore, Andreas Schlüter, Alexander Sczyrba, Elena Maestri, Nelson Marmiroli, Daniel Neuhoff, Joseph Nesme, Søren Sørensen, Giuseppe Aprea, Chiara Nobili, Ombretta Presenti, Giusto Giovannetti, Caterina Giovannetti, Anne Pihlanto, Andrea Brunori, Annamaria Bevivino. Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms. 2021; 9 (2):426.

Chicago/Turabian Style

Silvia Tabacchioni; Stefania Passato; Patrizia Ambrosino; LiRen Huang; Marina Caldara; Cristina Cantale; Jonas Hett; Antonella Del Fiore; Alessia Fiore; Andreas Schlüter; Alexander Sczyrba; Elena Maestri; Nelson Marmiroli; Daniel Neuhoff; Joseph Nesme; Søren Sørensen; Giuseppe Aprea; Chiara Nobili; Ombretta Presenti; Giusto Giovannetti; Caterina Giovannetti; Anne Pihlanto; Andrea Brunori; Annamaria Bevivino. 2021. "Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture." Microorganisms 9, no. 2: 426.

Journal article
Published: 22 October 2020 in Sustainability
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Productivity and sustainability of tropical forest plantations greatly rely on regulation of ecosystem functioning and nutrient cycling, i.e., the link between plant growth, nutrient availability, and the microbial community structure. So far, these interactions have never been evaluated in the Acacia and Eucalyptus forest planted on infertile soils in the Congolese coastal plains. In the present work, the soil bacterial community has been investigated by metabarcoding of the 16S rRNA bacterial gene in different stands of monoculture and mixed-species plantation to evaluate the potential of nitrogen-fixing trees on nutrient and bacterial structure. At the phylum level, the soil bacterial community was dominated by Actinobacteria, followed by Proteobacteria, Firmicutes, and Acidobacteria. A principal coordinate analysis revealed that bacterial communities from pure Eucalyptus, compared to those from plantations containing Acacia in pure and mixed-species stands, showed different community composition (beta-diversity). Regardless of the large variability of the studied soils, the prevalence of Firmicutes phylum, and lower bacterial richness and phylogenic diversity were reported in stands containing Acacia relative to the pure Eucalyptus. Distance-based redundancy analysis revealed a positive correlation of available phosphorus (P) and carbon/nitrogen (C/N) ratio with bacterial community structure. However, the Spearman correlation test revealed a broad correlation between the relative abundance of bacterial taxa and soil attributes, in particular with sulfur (S) and carbon (C), suggesting the important role of soil bacterial community in nutrient cycling in this type of forest management. Concerning mixed plantations, a shift in bacterial community structure was observed, probably linked to other changes, i.e., improvement in soil fertility (enhanced P and C dynamics in forest floor and soil, and increase in soil N status), and C sequestration in both soil and stand wood biomass with the great potential impact to mitigate climate change. Overall, our findings highlight the role of soil attributes, especially C, S, available P, and C/N ratio at a lesser extent, in driving the soil bacterial community in mixed-species plantations and its potential to improve soil fertility and to sustain Eucalyptus plantations established on the infertile and sandy soils of the Congolese coastal plains.

ACS Style

Lydie-Stella Koutika; Alessia Fiore; Silvia Tabacchioni; Giuseppe Aprea; Arthur Prudêncio De Araujo Pereira; Annamaria Bevivino. Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains. Sustainability 2020, 12, 8763 .

AMA Style

Lydie-Stella Koutika, Alessia Fiore, Silvia Tabacchioni, Giuseppe Aprea, Arthur Prudêncio De Araujo Pereira, Annamaria Bevivino. Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains. Sustainability. 2020; 12 (21):8763.

Chicago/Turabian Style

Lydie-Stella Koutika; Alessia Fiore; Silvia Tabacchioni; Giuseppe Aprea; Arthur Prudêncio De Araujo Pereira; Annamaria Bevivino. 2020. "Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains." Sustainability 12, no. 21: 8763.

Journal article
Published: 04 July 2020 in Microorganisms
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Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.

ACS Style

Giovanni Bacci; Giovanni Taccetti; Daniela Dolce; Federica Armanini; Nicola Segata; Francesca Di Cesare; Vincenzina Lucidi; Ersilia Fiscarelli; Patrizia Morelli; Rosaria Casciaro; Anna Negroni; Alessio Mengoni; Annamaria Bevivino. Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms 2020, 8, 1003 .

AMA Style

Giovanni Bacci, Giovanni Taccetti, Daniela Dolce, Federica Armanini, Nicola Segata, Francesca Di Cesare, Vincenzina Lucidi, Ersilia Fiscarelli, Patrizia Morelli, Rosaria Casciaro, Anna Negroni, Alessio Mengoni, Annamaria Bevivino. Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms. 2020; 8 (7):1003.

Chicago/Turabian Style

Giovanni Bacci; Giovanni Taccetti; Daniela Dolce; Federica Armanini; Nicola Segata; Francesca Di Cesare; Vincenzina Lucidi; Ersilia Fiscarelli; Patrizia Morelli; Rosaria Casciaro; Anna Negroni; Alessio Mengoni; Annamaria Bevivino. 2020. "Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease." Microorganisms 8, no. 7: 1003.

Journal article
Published: 27 June 2020 in Forest Ecosystems
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Background Land-use change and forest management may alter soil organic matter (SOM) and nutrient dynamics, due in part to alterations in litter input and quality. Acacia was introduced in eucalypt plantations established in the Congolese coastal plains to improve soil fertility and tree growth. Eucalypt trees were expected to benefit from N2 fixed by acacia. However, some indicators suggest a perturbation in SOM and P dynamics might affect the sustainability of the system in the medium and long term. In tropical environments, most of the nutrient processes are determined by the high rates of organic matter (OM) mineralization. Therefore, SOM stability might play a crucial role in regulating soil-plant processes. In spite of this, the relationship between SOM quality, C and other nutrient dynamics are not well understood. In the present study, OM quality and P forms in forest floor and soil were investigated to get more insight on the C and P dynamics useful to sustainable management of forest plantations. Methods Thermal analysis (differential scanning calorimetry (DSC) and thermogravimetry (TGA)) and nuclear magnetic resonance (solid state 13C CPMASS and NMR and 31P-NMR) spectroscopy have been applied to partially decomposed forest floor and soils of pure acacia and eucalypt, and mixed-species acacia-eucalypt stands. Results Thermal analysis and 13C NMR analysis revealed a more advanced stage of humification in forest floor of acacia-eucalypt stands, suggesting a greater microbial activity in its litter. SOM were related to the OM recalcitrance of the forest floor, indicating this higher microbial activity of the forest floor in this stand might be favouring the incorporation of C into the mineral soil. Conclusions In relation with the fast mineralization in this environment, highly soluble orthophosphate was the dominant P form in both forest floor and soils. However, the mixed-species forest stands immobilized greater P in organic forms, preventing the P losses by leaching and contributing to sustain the P demand in the medium term. This shows that interactions between plants, microorganisms and soil can sustain the demand of this ecosystem. For this, the forest floor plays a key role in tightening the P cycle, minimizing the P losses.

