1
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Hauptfeld E, Pappas N, van Iwaarden S, Snoek BL, Aldas-Vargas A, Dutilh BE, von Meijenfeldt FAB. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nat Commun 2024; 15:3373. [PMID: 38643272 PMCID: PMC11032395 DOI: 10.1038/s41467-024-47155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
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Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sandra van Iwaarden
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Rosalind Franklin Strasse 1, 07743, Jena, Germany.
| | - F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790AB, Den Burg, The Netherlands.
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2
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Nie W, Qiu T, Wei Y, Ding H, Guo Z, Qiu J. Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies. Brief Bioinform 2024; 25:bbae117. [PMID: 38555471 PMCID: PMC10981677 DOI: 10.1093/bib/bbae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/15/2024] [Accepted: 03/02/2024] [Indexed: 04/02/2024] Open
Abstract
Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable therapeutic phages that are capable of infecting pathogens from massive phage databases has been a principal step in phage therapy design. Experimental methods to identify phage-host interaction (PHI) are time-consuming and expensive; high-throughput computational method to predict PHI is therefore a potential substitute. Here, we systemically review bioinformatic methods for predicting PHI, introduce reference databases and in silico models applied in these methods and highlight the strengths and challenges of current tools. Finally, we discuss the application scope and future research direction of computational prediction methods, which contribute to the performance improvement of prediction models and the development of personalized phage therapy.
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Affiliation(s)
- Wanchun Nie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital; Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Yiwen Wei
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hao Ding
- Institute of Clinical Science, Zhongshan Hospital; Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Zhixiang Guo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
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3
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Ide-Pérez MR, Sánchez-Reyes A, Folch-Mallol JL, Sánchez-Carbente MDR. Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLoS One 2024; 19:e0297232. [PMID: 38354109 PMCID: PMC10866521 DOI: 10.1371/journal.pone.0297232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024] Open
Abstract
Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.
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Affiliation(s)
- Martín R. Ide-Pérez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ayixon Sánchez-Reyes
- Investigador por México-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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4
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Koslicki D, White S, Ma C, Novikov A. YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics 2024; 40:btae047. [PMID: 38268451 PMCID: PMC10868342 DOI: 10.1093/bioinformatics/btae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/05/2024] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
MOTIVATION In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low-abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. RESULTS We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of ANI, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. AVAILABILITY AND IMPLEMENTATION The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.
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Affiliation(s)
- David Koslicki
- Department of Computer Science and Engineering, Pennsylvania State University, State College, PA 16802, United States
- Department of Biology, Pennsylvania State University, State College, PA 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA
- One Health Microbiome Center, Pennsylvania State University, State College, PA 16802, United States
| | - Stephen White
- Department of Mathematics, Pennsylvania State University, State College, PA 16802, United States
| | - Chunyu Ma
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA
| | - Alexei Novikov
- Department of Mathematics, Pennsylvania State University, State College, PA 16802, United States
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5
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Berthold M, Albrecht M, Campbell DA, Omar NM. Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes. Microbiol Resour Announc 2023; 12:e0046023. [PMID: 37943043 PMCID: PMC10720521 DOI: 10.1128/mra.00460-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Cyanobium and Synechococcus are prominent, globally distributed cyanobacteria genera with ecological significance. Here, we report the genomes of the marine Synechococcus sp. CCMP836 and two strains of Cyanobium (CZS25K and CZS48M) along with the genomes of 17 co-occurring proteobacteria. These genomes will improve the strain-specific ecological positions.
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Affiliation(s)
| | - Martin Albrecht
- Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | | | - Naaman M. Omar
- Department of Biology, Mount Allison University, Sackville, Canada
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6
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Garber ME, Frank V, Kazakov AE, Incha MR, Nava AA, Zhang H, Valencia LE, Keasling JD, Rajeev L, Mukhopadhyay A. REC protein family expansion by the emergence of a new signaling pathway. mBio 2023; 14:e0262223. [PMID: 37991384 PMCID: PMC10746176 DOI: 10.1128/mbio.02622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE We explore when and why large classes of proteins expand into new sequence space. We used an unsupervised machine learning approach to observe the sequence landscape of REC domains of bacterial response regulator proteins. We find that within-gene recombination can switch effector domains and, consequently, change the regulatory context of the duplicated protein.
