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Ferravante C, Arslan‐Gatz BS, Dell'Annunziata F, Palumbo D, Lamberti J, Alexandrova E, Di Rosa D, Strianese O, Giordano A, Palo L, Giurato G, Salzano FA, Galdiero M, Weisz A, Franci G, Rizzo F, Folliero V. Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID-19. J Med Virol 2022; 94:5567-5573. [PMID: 35831579 PMCID: PMC9349744 DOI: 10.1002/jmv.27998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 12/15/2022]
Abstract
In December 2019, several patients were hospitalized and diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which subsequently led to a global pandemic. To date, there are no studies evaluating the relationship between the respiratory phageome and the SARS-CoV-2 infection. The current study investigated the phageome profiles in the nasopharyngeal swabs collected from 55 patients during the three different waves of coronavirus disease 2019 (COVID-19) in the Campania Region (Southern Italy). Data obtained from the taxonomic profiling show that phage families belonging to the order Caudovirales have a high abundance in the patient samples. Moreover, the severity of the COVID-19 infection seems to be correlated with the phage abundance.
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Affiliation(s)
- Carlo Ferravante
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Berin S. Arslan‐Gatz
- Department of Experimental MedicineUniversity of Campania “Luigi Vanvitelli”NaplesItaly
| | | | - Domenico Palumbo
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Jessica Lamberti
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Elena Alexandrova
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Domenico Di Rosa
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Oriana Strianese
- Genome Research Center for Health ‐ CRGSCampus of Medicine ‐ University of SalernoBaronissiItaly
| | - Alessandro Giordano
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Luigi Palo
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly,Genome Research Center for Health ‐ CRGSCampus of Medicine ‐ University of SalernoBaronissiItaly
| | - Francesco A. Salzano
- Department of Medicine, Surgery and DentistryUniversity of SalernoBaronissiItaly
| | - Massimiliano Galdiero
- Department of Experimental MedicineUniversity of Campania “Luigi Vanvitelli”NaplesItaly
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly,Genome Research Center for Health ‐ CRGSCampus of Medicine ‐ University of SalernoBaronissiItaly,Medical Genomics Program, AOU ‘S. Giovanni di Dio e Ruggi d'Aragona’University of SalernoSalernoItaly
| | - Gianluigi Franci
- Department of Medicine, Surgery and DentistryUniversity of SalernoBaronissiItaly
| | - Francesca Rizzo
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana', Laboratory of Molecular Medicine and GenomicsUniversity of SalernoBaronissiItaly,Genome Research Center for Health ‐ CRGSCampus of Medicine ‐ University of SalernoBaronissiItaly
| | - Veronica Folliero
- Department of Experimental MedicineUniversity of Campania “Luigi Vanvitelli”NaplesItaly
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De Angelis F, Romboni M, Veltre V, Catalano P, Martínez-Labarga C, Gazzaniga V, Rickards O. First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD). Genes (Basel) 2022; 13:genes13010136. [PMID: 35052476 PMCID: PMC8774527 DOI: 10.3390/genes13010136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.
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Affiliation(s)
- Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
- Correspondence: ; Tel.: +39-0672594350
| | - Marco Romboni
- Department of Biology, University of Pisa, 56121 Pisa, Italy;
| | - Virginia Veltre
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Paola Catalano
- Former Servizio di Antropologia, Soprintendenza Speciale Archeologia, Belle Arti e Paesaggio di Roma, 00185 Roma, Italy;
| | - Cristina Martínez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
| | - Valentina Gazzaniga
- Unità di Storia della Medicina e Bioetica, Sapienza University of Rome, 00185 Roma, Italy;
| | - Olga Rickards
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
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Ferravante C, Sanna G, Melone V, Fromentier A, Rocco T, D'Agostino Y, Lamberti J, Alexandrova E, Pecoraro G, Pagliano P, Astorri R, Manzin A, Weisz A, Giurato G, Galdiero M, Rizzo F, Franci G. Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania region of Italy. J Med Virol 2022; 94:2275-2283. [PMID: 34989406 PMCID: PMC9015490 DOI: 10.1002/jmv.27571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/14/2021] [Accepted: 12/30/2021] [Indexed: 01/08/2023]
Abstract
From December 2019, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS‐CoV‐2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS‐CoV‐2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient's cohort from the Campania region (Southern Italy). Results show coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only 2% of the cases (2/89) identified respiratory viruses. The severe acute respiratory syndrome coronavirus 2 infection is considered a major global threat that is still spreading around the world. Nasopharyngeal swabs samples were collected from the Campania region cohort of 89 Covid‐19 patients. Descriptive analysis of respiratory virome was carried out with the HOME‐BIO pipeline, that performed viral taxonomy profiling. It detected coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae family. Only 2% of the cases (2/89) identified respiratory viruses.
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Affiliation(s)
- Carlo Ferravante
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Viola Melone
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Aurore Fromentier
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Teresa Rocco
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Ylenia D'Agostino
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Jessica Lamberti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Elena Alexandrova
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Giovanni Pecoraro
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
| | - Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
| | - Roberta Astorri
- Department of Mental Health and Public Medicine, Infection Disease Unit, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Francesca Rizzo
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Genome Research Center for Health (CRGS), University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy.,Medical Genomics Program, Clinical Microbiology Program, Infectivology and NAT Molecular Biology Units, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, Salerno, Italy
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Raj A, Kumar A, Dames JF. Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability. Front Microbiol 2021; 12:791723. [PMID: 35003022 PMCID: PMC8733403 DOI: 10.3389/fmicb.2021.791723] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022] Open
Abstract
Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.
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Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, India
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Joanna Felicity Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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