ACS Style

Lydie-Stella Koutika; Lorenzo Cafiero; Annamaria Bevivino; Agustín Merino. Organic matter quality of forest floor as a driver of C and P dynamics in acacia and eucalypt plantations established on a Ferralic Arenosols, Congo. Forest Ecosystems 2020, 7, 1 -15.

AMA Style

Lydie-Stella Koutika, Lorenzo Cafiero, Annamaria Bevivino, Agustín Merino. Organic matter quality of forest floor as a driver of C and P dynamics in acacia and eucalypt plantations established on a Ferralic Arenosols, Congo. Forest Ecosystems. 2020; 7 (1):1-15.

Chicago/Turabian Style

Lydie-Stella Koutika; Lorenzo Cafiero; Annamaria Bevivino; Agustín Merino. 2020. "Organic matter quality of forest floor as a driver of C and P dynamics in acacia and eucalypt plantations established on a Ferralic Arenosols, Congo." Forest Ecosystems 7, no. 1: 1-15.

Conference paper
Published: 22 February 2020 in Lecture Notes in Electrical Engineering
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The detection of fungal contaminations, specifically moulds, in tomato sauce stored in the refrigerator is of great importance and very attractive in smart emerging applications. Using an electronic nose (e-nose) and a Fourier transform infrared (FTIR) spectrometer, we examined two sampling methods to early detect fungal contamination: the first method looks at the accumulated headspace while the second one at the actual headspace. Interestingly, we found that we can use only one sensor to detect the moulds even before their visual development.

ACS Style

Domenico Palumbo; Luigi Quercia; Antonella Del Fiore; Patrizia De Rossi; Annamaria Bevivino. The Best Approach for Early Detection of Fungi in Tomato Sauce. Lecture Notes in Electrical Engineering 2020, 239 -246.

AMA Style

Domenico Palumbo, Luigi Quercia, Antonella Del Fiore, Patrizia De Rossi, Annamaria Bevivino. The Best Approach for Early Detection of Fungi in Tomato Sauce. Lecture Notes in Electrical Engineering. 2020; ():239-246.

Chicago/Turabian Style

Domenico Palumbo; Luigi Quercia; Antonella Del Fiore; Patrizia De Rossi; Annamaria Bevivino. 2020. "The Best Approach for Early Detection of Fungi in Tomato Sauce." Lecture Notes in Electrical Engineering , no. : 239-246.

Original research article
Published: 10 December 2019 in Frontiers in Microbiology
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Biochar shapes the soil environment and plant growth. Nevertheless, the mechanisms associated with an improved plant biomass and soil microbiome in low metal-contaminated soils are still unclear. In this study, the influence of biochar on soil physico-chemical properties, plant performance, and rhizosphere microbiota in durum wheat was investigated at the above- and belowground levels. Two kinds of biochar from different feedstocks (wood chips and wheat straw pellets) and two Italian durum wheat varieties, Duilio and Marco Aurelio, were analyzed in a greenhouse using a low-nutrient gleyic fluvisol containing a very small amount of Pb and Zn. Four different treatments were performed: soil-only control (C), soil amended with woody biochar equilibrated with nutrient solution (B1+) and non-activated (B1−), and soil amended with non-activated (B2−) wheat straw biochar. Seven weeks after seed germination, (1) the physico-chemical properties of soil, biochars, and mixtures were assessed; (2) the fresh and dry weight of aboveground plant tissues and roots and other morphometric traits were measured; and (3) metabarcoding of the 16S rRNA bacterial gene was performed on rhizosphere soil samples. The results showed that the biochar from wheat straw had stronger impact on both durum varieties, with higher electrical conductivity, higher levels of available K and Na, and a substantial increase of dissolved Na+, K+, and Cl− ions in pore water. Generally, biochar amendment decreased Zn availability for the plants. In addition, biochar improved plant growth in the early growth stage, and the more positive effect was achieved by combining wheat straw biochar with Marco Aurelio. Rhizosphere bacterial microbiota showed variation in alpha diversity only due to treatment; on the other hand, the differential analysis showed consistent variation among samples with significant effects on amplicon sequence variant (ASV) abundance due to the specific biochar treatment as well as the genotype. The pure B1−, due to its scarce nutrient content with respect to the richer types (B1+ and B2−), had a negative impact on microbiota richness. Our study highlights that an appropriate combination of biochar feedstock and crop species may lead to superior yield.

ACS Style

Arianna Latini; Giovanni Bacci; Manuel Teodoro; Daniele Mirabile Gattia; Annamaria Bevivino; Lukáš Trakal. The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil. Frontiers in Microbiology 2019, 10, 2694 .

AMA Style

Arianna Latini, Giovanni Bacci, Manuel Teodoro, Daniele Mirabile Gattia, Annamaria Bevivino, Lukáš Trakal. The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil. Frontiers in Microbiology. 2019; 10 ():2694.

Chicago/Turabian Style

Arianna Latini; Giovanni Bacci; Manuel Teodoro; Daniele Mirabile Gattia; Annamaria Bevivino; Lukáš Trakal. 2019. "The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil." Frontiers in Microbiology 10, no. : 2694.

Journal article
Published: 04 September 2019 in Forest Ecosystems
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Afforestation of savannas in the Congolese coastal plains with eucalypt has provided wood pulp for industry and fuel energy for the local population. Typically, following afforestation, Acacia mangium are introduced to improve soil fertility and sustain productivity. Through investigations of particulate organic matter (POM), potential soil organic matter (SOM) quality was assessed in acacia and eucalypt plantations along rotations. Nutrients in POM (4000–50 μm) in the 0–5 cm soil layer were measured after five years into the second rotation (R2Y5) in relation to soil pH and P availability. Data were compared to those at the end of the first 7-year-rotation (R1Y7) and after two years into the second rotation (R2Y2) to evaluate overall SOM quality in the topsoil. At R2Y5, soil pH was higher in the pure eucalypt stands (100E) than in stands containing acacia, either in monoculture (100A) or evenly mixed with eucalypt (50A50E). Coarse POM (cPOM, 4000–250 μm) beneath 100A had the highest N concentration (1.71%), followed by those beneath 50A50E (1.42%) and 100E (1.30%). Higher N was always found in the stands containing acacia. Lower sulphur (S) concentrations and P availabilities were observed in cPOM (50A50E). The greatest amount of coarse (414.7 g) and fine (214.5 g) forest floor litter were found in 100A stands, whereas higher C concentrations were found in the 100E stands for coarse forest floor litter (36.5%) and in the 50A50E stands for fine forest floor litter (38.7%). The decrease in cPOM N and C concentrations were lower than 20% (R1Y7) and 26% (R2Y5) relative to the younger stage (R2Y2). This tendency was more pronounced in fine POM (250–50 μm) and organo-mineral fraction (< 50 μm). The main changes occurred in cPOM beneath stands containing acacia while higher weight of forest floor litter was found in 100A. Soil pH decreased in stands containing acacia. Overall N and C dynamics was enhanced in older stands (R2Y5) than in the younger stands (R2Y2). This may reveal a creation of more labile SOM with lower N and C concentrations in POM fractions in the surface layer, i.e., an ecosystem with a lower potential to mitigate climate change along rotations.

