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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Correction: Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024:10.1038/s41388-024-03018-z. [PMID: 38580705 DOI: 10.1038/s41388-024-03018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024; 43:1127-1148. [PMID: 38396294 PMCID: PMC10997506 DOI: 10.1038/s41388-024-02974-w] [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: 11/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.
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Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. Chemosphere 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
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Taylor BC, Sheikh Andalibi M, Wandro S, Weldon KC, Sepich-Poore GD, Carpenter CS, Fraraccio S, Franklin D, Iudicello JE, Letendre S, Gianella S, Grant I, Ellis RJ, Heaton RK, Knight R, Swafford AD. Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome. Microorganisms 2023; 11:1022. [PMID: 37110445 PMCID: PMC10146336 DOI: 10.3390/microorganisms11041022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Inter-individual differences in the gut microbiome are linked to alterations in inflammation and blood-brain barrier permeability, which may increase the risk of depression in people with HIV (PWH). The microbiome profile of blood, which is considered by many to be typically sterile, remains largely unexplored. We aimed to characterize the blood plasma microbiome composition and assess its association with major depressive disorder (MDD) in PWH and people without HIV (PWoH). In this cross-sectional, observational cohort, we used shallow-shotgun metagenomic sequencing to characterize the plasma microbiome of 151 participants (84 PWH and 67 PWoH), all of whom underwent a comprehensive neuropsychiatric assessment. The microbial composition did not differ between PWH and PWoH or between participants with MDD and those without it. Using the songbird model, we computed the log ratio of the highest and lowest 30% of the ranked classes associated with HIV and MDD. We found that HIV infection and lifetime MDD were enriched in a set of differentially abundant inflammatory classes, such as Flavobacteria and Nitrospira. Our results suggest that the circulating plasma microbiome may increase the risk of MDD related to dysbiosis-induced inflammation in PWH. If confirmed, these findings may indicate new biological mechanisms that could be targeted to improve treatment of MDD in PWH.
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Affiliation(s)
- Bryn C. Taylor
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA 92093, USA
| | - Mohammadsobhan Sheikh Andalibi
- Departments of Neurosciences and Psychiatry, HIV Neurobehavioral Research Center, University of California, San Diego, CA 92093, USA; (M.S.A.)
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Kelly C. Weldon
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA 92093, USA
| | | | - Carolina S. Carpenter
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Donald Franklin
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Jennifer E. Iudicello
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Scott Letendre
- Departments of Medicine and Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Sara Gianella
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA 92093, USA
| | - Igor Grant
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, HIV Neurobehavioral Research Center, University of California, San Diego, CA 92093, USA; (M.S.A.)
| | - Robert K. Heaton
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, San Diego, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
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Fraraccio S, Wandro S, Singh-Taylor A, Miller-Montgomery S, Adams E, Knight R, Segal LN, Pass HI, Sepich-Poore GD. Abstract 5713: Assessing the real-world utility of cell-free microbial DNA in diagnosing early-stage lung cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Links between cancer and microbes date back four millennia (Sepich-Poore et al. 2021. Science). Recently, we found that microbial DNA is detectable in tumor tissues and patient blood from many human cancer types (Poore et al. 2020. Nature). These intratumoral and bloodborne microbiomes were distinct between cancer types, between normal and malignant tissues, and present in cell-free plasma samples. However, the practical utility of cell-free microbial DNA (cf-mbDNA) as a bona fide liquid biopsy diagnostic, including its applicability in early-stage disease in treatment-naïve individuals, distinguishing histological subtypes, and discriminating against non-cancer-but-diseased patients remains unknown. Thus, we constructed an age and sex-matched cohort of >1000 individuals with lung cancer, lung disease, and no disease (healthy) to evaluate the utility of a cf-mbDNA-driven liquid biopsy diagnostic.
Methods: Shallow shotgun metagenomic sequencing with gold-standard positive and negative controls was performed using 400 µL of patient plasma. Direct genome alignments separated human and microbial reads, and generated genome-wide binned and species-level abundances, respectively. Novel taxonomic diversity was captured by additionally performing de novo co-assemblies in tandem with tumor and blood samples from The Cancer Genome Atlas (TCGA). Multi-modal, stacked machine learning classifiers then evaluated the diagnostic performance of microbial-only and multi-species (microbial + human) information.