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Affiliation(s)
- Megan E. Garber
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vered Frank
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew R. Incha
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Alberto A. Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Luis E. Valencia
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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7
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Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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8
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Doane MP, Reed MB, McKerral J, Farias Oliveira Lima L, Morris M, Goodman AZ, Johri S, Papudeshi B, Dillon T, Turnlund AC, Peterson M, Mora M, de la Parra Venegas R, Pillans R, Rohner CA, Pierce SJ, Legaspi CG, Araujo G, Ramirez-Macias D, Edwards RA, Dinsdale EA. Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome. Sci Rep 2023; 13:12747. [PMID: 37550406 PMCID: PMC10406844 DOI: 10.1038/s41598-023-39184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.
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Affiliation(s)
| | - Michael B Reed
- North Carolina Agricultural and Technical State University, Greensboro, NC, USA
| | | | | | - Megan Morris
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Shaili Johri
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | | | | | - Abigail C Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD, Australia
| | | | - Maria Mora
- San Diego State University, San Diego, CA, USA
| | | | | | | | | | | | - Gonzalo Araujo
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
- Marine Research and Conservation Foundation, Lydeard St Lawrence, Somerset, UK
| | - Deni Ramirez-Macias
- Tiburon Ballena Mexico de Conciencia Mexico, La Paz, Baja California Sur, Mexico
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9
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Kerr EN, Papudeshi B, Haggerty M, Wild N, Goodman AZ, Lima LFO, Hesse RD, Skye A, Mallawaarachchi V, Johri S, Parker S, Dinsdale EA. Stingray epidermal microbiomes are species-specific with local adaptations. Front Microbiol 2023; 14:1031711. [PMID: 36937279 PMCID: PMC10017458 DOI: 10.3389/fmicb.2023.1031711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.
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Affiliation(s)
- Emma N. Kerr
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- *Correspondence: Emma N. Kerr,
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Miranda Haggerty
- California Department of Fish and Wildlife, San Diego, CA, United States
| | - Natasha Wild
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Asha Z. Goodman
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Lais F. O. Lima
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Ryan D. Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Amber Skye
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Shaili Johri
- Hopkins Maine Station, Stanford University, Stanford, CA, United States
| | - Sophia Parker
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Elizabeth A. Dinsdale,
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10
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Sarwal V, Brito J, Mangul S, Koslicki D. TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. Gigascience 2022; 12:giad008. [PMID: 36852763 PMCID: PMC9972184 DOI: 10.1093/gigascience/giad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/12/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Metagenomic taxonomic profiling aims to predict the identity and relative abundance of taxa in a given whole-genome sequencing metagenomic sample. A recent surge in computational methods that aim to accurately estimate taxonomic profiles, called taxonomic profilers, has motivated community-driven efforts to create standardized benchmarking datasets and platforms, standardized taxonomic profile formats, and a benchmarking platform to assess tool performance. While this standardization is essential, there is currently a lack of tools to visualize the standardized output of the many existing taxonomic profilers. Thus, benchmarking studies rely on a single-value metrics to compare performance of tools and compare to benchmarking datasets. This is one of the major problems in analyzing metagenomic profiling data, since single metrics, such as the F1 score, fail to capture the biological differences between the datasets. FINDINGS Here we report the development of TAMPA (Taxonomic metagenome profiling evaluation), a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community. We demonstrate the unique ability of TAMPA to generate a novel biological hypothesis by highlighting the taxonomic differences between samples otherwise missed by commonly utilized metrics. CONCLUSION In this study, we show that TAMPA can help visualize the output of taxonomic profilers, enabling biologists to effectively choose the most appropriate profiling method to use on their metagenomics data. TAMPA is available on GitHub, Bioconda, and Galaxy Toolshed at https://github.com/dkoslicki/TAMPA and is released under the MIT license.
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Affiliation(s)
- Varuni Sarwal
- Department of Computer Science, University of California–Los Angeles, Los Angeles, CA 90095, USA
| | - Jaqueline Brito
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences,University of Southern California, Los Angeles, CA 90089, USA
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences,University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - David Koslicki
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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11
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Goodman AZ, Papudeshi B, Doane MP, Mora M, Kerr E, Torres M, Nero Moffatt J, Lima L, Nosal AP, Dinsdale E. Epidermal Microbiomes of Leopard Sharks ( Triakis semifasciata) Are Consistent across Captive and Wild Environments. Microorganisms 2022; 10:microorganisms10102081. [PMID: 36296361 PMCID: PMC9610875 DOI: 10.3390/microorganisms10102081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.