ACS Style

Lydie-Stella Koutika; Sylvain Ngoyi; Lorenzo Cafiero; Annamaria Bevivino. Soil organic matter quality along rotations in acacia and eucalypt plantations in the Congolese coastal plains. Forest Ecosystems 2019, 6, 1 -13.

AMA Style

Lydie-Stella Koutika, Sylvain Ngoyi, Lorenzo Cafiero, Annamaria Bevivino. Soil organic matter quality along rotations in acacia and eucalypt plantations in the Congolese coastal plains. Forest Ecosystems. 2019; 6 (1):1-13.

Chicago/Turabian Style

Lydie-Stella Koutika; Sylvain Ngoyi; Lorenzo Cafiero; Annamaria Bevivino. 2019. "Soil organic matter quality along rotations in acacia and eucalypt plantations in the Congolese coastal plains." Forest Ecosystems 6, no. 1: 1-13.

Case report
Published: 29 August 2019 in BMC Pulmonary Medicine
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Burkholderia contaminans is one of the 20 closely related bacterial of the Burkholderia cepacia complex, a group of bacteria that are ubiquitous in the environment and capable of infecting people with cystic fibrosis (CF). This species is an emerging pathogen and it has been widely isolated from CF patients in Argentina, Spain, Portugal, Australia, Canada, USA with a low prevalence in Ireland, France, Russia, Switzerland, Czech Republic, and Italy. This is the first report of B. contaminans affecting two Italian CF patients attending the same CF Centre. We correlate B. contaminans colonisation with lung function decline and co-infection with other clinically relevant CF pathogens. B. contaminans was identified by Multi Locus Sequence Typing in routine sputum analysis of two Caucasian CF women homozygous for Phe508del CFTR mutation. Sequence Type 102 was detected in both strains. It is known that B. contaminans ST102 was isolated both from CF and non-CF patients, with an intercontinental spread across the world. Random Amplified Polymorphic DNA analysis revealed the genetic relatedness between the two strains. We examined their susceptibility to antimicrobial agents, comparing the latter with that recorded for other B. contaminans isolated from different countries. We also described key virulence factors possibly linked with a clinical outcome. Specifically, we attempted to correlate colonization with the incidence of acute exacerbation of symptoms and lung function decline. This case presentation suggests that acquisition of B. contaminans ST102 is not directly associated with a lung function decline. We retain that the presence of other CF pathogens (i.e. MRSA and Trichosporon) along with B. contaminans ST102 might have contributed to the worsening of clinical conditions in our CF patients. The circumstances leading to the establishment of B. contaminans ST102 infections are still unknown. We highlight the importance to proper detect and typing bacteria implicated in CF infection by using molecular techniques.

ACS Style

Daniela Savi; Serena Quattrucci; Maria Trancassini; Claudia Dalmastri; Riccardo V. De Biase; Marta Maggisano; Paolo Palange; Annamaria Bevivino. Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report. BMC Pulmonary Medicine 2019, 19, 1 -8.

AMA Style

Daniela Savi, Serena Quattrucci, Maria Trancassini, Claudia Dalmastri, Riccardo V. De Biase, Marta Maggisano, Paolo Palange, Annamaria Bevivino. Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report. BMC Pulmonary Medicine. 2019; 19 (1):1-8.

Chicago/Turabian Style

Daniela Savi; Serena Quattrucci; Maria Trancassini; Claudia Dalmastri; Riccardo V. De Biase; Marta Maggisano; Paolo Palange; Annamaria Bevivino. 2019. "Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report." BMC Pulmonary Medicine 19, no. 1: 1-8.

Review
Published: 19 August 2019 in Trends in Molecular Medicine
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Despite over a decade of cystic fibrosis (CF) microbiome research, much remains to be learned about the overall composition, metabolic activities, and pathogenicity of the microbes in CF airways, limiting our understanding of the respiratory microbiome's relation to disease. Systems-level integration and modeling of host–microbiome interactions may allow us to better define the relationships between microbiological characteristics, disease status, and treatment response. In this way, modeling could pave the way for microbiome-based development of predictive models, individualized treatment plans, and novel therapeutic approaches, potentially serving as a paradigm for approaching other chronic infections. In this review, we describe the challenges facing this effort and propose research priorities for a systems biology approach to CF lung disease.

ACS Style

Annamaria Bevivino; Giovanni Bacci; Pavel Drevinek; Maria Nelson; Lucas Hoffman; Alessio Mengoni. Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends in Molecular Medicine 2019, 25, 1110 -1122.

AMA Style

Annamaria Bevivino, Giovanni Bacci, Pavel Drevinek, Maria Nelson, Lucas Hoffman, Alessio Mengoni. Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends in Molecular Medicine. 2019; 25 (12):1110-1122.

Chicago/Turabian Style

Annamaria Bevivino; Giovanni Bacci; Pavel Drevinek; Maria Nelson; Lucas Hoffman; Alessio Mengoni. 2019. "Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration." Trends in Molecular Medicine 25, no. 12: 1110-1122.

Preprint
Published: 15 April 2019
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Although the cystic fibrosis (CF) lung microbiome has been characterized in several studies, little is still known about the functions harboured by those bacteria, and how they change with disease status and antibiotic treatment. The aim of this study was to investigate the taxonomic and functional temporal dynamics of airways microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with chronic P. aeruginosa infection, for a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing either strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes during exacerbations and following antibiotic treatment. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of traditional CF pathogens, including P. aeruginosa, and emerging pathogens. Sputum microbiome was found to be extraordinarily resilient following antibiotic treatment, with rapid recovery of taxa and metagenome-associated gene functions. In particular, a large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status or antibiotic treatment, and constantly detected in the lung microbiome of all subjects independently from known antibiotic exposure, suggesting an overall microbiome-associated functions stability despite taxonomic fluctuations of the communities. IMPORTANCE While the dynamics of CF sputum microbial composition were highly patient-specific, the overall sputum metagenome composition was stable, showing a high resilience along time and antibiotic exposure. The high degree of redundancy in the CF lung microbiome could testifies ecological aspects connected to the disease that were never considered so far, as the large core-set of genes shared between patients despite observed differences in clinical status or antibiotic treatment. Investigations on the actual functionality (e.g. by metatranscriptomics) of the identified core-set of genes could provide clues on genetic function of the microbiome to be targeted in future therapeutic treatments.

ACS Style

Giovanni Bacci; Giovanni Taccetti; Daniela Dolce; Federica Armanini; Nicola Segata; Francesca Di Cesare; Vincenzina Lucidi; Ersilia Vita Fiscarelli; Patrizia Morelli; Rosaria Casciaro; Anna Negroni; Alessio Mengoni; Annamaria Bevivino. Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa. 2019, 609057 .

AMA Style

Giovanni Bacci, Giovanni Taccetti, Daniela Dolce, Federica Armanini, Nicola Segata, Francesca Di Cesare, Vincenzina Lucidi, Ersilia Vita Fiscarelli, Patrizia Morelli, Rosaria Casciaro, Anna Negroni, Alessio Mengoni, Annamaria Bevivino. Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa. . 2019; ():609057.