Results: Cf-mbDNA provides strong diagnostic performance in treatment-naïve, cancer-bearing individuals versus age and sex-matched healthy controls, as early as stage I disease (AUROCs≥0.90). Furthermore, cf-mbDNA outperforms histological classification compared to human genomic information. Multi-species models paired with routinely-available clinicodemographic information provided robust discrimination of lung cancer versus lung diseases (AUROC≥0.80). Importantly, the addition of cell-free microbial information produced an integrated model surpassing the diagnostic performance of PET-CT and clinical risk models for lung nodule malignancy determination in a blinded validation cohort of Stage I lung cancer and non-cancer lung disease samples.
Conclusion: Cf-mbDNA features comprise a novel class of biomarkers that are combinable with host analytes, and show promise for real-world, early-stage, lung cancer diagnosis.
Citation Format: Serena Fraraccio, Stephen Wandro, Akanksha Singh-Taylor, Sandrine Miller-Montgomery, Eddie Adams, Rob Knight, Leopoldo N. Segal, Harvey I. Pass, Gregory D. Sepich-Poore. Assessing the real-world utility of cell-free microbial DNA in diagnosing early-stage lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5713.
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Affiliation(s)
| | | | | | | | | | - Rob Knight
- 2University of California San Diego, San Diego, CA
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Desmarais M, Fraraccio S, Dolinova I, Ridl J, Strnad H, Kubatova H, Sevcu A, Suman J, Strejcek M, Uhlik O. Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. Antonie Van Leeuwenhoek 2022; 115:1041-1057. [PMID: 35701646 DOI: 10.1007/s10482-022-01752-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.
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Affiliation(s)
- Miguel Desmarais
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Iva Dolinova
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
- Department of Genetics and Molecular Diagnostics, Regional Hospital Liberec, Liberec, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Kubatova
- State Office for Nuclear Safety, Prague, Czech Republic
| | - Alena Sevcu
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic.
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Sepich-Poore G, Fraraccio S, Wandro S, Miller-Montgomery S, Knight R, Adams E. FP05.04 Robust Discrimination of Lung Cancer via Microbial DNA Detection and Machine Learning Classification. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques 2021; 70:149-159. [PMID: 33512248 PMCID: PMC7931620 DOI: 10.2144/btn-2020-0153] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics & Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, University of California, San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
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9
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Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. bioRxiv 2020:2020.11.13.370387. [PMID: 33200135 PMCID: PMC7668742 DOI: 10.1101/2020.11.13.370387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols. Accession numbers Raw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub ( github.com/justinshaffer/Extraction_test_MagMAX ). Methods summary To allow for downstream applications involving RNA-based organisms such as SARS-CoV-2, we compared the two extraction protocols designed to extract DNA and RNA against our previously established protocol for extracting only DNA for microbial community analyses. Across 10 diverse sample types, one of the two protocols was equivalent or better than our established DNA-based protocol. Our conclusion is based on per-sample comparisons of DNA and RNA yield, the number of quality sequences generated, microbial community alpha- and beta-diversity and taxonomic composition, the limit of detection, and extent of well-to-well contamination.
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10
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Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 2020; 579:567-574. [PMID: 32214244 PMCID: PMC7500457 DOI: 10.1038/s41586-020-2095-1] [Citation(s) in RCA: 575] [Impact Index Per Article: 143.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1-10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia-IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.
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Affiliation(s)
- Gregory D Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Beerse, Belgium
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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11
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Ridl J, Suman J, Fraraccio S, Hradilova M, Strejcek M, Cajthaml T, Zubrova A, Macek T, Strnad H, Uhlik O. Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants. Stand Genomic Sci 2018; 13:3. [PMID: 29435100 PMCID: PMC5796565 DOI: 10.1186/s40793-017-0306-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/06/2017] [Indexed: 12/25/2022] Open
Abstract
In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the β-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level.
