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Gaur VK, Gupta S, Pandey A. Evolution in mitigation approaches for petroleum oil-polluted environment: recent advances and future directions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:61821-61837. [PMID: 34420173 DOI: 10.1007/s11356-021-16047-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Increasing petroleum consumption and a rise in incidental oil spillages have become global concerns owing to their aquatic and terrestrial toxicity. Various physicochemical and biological treatment strategies have been studied to tackle them and their impact on environment. One of such approaches in this regard is the use of microbial processes due to their being "green" and also apparent low cost and high effectiveness. This review presents the advancement in the physical and biological remediation methods and their progressive efficacy if employed in combination of hybrid modes. The use of biosurfactants and/or biochar along with microbes seems to be a more effective bioremediation approach as compared to their individual effects. The lacuna in research at community or molecular level has been overcome by the recent introduction of "-omics" technology in hydrocarbon degradation. Thus, the review further focuses on presenting the state-of-art information on the advancement of petroleum bioremediation strategies and identifies the research gaps for achieving total mitigation of petroleum oil.
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Affiliation(s)
- Vivek Kumar Gaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India.
- Centre for Energy and Environmental Sustainability, Lucknow, 226029, India.
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2
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Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages. mBio 2022; 13:e0065122. [PMID: 35532161 PMCID: PMC9239159 DOI: 10.1128/mbio.00651-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although we know the generally appreciated significant roles of microbes in sea ice and polar waters, detailed studies of virus-host systems from such environments have been so far limited by only a few available isolates. Here, we investigated infectivity under various conditions, infection cycles, and genetic diversity of the following Antarctic sea ice bacteriophages: Paraglaciecola Antarctic GD virus 1 (PANV1), Paraglaciecola Antarctic JLT virus 2 (PANV2), Octadecabacter Antarctic BD virus 1 (OANV1), and Octadecabacter Antarctic DB virus 2 (OANV2). The phages infect common sea ice bacteria belonging to the genera Paraglaciecola or Octadecabacter. Although the phages are marine and cold-active, replicating at 0°C to 5°C, they all survived temporal incubations at ≥30°C and remained infectious without any salts or supplemented only with magnesium, suggesting a robust virion assembly maintaining integrity under a wide range of conditions. Host recognition in the cold proved to be effective, and the release of progeny viruses occurred as a result of cell lysis. The analysis of viral genome sequences showed that nearly one-half of the gene products of each virus are unique, highlighting that sea ice harbors unexplored virus diversity. Based on predicted genes typical for tailed double-stranded DNA phages, we suggest placing the four studied viruses in the class Caudoviricetes. Searching against viral sequences from metagenomic assemblies, we revealed that related viruses are not restricted to Antarctica but are also found in distant marine environments.
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3
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, Zhang Y, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabj1453. [PMID: 34215592 PMCID: PMC11057702 DOI: 10.1126/sciadv.abj1453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Tian
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Zhang C, Meckenstock RU, Weng S, Wei G, Hubert CRJ, Wang JH, Dong X. Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition. FEMS Microbiol Ecol 2021; 97:6171024. [PMID: 33720296 DOI: 10.1093/femsec/fiab045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology, University Duisburg-Essen, Universitätsstrasse 5, Essen 45141, Germany
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Siming District, Xiamen 361005, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N1N4, Canada
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 2 Daxue Road, XiangZhou District, Zhuhai 519000, China
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Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
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Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
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Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary. PLoS One 2019; 14:e0217431. [PMID: 31170168 PMCID: PMC6553723 DOI: 10.1371/journal.pone.0217431] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterioplankton play a key role in the global cycling of elements. To characterize the effects of hypoxia on bacterioplankton, bacterial community structure and function were investigated in the Changjiang Estuary. Water samples were collected from three layers (surface, middle, and bottom) at ten sampling sites in the Changjiang Estuary hypoxic and non-hypoxic zones. The community structure was analyzed using high-throughput sequencing of 16S rDNA genes, and the predictive metagenomic approach was used to investigate the functions of the bacterial community. Co-occurrence networks are constructed