Chicago/Turabian Style

Giovanni Bacci; Giovanni Taccetti; Daniela Dolce; Federica Armanini; Nicola Segata; Francesca Di Cesare; Vincenzina Lucidi; Ersilia Vita Fiscarelli; Patrizia Morelli; Rosaria Casciaro; Anna Negroni; Alessio Mengoni; Annamaria Bevivino. 2019. "Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa." , no. : 609057.

Journal article
Published: 20 October 2018 in International Journal of Molecular Sciences
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Different steps and conditions for DNA extraction for microbiota analysis in sputum have been reported in the literature. We aimed at testing both dithiothreitol (DTT) and enzymatic treatments of sputum samples and identifying the most suitable DNA extraction technique for the microbiota analysis of sputum. Sputum treatments with and without DTT were compared in terms of their median levels and the coefficient of variation between replicates of both DNA extraction yield and real-time PCR for the 16S rRNA gene. Treatments with and without lysozyme and lysostaphin were compared in terms of their median levels of real-time PCR for S. aureus. Two enzyme-based and three beads-based techniques for DNA extraction were compared in terms of their DNA extraction yield, real-time PCR for the 16S rRNA gene and microbiota analysis. DTT treatment decreased the coefficient of variation between replicates of both DNA extraction yield and real-time PCR. Lysostaphin (either 0.18 or 0.36 mg/mL) and lysozyme treatments increased S. aureus detection. One enzyme-based kit offered the highest DNA yield and 16S rRNA gene real-time PCR with no significant differences in terms of alpha-diversity indexes. A condition using both DTT and lysostaphin/lysozyme treatments along with an enzymatic kit seems to be preferred for the microbiota analysis of sputum samples.

ACS Style

Leonardo Terranova; Martina Oriano; Antonio Teri; Luca Ruggiero; Camilla Tafuro; Paola Marchisio; Andrea Gramegna; Martina Contarini; Elisa Franceschi; Samantha Sottotetti; Lisa Cariani; Annamaria Bevivino; James D. Chalmers; Stefano Aliberti; Francesco Blasi. How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis. International Journal of Molecular Sciences 2018, 19, 3256 .

AMA Style

Leonardo Terranova, Martina Oriano, Antonio Teri, Luca Ruggiero, Camilla Tafuro, Paola Marchisio, Andrea Gramegna, Martina Contarini, Elisa Franceschi, Samantha Sottotetti, Lisa Cariani, Annamaria Bevivino, James D. Chalmers, Stefano Aliberti, Francesco Blasi. How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis. International Journal of Molecular Sciences. 2018; 19 (10):3256.

Chicago/Turabian Style

Leonardo Terranova; Martina Oriano; Antonio Teri; Luca Ruggiero; Camilla Tafuro; Paola Marchisio; Andrea Gramegna; Martina Contarini; Elisa Franceschi; Samantha Sottotetti; Lisa Cariani; Annamaria Bevivino; James D. Chalmers; Stefano Aliberti; Francesco Blasi. 2018. "How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis." International Journal of Molecular Sciences 19, no. 10: 3256.

Review article
Published: 05 June 2018 in Frontiers in Microbiology
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Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

ACS Style

Jesús Mercado-Blanco; Isabel Abrantes; Anna Barra Caracciolo; Annamaria Bevivino; Aurelio Ciancio; Paola Grenni; Katarzyna Hrynkiewicz; László Kredics; Diogo N. Proença. Belowground Microbiota and the Health of Tree Crops. Frontiers in Microbiology 2018, 9, 1006 .

AMA Style

Jesús Mercado-Blanco, Isabel Abrantes, Anna Barra Caracciolo, Annamaria Bevivino, Aurelio Ciancio, Paola Grenni, Katarzyna Hrynkiewicz, László Kredics, Diogo N. Proença. Belowground Microbiota and the Health of Tree Crops. Frontiers in Microbiology. 2018; 9 ():1006.

Chicago/Turabian Style

Jesús Mercado-Blanco; Isabel Abrantes; Anna Barra Caracciolo; Annamaria Bevivino; Aurelio Ciancio; Paola Grenni; Katarzyna Hrynkiewicz; László Kredics; Diogo N. Proença. 2018. "Belowground Microbiota and the Health of Tree Crops." Frontiers in Microbiology 9, no. : 1006.

Meeting abstracts
Published: 16 January 2018 in Italian Journal of Pediatrics
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The human body contains complex communities of microorganisms that play an important role in human health. In the last decade, next-generation sequencing (NGS) was employed to decipher the structure and composition of the human microbiome, defined as the totality of microbes, their genomes and interactions in a defined environment. Cystic Fibrosis (CF) disease affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract [1]. An increasing number of studies have revealed a cross-talk between the two compartiments as exemplified by intestinal complications during respiratory disease and vice versa. Although so far mechanisms through which the lung could influence the gut environment are unclear, the existence of the gut–lung axis could open up new possibilities for therapeutic approaches to respiratory diseases. A growing body of evidence suggests that the gastrointestinal (GI) microbiome in people with CF is altered. These dysbioses contribute to disease manifestations in many organs, both within and beyond the GI tract [2]. In this lecture, I highlight how changes in the intestinal microenvironment, with a particular focus on the intestinal microbiota, impact upon respiratory disease. Together with reported benefits for respiratory exacerbations, such as a reduced rate of pulmonary exacerbations and upper respiratory tract infections in patients with CF, the administration of probiotcs may globally modify the GI microbiome, thus promoting bacterial communities that modulate host immune responses [3]. Observations from clinical trials of probiotics in CF patient revealed the probiotics can ameliorate the dysbiosis of CF, reducing the proteobacterial populations in the gut microbiota, as well as decreasing gut inflammation and the number of pulmonary exacerbations. References 1. Burke DG, Fouhy F, Harrison MJ, et al. The altered gut microbiota in adults with cystic fibrosis. BMC Microbiology. 2017;17:58. 2. He Y, Wen Q, Yao F, et al. Gut–lung axis: The microbial contributions and clinical implications. Critical Reviews in Microbiology. 2017; 43:81-95. 3. Van Biervliet S, Declercq D, Somerse S. Clinical effects of probiotics in cystic fibrosis patients: A systematic review. Clinical Nutrition ESPEN 2017;18: 37-43. Cystic Fibrosis (CF) occurs most frequently in caucasian populations. Although less common, this disorder have been reported in all the ethnicities. Currently, there are more than 2000 described sequence variations in CFTR gene, uniformly distributed and including variants pathogenic and benign (CFTR1:www.genet.sickkids.on.ca/). To date, only a subset have been firmily established as variants annotated as disease-causing (CFTR2: www.cftr2.org). The spectrum and the frequency of individual CFTR variants, however, vary among specific ethnic groups and geographic areas. Genetic screening for CF with standard panels of CFTR mutations is widely used for the diagnosis of CF in newborns and symptomatic patients, and to diagnose CF carrier status. These screening panels have an high diagnostic sensitivity (around 85%) for CFTR mutations in caucasians populations but very low for non caucasians. Developed in the last decade, Next-Generation Sequencing (NGS) has been the last breakthrough technology in genetic studies with a substantial reduction in cost per sequenced base and a considerable enhancement of the sequence generation capabilities. Extended CFTR gene sequencing in NGS includes all the coding regions, the splicing sites and their flankig intronic regions, deep intronic regions where are localized known mutations, the promoter and the 5'-3' UTR regions. NGS allows the analysis of many samples concurrently in a shorter period of time compared to Sanger method . Moreover, NGS platforms are able to identify CFTR copy number variation (CNVs), not detected by Sanger sequencing. This technology has provided new and reliable approaches to molecular diagnosis of CF and CFTR-Related Disorders. It also allows to improve the diagnostic sensitivity of newborn and carrier screening molecular tests. In fact, bioinformatics tools suitable for all the NGS platforms can filter data generated from the gene sequencing, and analyze only mutations with well-established disease liability. This approach allows the development of targeted mutations panels with a higher number of frequent CF mutations for the target population compared to the standard panels and a consequent enhancement of the diagnostic sensitivity. Moreover, in the emerging challenge of diagnosing CF in non caucasians patients, the possibility of customize a NGS targeted mutations panel should increase the diagnostic sensitivity when the target population has different ethnicities. Background The life expectancy of patient with Cystic Fibrosis (CF) is increased in the last forty years. As result, extrapulmonary complication increased such as urinary incontinence (UI). The UI in patient with CF is probably connected with the increasing of pressure on the pelvic floor during coughing. This report sums up published articles concerning the prevalence, severity, impact and management of UI, in patients with CF. Materials and methods References were identified searching Medline, Embase and PubMed using the medical subject headings ‘cystic fibrosis’ AND ‘urinary incontinence’. Articles concerning UI prevalence, impact on quality of life and treatment were included. Results The UI’s prevalence ranged from 30-69% for women and 19-49% for girls. In adult men, UI’s prevalence ranges from 5% to 15% [1,2]. UI has a negative effect on the performance of airway clearance, exercise and/or spirometry, and has variable impact on patients’ lifestyle. There is limited evidence about the prevention and treatment of UI in CF, but the pelvic floor exercises are effective at reducing leakage in the short time [3]. Optimal positioning and posture advice during...