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Affiliation(s)
- Asha Z. Goodman
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Correspondence: (A.Z.G.); (E.D.)
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
| | - Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Emma Kerr
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Melissa Torres
- Scripps Institution of Oceanography, Universtity of California, San Diego, CA 92093, USA
| | - Jennifer Nero Moffatt
- Scripps Institution of Oceanography, Universtity of California, San Diego, CA 92093, USA
| | - Lais Lima
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Andrew P. Nosal
- Department of Biology, Point Loma Nazarene University, San Diego, CA 92106, USA
| | - Elizabeth Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
- Correspondence: (A.Z.G.); (E.D.)
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12
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Fernández-López M, Sánchez-Reyes A, Barcelos C, Sidón-Ceseña K, Leite RB, Lago-Lestón A. Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes. Antibiotics (Basel) 2022; 11:antibiotics11070887. [PMID: 35884142 PMCID: PMC9311598 DOI: 10.3390/antibiotics11070887] [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] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.
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Affiliation(s)
- Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca 62209, Mexico;
| | - Ayixon Sánchez-Reyes
- CONACYT-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico;
| | - Clara Barcelos
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Karla Sidón-Ceseña
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Ricardo B. Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal;
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
- Correspondence:
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13
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Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods 2022; 19:429-440. [PMID: 35396482 PMCID: PMC9007738 DOI: 10.1038/s41592-022-01431-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses. This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.
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Affiliation(s)
- Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Till Robin Lesker
- German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Gary Robertson
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | | | | | - Jan Buchmann
- Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany
| | - Aydin Buluç
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Bo Chen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | | | - Philip T L C Clausen
- National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark
| | - Alexandru Cristian
- Drexel University, Philadelphia, PA, USA.,Google Inc., Philadelphia, PA, USA
| | - Piotr Wojciech Dabrowski
- Robert Koch-Institut, Berlin, Germany.,Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany
| | | | - Rob Egan
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Eleazar Eskin
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Eugene Goltsman
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Melissa A Gray
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA
| | - Lars Hestbjerg Hansen
- University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark
| | - Steven Hofmeyr
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Pingqin Huang
- School of Computer Science, Fudan University, Shanghai, China
| | - Luiz Irber
- University of California, Davis, Davis, CA, USA
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Tue Sparholt Jørgensen
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.,Aarhus University, Department of Environmental Science, Roskilde, Denmark
| | - Silas D Kieser
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Axel Kola
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia
| | - Jason Kwan
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chenhao Li
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Fabio Malcher-Miranda
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Vanessa R Marcelino
- Sydney Medical School, The University of Sydney, Sydney, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | | | - Pierre Marijon
- Department of Computer Science, Inria, University of Lille, CNRS, Lille, France
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Daniel R Mende
- Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.,Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.,National University of Singapore, Singapore, Singapore
| | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leonid Oliker
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Vitor C Piro
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Evan R Rees
- University of Wisconsin-Madison, Madison, WI, USA
| | - Knut Reinert
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Bernhard Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.,Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Gail L Rosen
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.,Center for Biological Discovery from Big Data, Philadelphia, PA, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Varuni Sarwal
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Enrico Seiler
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Lizhen Shi
- Florida Polytechnic University, Lakeland, FL, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Ashleigh Thomas
- DOE Joint Genome Institute, Berkeley, CA, USA.,University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada
| | | | | | - Zhengyang Wang
- School of Computer Science, Fudan University, Shanghai, China
| | - Ziye Wang
- School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California at Merced, Merced, CA, USA
| | | | | | - Katherine Yelick
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Ronghui You
- School of Computer Science, Fudan University, Shanghai, China
| | - Georg Zeller
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | | | - Shanfeng Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Jie Zhu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Fantin Mesny
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Nathiana Smit
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Bremges
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. .,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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14
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Garber AI, Armbruster CR, Lee SE, Cooper VS, Bomberger JM, McAllister SM. SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs. BMC Genomics 2022; 23:202. [PMID: 35279076 PMCID: PMC8917688 DOI: 10.1186/s12864-022-08382-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences. RESULTS While many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semi-automated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias. CONCLUSIONS The output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.