to investigate the relationship between different bacterioplankton. The results showed that community composition in hypoxic and non-hypoxic zones were markedly different. The diversity and richness of bacterial communities in the bottom layer (hypoxic zone) were remarkably higher than that of the surface layer (non-hypoxic). In the non-hypoxic zone, it was found that Proteobacteria, Bacteroidetes, and Flavobacteriia were the dominant groups while Alphaproteobacteria, SAR406 and Deltaproteobacteria were the dominant groups in the hypoxic zone. From the RDA analysis, it was shown that dissolved oxygen (DO) explained most of the bacterial community variation in the redundancy analysis targeting only hypoxia zones, whereas nutrients and salinity explained most of the variation across all samples in the Changjiang Estuary. To understand the genes involved in nitrogen metabolism, an analysis of the oxidation state of nitrogen was performed. The results showed that the bacterial community in the surface layer (non-hypoxic) had more genes involved in dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, and anammox, while that in the middle and bottom layers (hypoxic zone) had more abundant genes associated with nitrogen fixation and nitrification. Co-occurrence networks revealed that microbial assemblages in the middle and bottom layers shared more niche spaces than in the surface layer (non-hypoxic zone). The environmental heterogeneity in the hypoxic and non-hypoxic zones might be important environmental factors that determine the bacterial composition in these two zones.
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7
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Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol 2019; 4:603-613. [PMID: 30833729 PMCID: PMC6453112 DOI: 10.1038/s41564-019-0363-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022]
Abstract
Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘Ca. Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.
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Cabral L, Pereira de Sousa ST, Júnior GVL, Hawley E, Andreote FD, Hess M, de Oliveira VM. Microbial functional responses to long-term anthropogenic impact in mangrove soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:231-239. [PMID: 29807296 DOI: 10.1016/j.ecoenv.2018.04.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery.
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Affiliation(s)
- Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sanderson Tarciso Pereira de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Erik Hawley
- Washington State University, Pullman, WA, USA
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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9
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Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 2018; 3:836-843. [PMID: 29807988 PMCID: PMC6786971 DOI: 10.1038/s41564-018-0171-1] [Citation(s) in RCA: 664] [Impact Index Per Article: 110.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/27/2018] [Indexed: 11/30/2022]
Abstract
Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.
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Affiliation(s)
- Christian M K Sieber
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Allison Sharrar
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, CA, USA
| | - Susannah G Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG. MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. Bioinformatics 2016; 32:2760-7. [PMID: 27259541 DOI: 10.1093/bioinformatics/btw312] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/16/2016] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION High-throughput metagenomic sequencing has revolutionized our view on the structure and metabolic potential of microbial communities. However, analysis of metagenomic composition is often complicated by the high complexity of the community and the lack of related reference genomic sequences. As a start point for comparative metagenomic analysis, the researchers require efficient means for assessing pairwise similarity of the metagenomes (beta-diversity). A number of approaches were used to address this task, however, most of them have inherent disadvantages that limit their scope of applicability. For instance, the reference-based methods poorly perform on metagenomes from previously unstudied niches, while composition-based methods appear to be too abstract for straightforward interpretation and do not allow to identify the differentially abundant features. RESULTS We developed MetaFast, an approach that allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. For multiple metagenomes, the resulting representation is used to obtain a pairwise similarity matrix. The dimensional structure of the metagenomic components preserved in our algorithm reflects the inherent subspecies-level diversity of microbiota. The method is computationally efficient and especially promising for an analysis of metagenomes from novel environmental niches. AVAILABILITY AND IMPLEMENTATION Source code and binaries are freely available for download at https://github.com/ctlab/metafast The code is written in Java and is platform independent (tested on Linux and Windows x86_64). CONTACT ulyantsev@rain.ifmo.ru SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Veronika B Dubinkina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Dmitry G Alexeev
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
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