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Affiliation(s)
- Jakub Ridl
- 1Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jachym Suman
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Serena Fraraccio
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Miluse Hradilova
- 1Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michal Strejcek
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomas Cajthaml
- 3Laboratory of Environmental Biotechnology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrea Zubrova
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomas Macek
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Hynek Strnad
- 1Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Ondrej Uhlik
- 2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
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12
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Leewis MC, Uhlik O, Fraraccio S, McFarlin K, Kottara A, Glover C, Macek T, Leigh MB. Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil. Front Microbiol 2016; 7:837. [PMID: 27313574 PMCID: PMC4889597 DOI: 10.3389/fmicb.2016.00837] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/18/2016] [Indexed: 01/12/2023] Open
Abstract
Despite decades of research there is limited understanding of how vegetation impacts the ability of microbial communities to process organic contaminants in soil. Using a combination of traditional and molecular assays, we examined how phytoremediation with willow and/or fertilization affected the microbial community present and active in the transformation of diesel contaminants. In a pot study, willow had a significant role in structuring the total bacterial community and resulted in significant decreases in diesel range organics (DRO). However, stable isotope probing (SIP) indicated that fertilizer drove the differences seen in community structure and function. Finally, analysis of the total variance in both pot and SIP experiments indicated an interactive effect between willow and fertilizer on the bacterial communities. This study clearly demonstrates that a willow native to Alaska accelerates DRO degradation, and together with fertilizer, increases aromatic degradation by shifting microbial community structure and the identity of active naphthalene degraders.
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Affiliation(s)
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Czech Republic
| | - Kelly McFarlin
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks AK, USA
| | - Anastasia Kottara
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Czech Republic
| | - Catherine Glover
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks AK, USA
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Czech Republic
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks AK, USA
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13
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Valentino F, Morgan-Sagastume F, Fraraccio S, Corsi G, Zanaroli G, Werker A, Majone M. Sludge minimization in municipal wastewater treatment by polyhydroxyalkanoate (PHA) production. Environ Sci Pollut Res Int 2015; 22:7281-7294. [PMID: 24996948 DOI: 10.1007/s11356-014-3268-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/27/2014] [Indexed: 05/28/2023]
Abstract
An innovative approach has been recently proposed in order to link polyhydroxyalkanoates (PHA) production with sludge minimization in municipal wastewater treatment, where (1) a sequencing batch reactor (SBR) is used for the simultaneous municipal wastewater treatment and the selection/enrichment of biomass with storage ability and (2) the acidogenic fermentation of the primary sludge is used to produce a stream rich in volatile fatty acids (VFAs) as the carbon source for the following PHA accumulation stage. The reliability of the proposed process has been evaluated at lab scale by using substrate synthetic mixtures for both stages, simulating a low-strength municipal wastewater and the effluent from primary sludge fermentation, respectively. Six SBR runs were performed under the same operating conditions, each time starting from a new activated sludge inoculum. In every SBR run, despite the low VFA content (10% chemical oxygen demand, COD basis) of the substrate synthetic mixture, a stable feast-famine regime was established, ensuring the necessary selection/enrichment of the sludge and soluble COD removal to 89%. A good process reproducibility was observed, as also confirmed by denaturing gradient gel electrophoresis (DGGE) analysis of the microbial community, which showed that a high similarity after SBR steady-state had been reached. The main variation factors of the storage properties among different runs were uncontrolled changes of settling properties which in turn caused variations of both sludge retention time and specific organic loading rate. In the following accumulation batch tests, the selected/enriched consortium was able to accumulate PHA with good rate (63 mg CODPHA g CODXa(-1) h(-1)) and yield (0.23 CODPHA CODΔS(-1)) in spite that the feeding solution was different from the acclimation one. Even though the PHA production performance still requires optimization, the proposed process has a good potential especially if coupled to minimization of both primary sludge (by its use as the VFA source for the PHA accumulation, via previous fermentation) and excess secondary sludge (by its use as the biomass source for the PHA accumulation).