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Affiliation(s)
- Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA.
| | - Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Sean M McAllister
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, WA, 98115, USA.
- The Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, 98105, USA.
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15
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Wan XH. Artificial intelligence reveals roles of gut microbiota in driving human colorectal cancer evolution. Artif Intell Cancer 2021; 2:69-78. [DOI: 10.35713/aic.v2.i5.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
With the rapid development of high-throughput sequencing and artificial intelligence (AI) techniques, gut mucosal microbiota begins to be recognized as critical drivers of human colorectal cancer (CRC). Various AI approaches have been designed to obtain effective information from enormous numbers of microbial cells residing in gut mucosal as well as cancer cells. These mainly include detection of microbial markers for early clinical diagnosis of stage-specific CRC, characterization of pathogenic bacterial activities via genomic and transcriptomic analyses, and prediction of interplay between bacterial drivers and host immune systems. Here I review the current progresses of AI applications in profiling gut microbiomes linked to CRC initiation and development. I further look forward to future AI research for improving our understanding of the roles of gut microbiota in CRC evolution.
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Affiliation(s)
- Xue-Hua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
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16
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Ramanathan N, Ramamurthy J, Natarajan G. Numerical Characterization of DNA Sequences for Alignment-free Sequence Comparison - A Review. Comb Chem High Throughput Screen 2021; 25:365-380. [PMID: 34382516 DOI: 10.2174/1386207324666210811101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Biological macromolecules namely, DNA, RNA, and protein have their building blocks organized in a particular sequence and the sequential arrangement encodes evolutionary history of the organism (species). Hence, biological sequences have been used for studying evolutionary relationships among the species. This is usually carried out by multiple sequence algorithms (MSA). Due to certain limitations of MSA, alignment-free sequence comparison methods were developed. The present review is on alignment-free sequence comparison methods carried out using numerical characterization of DNA sequences. <P> Discussion: The graphical representation of DNA sequences by chaos game representation and other 2-dimesnional and 3-dimensional methods are discussed. The evolution of numerical characterization from the various graphical representations and the application of the DNA invariants thus computed in phylogenetic analysis is presented. The extension of computing molecular descriptors in chemometrics to the calculation of new set of DNA invariants and their use in alignment-free sequence comparison in a N-dimensional space and construction of phylogenetic tress is also reviewed. <P> Conclusion: The phylogenetic tress constructed by the alignment-free sequence comparison methods using DNA invariants were found to be better than those constructed using alignment-based tools such as PHLYIP and ClustalW. One of the graphical representation methods is now extended to study viral sequences of infectious diseases for the identification of conserved regions to design peptide-based vaccine by combining numerical characterization and graphical representation.
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Affiliation(s)
- Natarajan Ramanathan
- Department of Chemistry, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Jayalakshmi Ramamurthy
- Department of Computer Science, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Ganapathy Natarajan
- Department of Mechanical Engineering and Industrial Engineering, University of Wisconsin, Platteville, WI 53818. United States
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17
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Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass. Appl Environ Microbiol 2021; 87:e0042521. [PMID: 33990301 DOI: 10.1128/aem.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.
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18
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Franciosa I, Ferrocino I, Giordano M, Mounier J, Rantsiou K, Cocolin L. Specific metagenomic asset drives the spontaneous fermentation of Italian sausages. Food Res Int 2021; 144:110379. [PMID: 34053518 DOI: 10.1016/j.foodres.2021.110379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/17/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022]
Abstract
Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.
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Affiliation(s)
- Irene Franciosa
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy; Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Ilario Ferrocino
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Manuela Giordano
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Luca Cocolin
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy.
