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Gambarini V, Pantos O, Kingsbury JM, Weaver L, Handley KM, Lear G. PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation. Database (Oxford) 2022; 2022:6546196. [PMID: 35266524 PMCID: PMC9216477 DOI: 10.1093/database/baac008] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 01/04/2023]
Abstract
The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type they are reported to degrade. Each protein structure has been predicted in silico and can be visualized or downloaded for further investigation. In addition to standard database functionalities, such as searching, filtering and retrieving database records, we implemented several analytical tools that accept inputs, including gene, genome, metagenome, transcriptomes, metatranscriptomes and taxa table data. Users can now analyze their datasets for the presence of putative plastic-degrading species and potential plastic-degrading proteins and pathways from those species. Database URL:http://plasticdb.org.
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Affiliation(s)
- Victor Gambarini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand
| | - Olga Pantos
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Joanne M Kingsbury
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Louise Weaver
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand
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Lear G, Kingsbury JM, Franchini S, Gambarini V, Maday SDM, Wallbank JA, Weaver L, Pantos O. Plastics and the microbiome: impacts and solutions. Environ Microbiome 2021; 16:2. [PMID: 33902756 PMCID: PMC8066485 DOI: 10.1186/s40793-020-00371-w] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/28/2020] [Indexed: 05/12/2023]
Abstract
Global plastic production has increased exponentially since manufacturing commenced in the 1950's, including polymer types infused with diverse additives and fillers. While the negative impacts of plastics are widely reported, particularly on marine vertebrates, impacts on microbial life remain poorly understood. Plastics impact microbiomes directly, exerting toxic effects, providing supplemental carbon sources and acting as rafts for microbial colonisation and dispersal. Indirect consequences include increased environmental shading, altered compositions of host communities and disruption of host organism or community health, hormone balances and immune responses. The isolation and application of plastic-degrading microbes are of substantial interest yet little evidence supports the microbial biodegradation of most high molecular weight synthetic polymers. Over 400 microbial species have been presumptively identified as capable of plastic degradation, but evidence for the degradation of highly prevalent polymers including polypropylene, nylon, polystyrene and polyvinyl chloride must be treated with caution; most studies fail to differentiate losses caused by the leaching or degradation of polymer monomers, additives or fillers. Even where polymer degradation is demonstrated, such as for polyethylene terephthalate, the ability of microorganisms to degrade more highly crystalline forms of the polymer used in commercial plastics appears limited. Microbiomes frequently work in conjunction with abiotic factors such as heat and light to impact the structural integrity of polymers and accessibility to enzymatic attack. Consequently, there remains much scope for extremophile microbiomes to be explored as a source of plastic-degrading enzymes and microorganisms. We propose a best-practice workflow for isolating and reporting plastic-degrading taxa from diverse environmental microbiomes, which should include multiple lines of evidence supporting changes in polymer structure, mass loss, and detection of presumed degradation products, along with confirmation of microbial strains and enzymes (and their associated genes) responsible for high molecular weight plastic polymer degradation. Such approaches are necessary for enzymatic degraders of high molecular weight plastic polymers to be differentiated from organisms only capable of degrading the more labile carbon within predominantly amorphous plastics, plastic monomers, additives or fillers.
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Affiliation(s)
- G Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand.
