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Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB. Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nat Commun 2024; 15:1791. [PMID: 38424056 PMCID: PMC10904388 DOI: 10.1038/s41467-024-46033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
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Affiliation(s)
- Paula Istvan
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Einar Birkeland
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ekaterina Avershina
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Vahid Bemanian
- Pathology Department, Akershus University Hospital, Lørenskog, Norway
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Sonia Tarallo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Trine B Rounge
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
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Li Z, Rosenzweig R, Chen F, Qin J, Li T, Han J, Istvan P, Diaz-Reck D, Gelman F, Arye G, Ronen Z. Bioremediation of Petroleum-Contaminated Soils with Biosurfactant-Producing Degraders Isolated from the Native Desert Soils. Microorganisms 2022; 10:microorganisms10112267. [PMID: 36422337 PMCID: PMC9694877 DOI: 10.3390/microorganisms10112267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
A crude oil spill in 2014 resulted in extensive soil contamination of the hyper arid Evrona Nature Reserve in Israel's Negev Desert. The contaminated soils became highly hydrophobic, threatening the existence of plants in the habitat. We hypothesized that bioaugmenting the soil with indigenous biosurfactant-producing, hydrocarbon-degrading bacteria (HDB) would accelerate the reduction in the soil's hydrophobicity. We aimed to isolate and characterize biosurfactant-producing HDBs from the desert-contaminated soil and test if they can be used for augmenting the soil. Twelve hydrocarbon-degrading strains were isolated, identified as Pseudomonas, and classified as biosurfactants "producing" and "nonproducing". Inoculating 109 CFU/g of "producing" strains into the polluted soil resulted in a 99.2% reduction in soil hydrophobicity within seven days. At the same time, nonproducing strains reduced hydrophobicity by only 17%, while no change was observed in the untreated control. The microbial community in the inoculated soil was dominated by the introduced strains over 28 days, pointing to their persistence. Rhamnolipid biosynthesis gene rhlAB remained persistent in soil inoculated with biosurfactants, indicating in situ production. We propose that the success of the treatment is due to the use of inoculum enriched from the polluted soil.
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Affiliation(s)
- Zheng Li
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
- Geological Survey of Israel, 32 Yeshayahu Leibowitz St., Jerusalem 9692100, Israel; (R.R.); (F.G.)
| | - Ravid Rosenzweig
- Geological Survey of Israel, 32 Yeshayahu Leibowitz St., Jerusalem 9692100, Israel; (R.R.); (F.G.)
| | - Fengxian Chen
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (F.C.); (T.L.); (G.A.)
| | - Ji Qin
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
| | - Tianyi Li
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (F.C.); (T.L.); (G.A.)
| | - Jincheng Han
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
| | - Paula Istvan
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
| | - Damiana Diaz-Reck
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
| | - Faina Gelman
- Geological Survey of Israel, 32 Yeshayahu Leibowitz St., Jerusalem 9692100, Israel; (R.R.); (F.G.)
| | - Gilboa Arye
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (F.C.); (T.L.); (G.A.)
| | - Zeev Ronen
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be’er Sheva 8499000, Israel; (L.Z.); (J.Q.); (J.H.); (P.I.); (D.D.-R.)
- Correspondence:
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Lima RAT, De Oliveira G, Souza AA, Lopes FAC, Santana RH, Istvan P, Quirino BF, Barbosa J, De Freitas S, Garay AV, Krüger RH. Functional and structural characterization of a novel GH3 β-glucosidase from the gut metagenome of the Brazilian Cerrado termite Syntermes wheeleri. Int J Biol Macromol 2020; 165:822-834. [PMID: 33011259 DOI: 10.1016/j.ijbiomac.2020.09.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022]
Abstract
In this study, a GH3 family β-glucosidase (Bgl7226) from metagenomic sequences of the Syntermes wheeleri gut, a Brazilian Cerrado termite, was expressed, purified and characterized. The enzyme showed two optimum pHs (pH 7 and pH 10), and a maximum optimum temperature of about 40 °C using 4-Nitrophenyl β-D-glucopyranoside (pNPG) as substrate. Bgl7226 showed higher enzymatic activity at basic pH, but higher affinity (Km) at neutral pH. However, at neutral pH the Bgl7226 enzyme showed higher catalytic efficiency (kcat/Km) for pNPG substrate. Predictive analysis about the enzyme structure-function relationship by sequence alignment suggested the presence of multi-domains and conserved catalytic sites. Circular dichroism results showed that the secondary structure composition of the enzyme is pH-dependent. Small conformational changes occurred close to the optimum temperature of 40 o C, and seem important for the highest activity of Bgl7226 observed at pH 7 and 10. In addition, the small transition in the unfolding curves close to 40 o C is typical of intermediates associated with proteins structured in several domains. Bgl7226 has significant β-glucosidase activity which could be attractive for biotechnological applications, such as plant roots detoxification; specifically, our group is interested in cassava roots (Manihot esculenta) detoxification.