ACS Style

Annamaria Bevivino; Alessandra Coiana; Annalisa Fogazzi; Fabiana Timelli; Sandra Signorini; Marco Lucarelli; Patrizia Morelli; Rita Padoan; Barbara Giordani; Annalisa Amato; Fabio Majo; Gianluca Ferrari; Serena Quattrucci; Laura Minicucci; Giovanna Floridia; Gianna Puppo Fornaro; Domenica Taruscio; Marco Salvatore; Manuela Seia; Silvia Pierandrei; Giovanna Blaconà; Valentina Salvati; Giovanni Sette; Giuseppe Cimino; Federica Sangiuolo; Adriana Eramo; Mirella Collura; Elisa Parisi; Annalisa Ferlisi; Gabriella Traverso; Marcella Bertolino; Lisa Termini; Maria A. Orlando; Caterina Di Girgenti; Valeria Pavone; Maria A. Calamia; Maria G. Silvestro; Caterina Lo Piparo; Francesca Ficili; Carla Colombo; Elizabeth Tullis; Jane C. Davies; Charlotte McKee; Cynthia DeSouza; David Waltz; Jessica Savage; Marc Fisher; Rebecca Shilling; Sam Moskowitz; Sarah Robertson; Simon Tian; Jennifer L. Taylor-Cousar; Steven M. Rowe; Elisa Beccia; Annalucia Carbone; Maria Favia; Stefano Castellani; Antonella Angiolillo; Valeria Casavola; Massimo Conese; Bruno M. Cesana; Diego Falchetti; Fiorella Battistini; Elisabetta Bignamini; Cesare Braggion; Natalia Cirilli; Maria C. Lucanto; Vincenzina Lucidi; Antonio Manca; Valeria Raia; Novella Rotolo; Donatello Salvatore; Sonia Volpi; Erica Nazzari; Riccardo Guarise; Palmiro Mileto; Francesca Garbarino; Gianfranco Alicandro; Alberto Battezzati; Antonella M. Di Lullo; Marika Comegna; Felice Amato; Paola Iacotucci; Vincenzo Carnovale; Elena Cantone; Maurizio Iengo; Giuseppe Castaldo; Claudio Orlando; Alida Casale; Angela Sepe; Fabiola De Gregorio; Antonia De Matteo; Alice Castaldo; Chiara Cimbalo; Antonella Tosco; Daniela Savi; Michela Mordenti; Enea Bonci; Patrizia Troiani; Viviana D’Alù; Paolo Rossi; Monica Varchetta; Tamara Perelli; Serenella Bertasi; Paolo Palange; Lucia Tardino; Giuseppe F. Parisi; Anna Portale; Chiara Franzonello; Maria Papale; Salvatore Leonardi; Francesca Pennisi; Sabina M. Bruno; Giulia Licciardello; Giampiero Ferraguti; Manuela Sterrantino; Giancarlo Testino; Roberto Buzzetti; Cecilia Surace; Valentina M. Sofia; Nicola Ullmann; Antonio Novelli; Adriano Angioni; Renato Liguori; Francesca Manzoni; Chiara Di Palma; Sabrina Maietta; Federica Zarrilli; Vito Terlizzi; Federico Alghisi; Giuseppe Tuccio; Valentina Tradati; Eliana Di Stefano; Patrizia Dato; Maria G. Sciarrabone; Carmela Fondacaro; Federico Cresta; Valentina Baglioni; Silvia Garuti; Isabella Buffoni; Francesca Landi; Rosaria Casciaro; Daniela Girelli; Antonio Teri; Samantha Sottotetti; Arianna Biffi; Chiara Vignati; Monica D’Accico; Anna Maraschini; Milena Arghittu; Giovanna Pizzamiglio; Elisa Cariani; Daniela Dolce; Novella Ravenni; Silvia Campana; Erica Camera; Carlo Castellani; Giovanni Taccetti; Eleonora Calderone; Roberto Bandettini; Chiara Degli Innocenti; Chiara Castellani; Eleonora Masi; Maria Chiara Cavicchi; Beatrice Ferrari; Ramona Pezzotta; Piercarlo Poli; Serena Messali; Silvana Timpano; Erika Scaltriti; Stefano Pongolini; Simona Fiorentini; Silvia Bresci; Lorenzo Corsi; Beatrice Borchi; Annalisa Cavallo; Filippo Bartalesi; Massimo Pistolesi; Alessandro Bartoloni; Federica Arcoleo; Tiziana Pensabene; Giovanni Bacci; Federica Armanini; Ersilia V. Fiscarelli; Nicola Segata; Alessio Mengoni; Maria V. Di Toppa; Nicoleta Popa; Francesco Felicetti; Sonia Graziano; Riccardo Ciprandi; Rita Pescini; Guendalina Graffigna; Serena Barello; Paola Catastini; Salvatore De Masi; Lucia Guarnuto; Emanuela Di Liberti; Valentina Patti; Massimo Luca Castellazzi; Valeria Daccò; Laura Claut; Matteo Giuliari; Luana Vicentini; Fausto Tilotta; Antonella Paciaroni; Sabino Della Sala; Cristina Guerzoni; Elisa Andreatta; Grazia Dinnella; Orazia M. Granata; Tommaso S. Aronica; Mimì Crapisi; Donatella Fogazza; Luca Alessi; Flavia Mulè; Marcello Vitaliti; Mariarosaria Maresi; Andrea Catzola; Laura Salvadori; Carmela Colangelo; Giovanni Marsicovetere; Michele D’Andria; Domenica Passarella; Carmela Genovese; Stefania Barrale; Maria R. Bonaccorso; Annalisa D’Arpa. Abstracts from the 23rd Italian congress of Cystic Fibrosis and the 13th National congress of Cystic Fibrosis Italian Society. Italian Journal of Pediatrics 2018, 44, 1 -23.