| | - J M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
| | - S Franchini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - V Gambarini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - S D M Maday
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - J A Wallbank
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - L Weaver
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
| | - O Pantos
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
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Gambarini V, Pantos O, Kingsbury JM, Weaver L, Handley KM, Lear G. Phylogenetic Distribution of Plastic-Degrading Microorganisms. mSystems 2021; 6:e01112-20. [PMID: 33468707 PMCID: PMC7820669 DOI: 10.1128/msystems.01112-20] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/04/2021] [Indexed: 01/08/2023] Open
Abstract
The number of plastic-degrading microorganisms reported is rapidly increasing, making it possible to explore the conservation and distribution of presumed plastic-degrading traits across the diverse microbial tree of life. Putative degraders of conventional high-molecular-weight polymers, including polyamide, polystyrene, polyvinylchloride, and polypropylene, are spread widely across bacterial and fungal branches of the tree of life, although evidence for plastic degradation by a majority of these taxa appears limited. In contrast, we found strong degradation evidence for the synthetic polymer polylactic acid (PLA), and the microbial species related to its degradation are phylogenetically conserved among the bacterial family Pseudonocardiaceae We collated data on genes and enzymes related to the degradation of all types of plastic to identify 16,170 putative plastic degradation orthologs by mining publicly available microbial genomes. The plastic with the largest number of putative orthologs, 10,969, was the natural polymer polyhydroxybutyrate (PHB), followed by the synthetic polymers polyethylene terephthalate (PET) and polycaprolactone (PCL), with 8,233 and 6,809 orthologs, respectively. These orthologous genes were discovered in the genomes of 6,000 microbial species, and most of them are as yet not identified as plastic degraders. Furthermore, all these species belong to 12 different microbial phyla, of which just 7 phyla have reported degraders to date. We have centralized information on reported plastic-degrading microorganisms within an interactive and updatable phylogenetic tree and database to confirm the global and phylogenetic diversity of putative plastic-degrading taxa and provide new insights into the evolution of microbial plastic-degrading capabilities and avenues for future discovery.IMPORTANCE We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved. We found 16,170 putative plastic degradation orthologs in the genomes of 12 different phyla, which suggests a vast potential for the exploration of these traits in other taxa. Besides making the database available to the scientific community, we also created an interactive phylogenetic tree that can display all of the collated information, facilitating visualization and exploration of the data. Both the database and the tree are regularly updated to keep up with new scientific reports. We expect that our work will contribute to the field by increasing the understanding of the genetic diversity and evolution of microbial plastic-degrading traits.
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Affiliation(s)
- Victor Gambarini
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Olga Pantos
- The Institute of Environmental Science and Research, Ilam, Christchurch, New Zealand
| | - Joanne M Kingsbury
- The Institute of Environmental Science and Research, Ilam, Christchurch, New Zealand
| | - Louise Weaver
- The Institute of Environmental Science and Research, Ilam, Christchurch, New Zealand
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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de Aguiar CF, Castoldi A, Amano MT, Ignacio A, Terra FF, Cruz M, Felizardo RJF, Braga TT, Davanzo GG, Gambarini V, Antonio T, Antiorio ATFB, Hiyane MI, Morais da Fonseca D, Andrade-Oliveira V, Câmara NOS. Fecal IgA Levels and Gut Microbiota Composition Are Regulated by Invariant Natural Killer T Cells. Inflamm Bowel Dis 2020; 26:697-708. [PMID: 31819985 DOI: 10.1093/ibd/izz300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The gut microbiota is a key element to support host homeostasis and the development of the immune system. The relationship between the microbiota and immunity is a 2-way road, in which the microbiota contributes to the development/function of immune cells and immunity can affect the composition of microbes. In this context, natural killer T cells (NKT cells) are distinct T lymphocytes that play a role in gut immunity and are influenced by gut microbes. In our work, we investigated the involvement of invariant NKT cells (iNKT) in intestinal homeostasis. RESULTS We found that iNKT-deficient mice (iNKT-KO) had reduced levels of fecal IgA and an altered composition of the gut microbiota, with increased Bacteroidetes. The absence of iNKT cells also affected TGF-β1 levels and plasma cells, which were significantly reduced in knockout (KO) mice. In addition, when submitted to dextran sodium sulfate colitis, iNKT-KO mice had worsening of colitis when compared with wild-type (WT) mice. To further address iNKT cell contribution to intestinal homeostasis, we adoptively transferred iNKT cells to KO mice, and they were submitted to colitis. Transfer of iNKT cells improved colitis and restored fecal IgA levels and gut microbiota. CONCLUSIONS Our results indicate that intestinal NKT cells are important modulators of intestinal homeostasis and that gut microbiota composition may be a potential target in the management of inflammatory bowel diseases.
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Affiliation(s)
- Cristhiane Favero de Aguiar
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Angela Castoldi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Mariane T Amano
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil.,Instituto Sírio-Libanês de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo-SP, Brazil
| | - Aline Ignacio
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Fernanda Fernandes Terra
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Mario Cruz
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Raphael J F Felizardo
- Division of Nephrology, Department of Medicine, Federal University of São Paulo (UNIFESP), São Paulo-SP, Brazil
| | - Tárcio Teodoro Braga
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Gustavo Gastão Davanzo
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Victor Gambarini
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Tiago Antonio
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Ana Tada Fonseca Brasil Antiorio
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Meire Ioshie Hiyane
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Denise Morais da Fonseca
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Vinicius Andrade-Oliveira
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André-SP, Brazil
| | - Niels Olsen Saraiva Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil.,Division of Nephrology, Department of Medicine, Federal University of São Paulo (UNIFESP), São Paulo-SP, Brazil
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