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Affiliation(s)
- Francesco Valentino
- Department of Chemistry, "Sapienza" University of Rome, P.le Aldo Moro 5, 00185, Rome, RM, Italy,
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14
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Valentino F, Beccari M, Fraraccio S, Zanaroli G, Majone M. Feed frequency in a Sequencing Batch Reactor strongly affects the production of polyhydroxyalkanoates (PHAs) from volatile fatty acids. N Biotechnol 2014; 31:264-75. [DOI: 10.1016/j.nbt.2013.10.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 10/10/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
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15
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Frascari D, Bucchi G, Doria F, Rosato A, Tavanaie N, Salviulo R, Ciavarelli R, Pinelli D, Fraraccio S, Zanaroli G, Fava F. Development of an attached-growth process for the on-site bioremediation of an aquifer polluted by chlorinated solvents. Biodegradation 2013; 25:337-50. [DOI: 10.1007/s10532-013-9664-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/26/2013] [Indexed: 11/30/2022]
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16
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Frascari D, Zanaroli G, Bucchi G, Rosato A, Tavanaie N, Fraraccio S, Pinelli D, Fava F. Trichloroethylene aerobic cometabolism by suspended and immobilized butane-growing microbial consortia: a kinetic study. Bioresour Technol 2013; 144:529-538. [PMID: 23896437 DOI: 10.1016/j.biortech.2013.07.006] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/28/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
A kinetic study of butane uptake and trichloroethylene (TCE) aerobic cometabolism was conducted by two suspended-cell (15 and 30°C) and two attached-cell (15 and 30°C) consortia obtained from the indigenous biomass of a TCE-contaminated aquifer. The shift from suspended to attached cells resulted in an increase of butane (15 and 30°C) and TCE (15°C) biodegradation rates, and a significant decrease of butane inhibition on TCE biodegradation. The TCE 15°C maximum specific biodegradation rate was equal to 0.011 mg(TCE ) mg(protein)(-1) d(-1) with suspended cells and 0.021 mg(TCE) mg(protein)(-1) d(-1) with attached cells. The type of mutual butane/TCE inhibition depended on temperature and biomass conditions. On the basis of a continuous-flow simulation, a packed-bed PFR inoculated with the 15 or 30°C attached-cell consortium could attain a 99.96% conversion of the studied site's average TCE concentration with a 0.4-0.5-day hydraulic residence time, with a low effect of temperature on the TCE degradation performances.
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Affiliation(s)
- Dario Frascari
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Bologna, Italy.
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17
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Scoma A, Bertin L, Zanaroli G, Fraraccio S, Fava F. A physicochemical-biotechnological approach for an integrated valorization of olive mill wastewater. Bioresour Technol 2011; 102:10273-10279. [PMID: 21924896 DOI: 10.1016/j.biortech.2011.08.080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/16/2011] [Accepted: 08/19/2011] [Indexed: 05/31/2023]
Abstract
An integrated physicochemical-biotechnological approach for a multipurpose valorization of olive mill wastewaters was studied. More than 60% of the wastewater natural polyphenols were recovered through a solid phase extraction procedure, by employing Amberlite XAD16 resin as the adsorbent and ethanol as the biocompatible desorbing phase. Thereafter, the dephenolized effluent was fed to a mesophilic anaerobic acidogenic packed-bed biofilm reactor for the bioconversion of the organic leftover into volatile fatty acids (VFAs). A VFAs concentration of 19 gCODL(-1) was obtained, representing more than 70% of the COD occurring in the anaerobic effluent. The biotechnological process was assessed by means of bio-molecular analyses, which showed that the reactor packed bed was mostly colonized by bacteria of the Firmicutes phylogenetic group. The biorefinery scheme developed in this study allowed the obtainment of 1.59 g of polyphenols per liter of wastewater treated and 2.72 gCODL(-1) day(-1) of VFAs.
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Affiliation(s)
- Alberto Scoma
- Department of Civil, Environmental and Materials Engineering (DICAM), Unit of Environmental Biotechnology and Biorefineries, Faculty of Engineering, University of Bologna, via Terracini 28, 40131 Bologna, Italy.
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