AMA Style

Annamaria Bevivino, Alessandra Coiana, Annalisa Fogazzi, Fabiana Timelli, Sandra Signorini, Marco Lucarelli, Patrizia Morelli, Rita Padoan, Barbara Giordani, Annalisa Amato, Fabio Majo, Gianluca Ferrari, Serena Quattrucci, Laura Minicucci, Giovanna Floridia, Gianna Puppo Fornaro, Domenica Taruscio, Marco Salvatore, Manuela Seia, Silvia Pierandrei, Giovanna Blaconà, Valentina Salvati, Giovanni Sette, Giuseppe Cimino, Federica Sangiuolo, Adriana Eramo, Mirella Collura, Elisa Parisi, Annalisa Ferlisi, Gabriella Traverso, Marcella Bertolino, Lisa Termini, Maria A. Orlando, Caterina Di Girgenti, Valeria Pavone, Maria A. Calamia, Maria G. Silvestro, Caterina Lo Piparo, Francesca Ficili, Carla Colombo, Elizabeth Tullis, Jane C. Davies, Charlotte McKee, Cynthia DeSouza, David Waltz, Jessica Savage, Marc Fisher, Rebecca Shilling, Sam Moskowitz, Sarah Robertson, Simon Tian, Jennifer L. Taylor-Cousar, Steven M. Rowe, Elisa Beccia, Annalucia Carbone, Maria Favia, Stefano Castellani, Antonella Angiolillo, Valeria Casavola, Massimo Conese, Bruno M. Cesana, Diego Falchetti, Fiorella Battistini, Elisabetta Bignamini, Cesare Braggion, Natalia Cirilli, Maria C. Lucanto, Vincenzina Lucidi, Antonio Manca, Valeria Raia, Novella Rotolo, Donatello Salvatore, Sonia Volpi, Erica Nazzari, Riccardo Guarise, Palmiro Mileto, Francesca Garbarino, Gianfranco Alicandro, Alberto Battezzati, Antonella M. Di Lullo, Marika Comegna, Felice Amato, Paola Iacotucci, Vincenzo Carnovale, Elena Cantone, Maurizio Iengo, Giuseppe Castaldo, Claudio Orlando, Alida Casale, Angela Sepe, Fabiola De Gregorio, Antonia De Matteo, Alice Castaldo, Chiara Cimbalo, Antonella Tosco, Daniela Savi, Michela Mordenti, Enea Bonci, Patrizia Troiani, Viviana D’Alù, Paolo Rossi, Monica Varchetta, Tamara Perelli, Serenella Bertasi, Paolo Palange, Lucia Tardino, Giuseppe F. Parisi, Anna Portale, Chiara Franzonello, Maria Papale, Salvatore Leonardi, Francesca Pennisi, Sabina M. Bruno, Giulia Licciardello, Giampiero Ferraguti, Manuela Sterrantino, Giancarlo Testino, Roberto Buzzetti, Cecilia Surace, Valentina M. Sofia, Nicola Ullmann, Antonio Novelli, Adriano Angioni, Renato Liguori, Francesca Manzoni, Chiara Di Palma, Sabrina Maietta, Federica Zarrilli, Vito Terlizzi, Federico Alghisi, Giuseppe Tuccio, Valentina Tradati, Eliana Di Stefano, Patrizia Dato, Maria G. Sciarrabone, Carmela Fondacaro, Federico Cresta, Valentina Baglioni, Silvia Garuti, Isabella Buffoni, Francesca Landi, Rosaria Casciaro, Daniela Girelli, Antonio Teri, Samantha Sottotetti, Arianna Biffi, Chiara Vignati, Monica D’Accico, Anna Maraschini, Milena Arghittu, Giovanna Pizzamiglio, Elisa Cariani, Daniela Dolce, Novella Ravenni, Silvia Campana, Erica Camera, Carlo Castellani, Giovanni Taccetti, Eleonora Calderone, Roberto Bandettini, Chiara Degli Innocenti, Chiara Castellani, Eleonora Masi, Maria Chiara Cavicchi, Beatrice Ferrari, Ramona Pezzotta, Piercarlo Poli, Serena Messali, Silvana Timpano, Erika Scaltriti, Stefano Pongolini, Simona Fiorentini, Silvia Bresci, Lorenzo Corsi, Beatrice Borchi, Annalisa Cavallo, Filippo Bartalesi, Massimo Pistolesi, Alessandro Bartoloni, Federica Arcoleo, Tiziana Pensabene, Giovanni Bacci, Federica Armanini, Ersilia V. Fiscarelli, Nicola Segata, Alessio Mengoni, Maria V. Di Toppa, Nicoleta Popa, Francesco Felicetti, Sonia Graziano, Riccardo Ciprandi, Rita Pescini, Guendalina Graffigna, Serena Barello, Paola Catastini, Salvatore De Masi, Lucia Guarnuto, Emanuela Di Liberti, Valentina Patti, Massimo Luca Castellazzi, Valeria Daccò, Laura Claut, Matteo Giuliari, Luana Vicentini, Fausto Tilotta, Antonella Paciaroni, Sabino Della Sala, Cristina Guerzoni, Elisa Andreatta, Grazia Dinnella, Orazia M. Granata, Tommaso S. Aronica, Mimì Crapisi, Donatella Fogazza, Luca Alessi, Flavia Mulè, Marcello Vitaliti, Mariarosaria Maresi, Andrea Catzola, Laura Salvadori, Carmela Colangelo, Giovanni Marsicovetere, Michele D’Andria, Domenica Passarella, Carmela Genovese, Stefania Barrale, Maria R. Bonaccorso, Annalisa D’Arpa. Abstracts from the 23rd Italian congress of Cystic Fibrosis and the 13th National congress of Cystic Fibrosis Italian Society. Italian Journal of Pediatrics. 2018; 44 (1):1-23.