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Affiliation(s)
| | - Gideane De Oliveira
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Amanda Araújo Souza
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | | | - Renata Henrique Santana
- Instituto Federal de Brasília, Planaltina Campus, Brasília, DF 70910-900, Brazil; Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil
| | - Paula Istvan
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil; Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben- Gurion University of the Negev, Department of Environmental Hydrology & Microbiology, Israel
| | - Betania Ferraz Quirino
- Embrapa Agroenergy, Parque Estação Biológica (PqEB), PqEB s/n°, Brasília, DF 70770-901, Brazil
| | - João Barbosa
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Sonia De Freitas
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Aisel Valle Garay
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Ricardo Henrique Krüger
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
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Istvan P, Souza AA, Garay AV, Dos Santos DFK, de Oliveira GM, Santana RH, Lopes FAC, de Freitas SM, Barbosa JARG, Krüger RH. Structural and functional characterization of a novel lipolytic enzyme from a Brazilian Cerrado soil metagenomic library. Biotechnol Lett 2018; 40:1395-1406. [PMID: 30062528 DOI: 10.1007/s10529-018-2598-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/25/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To isolate putative lipase enzymes by screening a Cerrado soil metagenomic library with novel features. RESULTS Of 6720 clones evaluated, Clone W (10,000 bp) presented lipolytic activity and four predicted coding sequences, one of them LipW. Characterization of a predicted esterase/lipase, LipW, showed 28% sequence identity with an arylesterase from Pseudomonas fluorescens (pdb|3HEA) from protein database (PDB). Phylogenetic analysis showed LipW clustered with family V lipases; however, LipW was clustered in different subclade belonged to family V, suggesting a different subgroup of family V. In addition, LipW presented a difference in family V GH motif, a glycine replaced by a serine in GH motif. Estimated molecular weight and stokes radius values of LipW were 29,338.67-29,411.98 Da and 2.58-2.83 nm, respectively. Optimal enzyme activity was observed at pH 9.0-9.5 and at 40 °C. Circular dichroism analysis estimated secondary structures percentages as approximately 45% α-helix and 15% β-sheet, consistent with the 3D structure predicted by homology. CONCLUSION Our results demonstrate the isolation of novel family V lipolytic enzyme with biotechnological applications from a metagenomic library.
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Affiliation(s)
- Paula Istvan
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Amanda Araújo Souza
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Aisel Valle Garay
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Debora Farage Knupp Dos Santos
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Gideane Mendes de Oliveira
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Fabyano Alvares Cardoso Lopes
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Sonia Maria de Freitas
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil.
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Dos Santos DFK, Istvan P, Quirino BF, Kruger RH. Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments. Microb Ecol 2017; 73:479-491. [PMID: 27709246 DOI: 10.1007/s00248-016-0866-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 09/19/2016] [Indexed: 05/26/2023]
Abstract
Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.
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Affiliation(s)
| | - Paula Istvan
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Betania Ferraz Quirino
- Embrapa-Agroenergia, Brasília, DF, Brazil
- Universidade Católica de Brasília, Genomic Sciences and Biotechnology Program, Brasília, DF, Brazil
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dos Santos DFK, Istvan P, Noronha EF, Quirino BF, Krüger RH. New dioxygenase from metagenomic library from Brazilian soil: insights into antibiotic resistance and bioremediation. Biotechnol Lett 2015; 37:1809-17. [DOI: 10.1007/s10529-015-1861-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
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