Chicago/Turabian Style

Annamaria Bevivino; Alessandra Coiana; Annalisa Fogazzi; Fabiana Timelli; Sandra Signorini; Marco Lucarelli; Patrizia Morelli; Rita Padoan; Barbara Giordani; Annalisa Amato; Fabio Majo; Gianluca Ferrari; Serena Quattrucci; Laura Minicucci; Giovanna Floridia; Gianna Puppo Fornaro; Domenica Taruscio; Marco Salvatore; Manuela Seia; Silvia Pierandrei; Giovanna Blaconà; Valentina Salvati; Giovanni Sette; Giuseppe Cimino; Federica Sangiuolo; Adriana Eramo; Mirella Collura; Elisa Parisi; Annalisa Ferlisi; Gabriella Traverso; Marcella Bertolino; Lisa Termini; Maria A. Orlando; Caterina Di Girgenti; Valeria Pavone; Maria A. Calamia; Maria G. Silvestro; Caterina Lo Piparo; Francesca Ficili; Carla Colombo; Elizabeth Tullis; Jane C. Davies; Charlotte McKee; Cynthia DeSouza; David Waltz; Jessica Savage; Marc Fisher; Rebecca Shilling; Sam Moskowitz; Sarah Robertson; Simon Tian; Jennifer L. Taylor-Cousar; Steven M. Rowe; Elisa Beccia; Annalucia Carbone; Maria Favia; Stefano Castellani; Antonella Angiolillo; Valeria Casavola; Massimo Conese; Bruno M. Cesana; Diego Falchetti; Fiorella Battistini; Elisabetta Bignamini; Cesare Braggion; Natalia Cirilli; Maria C. Lucanto; Vincenzina Lucidi; Antonio Manca; Valeria Raia; Novella Rotolo; Donatello Salvatore; Sonia Volpi; Erica Nazzari; Riccardo Guarise; Palmiro Mileto; Francesca Garbarino; Gianfranco Alicandro; Alberto Battezzati; Antonella M. Di Lullo; Marika Comegna; Felice Amato; Paola Iacotucci; Vincenzo Carnovale; Elena Cantone; Maurizio Iengo; Giuseppe Castaldo; Claudio Orlando; Alida Casale; Angela Sepe; Fabiola De Gregorio; Antonia De Matteo; Alice Castaldo; Chiara Cimbalo; Antonella Tosco; Daniela Savi; Michela Mordenti; Enea Bonci; Patrizia Troiani; Viviana D’Alù; Paolo Rossi; Monica Varchetta; Tamara Perelli; Serenella Bertasi; Paolo Palange; Lucia Tardino; Giuseppe F. Parisi; Anna Portale; Chiara Franzonello; Maria Papale; Salvatore Leonardi; Francesca Pennisi; Sabina M. Bruno; Giulia Licciardello; Giampiero Ferraguti; Manuela Sterrantino; Giancarlo Testino; Roberto Buzzetti; Cecilia Surace; Valentina M. Sofia; Nicola Ullmann; Antonio Novelli; Adriano Angioni; Renato Liguori; Francesca Manzoni; Chiara Di Palma; Sabrina Maietta; Federica Zarrilli; Vito Terlizzi; Federico Alghisi; Giuseppe Tuccio; Valentina Tradati; Eliana Di Stefano; Patrizia Dato; Maria G. Sciarrabone; Carmela Fondacaro; Federico Cresta; Valentina Baglioni; Silvia Garuti; Isabella Buffoni; Francesca Landi; Rosaria Casciaro; Daniela Girelli; Antonio Teri; Samantha Sottotetti; Arianna Biffi; Chiara Vignati; Monica D’Accico; Anna Maraschini; Milena Arghittu; Giovanna Pizzamiglio; Elisa Cariani; Daniela Dolce; Novella Ravenni; Silvia Campana; Erica Camera; Carlo Castellani; Giovanni Taccetti; Eleonora Calderone; Roberto Bandettini; Chiara Degli Innocenti; Chiara Castellani; Eleonora Masi; Maria Chiara Cavicchi; Beatrice Ferrari; Ramona Pezzotta; Piercarlo Poli; Serena Messali; Silvana Timpano; Erika Scaltriti; Stefano Pongolini; Simona Fiorentini; Silvia Bresci; Lorenzo Corsi; Beatrice Borchi; Annalisa Cavallo; Filippo Bartalesi; Massimo Pistolesi; Alessandro Bartoloni; Federica Arcoleo; Tiziana Pensabene; Giovanni Bacci; Federica Armanini; Ersilia V. Fiscarelli; Nicola Segata; Alessio Mengoni; Maria V. Di Toppa; Nicoleta Popa; Francesco Felicetti; Sonia Graziano; Riccardo Ciprandi; Rita Pescini; Guendalina Graffigna; Serena Barello; Paola Catastini; Salvatore De Masi; Lucia Guarnuto; Emanuela Di Liberti; Valentina Patti; Massimo Luca Castellazzi; Valeria Daccò; Laura Claut; Matteo Giuliari; Luana Vicentini; Fausto Tilotta; Antonella Paciaroni; Sabino Della Sala; Cristina Guerzoni; Elisa Andreatta; Grazia Dinnella; Orazia M. Granata; Tommaso S. Aronica; Mimì Crapisi; Donatella Fogazza; Luca Alessi; Flavia Mulè; Marcello Vitaliti; Mariarosaria Maresi; Andrea Catzola; Laura Salvadori; Carmela Colangelo; Giovanni Marsicovetere; Michele D’Andria; Domenica Passarella; Carmela Genovese; Stefania Barrale; Maria R. Bonaccorso; Annalisa D’Arpa. 2018. "Abstracts from the 23rd Italian congress of Cystic Fibrosis and the 13th National congress of Cystic Fibrosis Italian Society." Italian Journal of Pediatrics 44, no. 1: 1-23.

Journal article
Published: 14 November 2017 in International Journal of Molecular Sciences
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Burkholderia cenocepacia is an important opportunistic pathogen in cystic fibrosis (CF) patients, and has also been isolated from natural environments. In previous work, we explored the virulence and pathogenic potential of environmental B. cenocepacia strains and demonstrated that they do not differ from clinical strains in some pathogenic traits. Here, we investigated the ability of the environmental B. cenocepacia Mex1 strain, isolated from the maize rhizosphere, to persist and increase its virulence after serial passages in a mouse model of chronic infection. B. cenocepacia Mex1 strain, belonging to the recA lineage IIIA, was embedded in agar beads and challenged into the lung of C57Bl/6 mice. The mice were sacrificed after 28 days from infection and their lungs were tested for bacterial loads. Agar beads containing the pool of B. cenocepacia colonies from the four sequential passages were used to infect the mice. The environmental B. cenocepacia strain showed a low incidence of chronic infection after the first passage; after the second, third and fourth passages in mice, its ability to establish chronic infection increased significantly and progressively up to 100%. Colonial morphology analysis and genetic profiling of the Mex1-derived clones recovered after the fourth passage from infected mice revealed that they were indistinguishable from the challenged strain both at phenotypic and genetic level. By testing the virulence of single clones in the Galleria mellonella infection model, we found that two Mex1-derived clones significantly increased their pathogenicity compared to the parental Mex1 strain and behaved similarly to the clinical and epidemic B. cenocepacia LMG16656T. Our findings suggest that serial passages of the environmental B. cenocepacia Mex1 strain in mice resulted in an increased ability to determine chronic lung infection and the appearance of clonal variants with increased virulence in non-vertebrate hosts.

ACS Style

Alessandra Bragonzi; Moira Paroni; Luisa Pirone; Ivan Coladarci; Fiorentina Ascenzioni; Annamaria Bevivino. Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice. International Journal of Molecular Sciences 2017, 18, 2417 .

AMA Style

Alessandra Bragonzi, Moira Paroni, Luisa Pirone, Ivan Coladarci, Fiorentina Ascenzioni, Annamaria Bevivino. Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice. International Journal of Molecular Sciences. 2017; 18 (11):2417.

Chicago/Turabian Style

Alessandra Bragonzi; Moira Paroni; Luisa Pirone; Ivan Coladarci; Fiorentina Ascenzioni; Annamaria Bevivino. 2017. "Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice." International Journal of Molecular Sciences 18, no. 11: 2417.

Conference paper
Published: 14 September 2017 in Soil Biological Communities and Ecosystem Resilience
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Soil is a complex and dynamic ecosystem whose functionality is related to the equilibrium existing among chemical, physical and biological parameters and the resident microbial communities. Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling, and have direct and indirect effects on both crop growth and quality, as well as on the sustainability of soil productivity. In addition, soil microorganisms substantially contribute to the resistance and resilience of agro-ecosystems to abiotic disturbance and stress. Therefore, changes in microbial communities may directly affect soil ecosystem function since microbes can respond rapidly to environmental changes because of the vastness of microbial biomass and diversity. An increasing number of studies have shown how environmental impacts that cause modifications in microbial community structure and diversity ultimately affect soil biological processes. Agricultural land management is one of most significant anthropogenic activities that substantially alter soil characteristics, including physical, chemical, and biological properties. The present chapter gives a picture of the effect of different agricultural management practices on soil microbial community structure and function. A case study on the effects of tillage and nitrogen fertilization on soil bacterial community structure is also reported.

ACS Style

Annamaria Bevivino; Claudia Dalmastri. Impact of Agricultural Land Management on Soil Bacterial Community: A Case Study in the Mediterranean Area. Soil Biological Communities and Ecosystem Resilience 2017, 77 -95.

AMA Style

Annamaria Bevivino, Claudia Dalmastri. Impact of Agricultural Land Management on Soil Bacterial Community: A Case Study in the Mediterranean Area. Soil Biological Communities and Ecosystem Resilience. 2017; ():77-95.

Chicago/Turabian Style

Annamaria Bevivino; Claudia Dalmastri. 2017. "Impact of Agricultural Land Management on Soil Bacterial Community: A Case Study in the Mediterranean Area." Soil Biological Communities and Ecosystem Resilience , no. : 77-95.

Article
Published: 11 August 2017 in Journal of the Science of Food and Agriculture
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Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry

ACS Style

Loretta Daddiego; Linda Bianco; Cristina Capodicasa; Fabrizio Carbone; Claudia Dalmastri; Lorenza Daroda; Antonella Del Fiore; Patrizia De Rossi; Mariasole Di Carli; Marcello Donini; Loredana Lopez; Alessio Mengoni; Patrizia Paganin; Gaetano Perrotta; Annamaria Bevivino. Omics approaches on fresh‐cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment. Journal of the Science of Food and Agriculture 2017, 98, 737 -750.

AMA Style

Loretta Daddiego, Linda Bianco, Cristina Capodicasa, Fabrizio Carbone, Claudia Dalmastri, Lorenza Daroda, Antonella Del Fiore, Patrizia De Rossi, Mariasole Di Carli, Marcello Donini, Loredana Lopez, Alessio Mengoni, Patrizia Paganin, Gaetano Perrotta, Annamaria Bevivino. Omics approaches on fresh‐cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment. Journal of the Science of Food and Agriculture. 2017; 98 (2):737-750.

Chicago/Turabian Style

Loretta Daddiego; Linda Bianco; Cristina Capodicasa; Fabrizio Carbone; Claudia Dalmastri; Lorenza Daroda; Antonella Del Fiore; Patrizia De Rossi; Mariasole Di Carli; Marcello Donini; Loredana Lopez; Alessio Mengoni; Patrizia Paganin; Gaetano Perrotta; Annamaria Bevivino. 2017. "Omics approaches on fresh‐cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment." Journal of the Science of Food and Agriculture 98, no. 2: 737-750.

Clinical trial
Published: 29 July 2017 in International Journal of Molecular Sciences
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In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.

ACS Style

Giovanni Bacci; Alessio Mengoni; Ersilia Fiscarelli; Nicola Segata; Giovanni Taccetti; Daniela Dolce; Patrizia Paganin; Patrizia Morelli; Vanessa Tuccio; Alessandra De Alessandri; Vincenzina Lucidi; Annamaria Bevivino. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. International Journal of Molecular Sciences 2017, 18, 1654 .

AMA Style

Giovanni Bacci, Alessio Mengoni, Ersilia Fiscarelli, Nicola Segata, Giovanni Taccetti, Daniela Dolce, Patrizia Paganin, Patrizia Morelli, Vanessa Tuccio, Alessandra De Alessandri, Vincenzina Lucidi, Annamaria Bevivino. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. International Journal of Molecular Sciences. 2017; 18 (8):1654.

Chicago/Turabian Style

Giovanni Bacci; Alessio Mengoni; Ersilia Fiscarelli; Nicola Segata; Giovanni Taccetti; Daniela Dolce; Patrizia Paganin; Patrizia Morelli; Vanessa Tuccio; Alessandra De Alessandri; Vincenzina Lucidi; Annamaria Bevivino. 2017. "A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease." International Journal of Molecular Sciences 18, no. 8: 1654.

Multicenter study
Published: 29 June 2016 in PLOS ONE
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Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.

ACS Style

Giovanni Bacci; Patrizia Paganin; Loredana Lopez; Chiara Vanni; Claudia Dalmastri; Cristina Cantale; Loretta Daddiego; Gaetano Perrotta; Daniela Dolce; Patrizia Morelli; Vanessa Tuccio; Alessandra De Alessandri; Ersilia Vita Fiscarelli; Giovanni Taccetti; Vincenzina Lucidi; Annamaria Bevivino; Alessio Mengoni. Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLOS ONE 2016, 11, e0156807 .

AMA Style

Giovanni Bacci, Patrizia Paganin, Loredana Lopez, Chiara Vanni, Claudia Dalmastri, Cristina Cantale, Loretta Daddiego, Gaetano Perrotta, Daniela Dolce, Patrizia Morelli, Vanessa Tuccio, Alessandra De Alessandri, Ersilia Vita Fiscarelli, Giovanni Taccetti, Vincenzina Lucidi, Annamaria Bevivino, Alessio Mengoni. Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLOS ONE. 2016; 11 (6):e0156807.

Chicago/Turabian Style

Giovanni Bacci; Patrizia Paganin; Loredana Lopez; Chiara Vanni; Claudia Dalmastri; Cristina Cantale; Loretta Daddiego; Gaetano Perrotta; Daniela Dolce; Patrizia Morelli; Vanessa Tuccio; Alessandra De Alessandri; Ersilia Vita Fiscarelli; Giovanni Taccetti; Vincenzina Lucidi; Annamaria Bevivino; Alessio Mengoni. 2016. "Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline." PLOS ONE 11, no. 6: e0156807.