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19
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Alipanahi B, Muggli MD, Jundi M, Noyes NR, Boucher C. Metagenome SNP calling via read-colored de Bruijn graphs. Bioinformatics 2021; 36:5275-5281. [PMID: 32049324 DOI: 10.1093/bioinformatics/btaa081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 01/08/2020] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Metagenomics refers to the study of complex samples containing of genetic contents of multiple individual organisms and, thus, has been used to elucidate the microbiome and resistome of a complex sample. The microbiome refers to all microbial organisms in a sample, and the resistome refers to all of the antimicrobial resistance (AMR) genes in pathogenic and non-pathogenic bacteria. Single-nucleotide polymorphisms (SNPs) can be effectively used to 'fingerprint' specific organisms and genes within the microbiome and resistome and trace their movement across various samples. However, to effectively use these SNPs for this traceability, a scalable and accurate metagenomics SNP caller is needed. Moreover, such an SNP caller should not be reliant on reference genomes since 95% of microbial species is unculturable, making the determination of a reference genome extremely challenging. In this article, we address this need. RESULTS We present LueVari, a reference-free SNP caller based on the read-colored de Bruijn graph, an extension of the traditional de Bruijn graph that allows repeated regions longer than the k-mer length and shorter than the read length to be identified unambiguously. LueVari is able to identify SNPs in both AMR genes and chromosomal DNA from shotgun metagenomics data with reliable sensitivity (between 91% and 99%) and precision (between 71% and 99%) as the performance of competing methods varies widely. Furthermore, we show that LueVari constructs sequences containing the variation, which span up to 97.8% of genes in datasets, which can be helpful in detecting distinct AMR genes in large metagenomic datasets. AVAILABILITY AND IMPLEMENTATION Code and datasets are publicly available at https://github.com/baharpan/cosmo/tree/LueVari. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bahar Alipanahi
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Martin D Muggli
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Musa Jundi
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Noelle R Noyes
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Christina Boucher
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
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20
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Bioinformatics Tools and Software. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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21
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Shah RM, McKenzie EJ, Rosin MT, Jadhav SR, Gondalia SV, Rosendale D, Beale DJ. An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. Metabolites 2020; 10:E94. [PMID: 32155792 PMCID: PMC7143645 DOI: 10.3390/metabo10030094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated perspective of the human gut microbiome and the linkages to human health will pave the way forward for delivering against the objectives of precision medicine, which is targeted to specific individuals and addresses the issues and mechanisms in situ.
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Affiliation(s)
- Rohan M. Shah
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Dutton Park, QLD 4102, Australia
| | - Elizabeth J. McKenzie
- Liggins Institute, The University of Auckland, Grafton, Auckland 1142, New Zealand; (E.J.M.); (M.T.R.)
| | - Magda T. Rosin
- Liggins Institute, The University of Auckland, Grafton, Auckland 1142, New Zealand; (E.J.M.); (M.T.R.)
| | - Snehal R. Jadhav
- Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, Burwood, VIC 3125, Australia;
| | - Shakuntla V. Gondalia
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | | | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Dutton Park, QLD 4102, Australia
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22
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Lima LFO, Weissman M, Reed M, Papudeshi B, Alker AT, Morris MM, Edwards RA, de Putron SJ, Vaidya NK, Dinsdale EA. Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network. mBio 2020; 11:e02691-19. [PMID: 32127450 PMCID: PMC7064765 DOI: 10.1128/mbio.02691-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
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Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, California, USA
- College of Biological Sciences, University of California Davis, Davis, California, USA
| | - Maya Weissman
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Micheal Reed
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Megan M Morris
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | | | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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23
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Bhatnagar S, Cowley ES, Kopf SH, Pérez Castro S, Kearney S, Dawson SC, Hanselmann K, Ruff SE. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. ENVIRONMENTAL MICROBIOME 2020; 15:3. [PMID: 33902727 PMCID: PMC8066431 DOI: 10.1186/s40793-019-0348-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/25/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. RESULTS Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. CONCLUSIONS The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.
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Affiliation(s)
- Srijak Bhatnagar
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Elise S. Cowley
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI USA
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO USA
| | - Sherlynette Pérez Castro
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
| | - Sean Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Scott C. Dawson
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA USA
| | | | - S. Emil Ruff
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
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24
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Silveira CB, Luque A, Roach TN, Villela H, Barno A, Green K, Reyes B, Rubio-Portillo E, Le T, Mead S, Hatay M, Vermeij MJ, Takeshita Y, Haas A, Bailey B, Rohwer F. Biophysical and physiological processes causing oxygen loss from coral reefs. eLife 2019; 8:49114. [PMID: 31793432 PMCID: PMC6890468 DOI: 10.7554/elife.49114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/27/2019] [Indexed: 12/25/2022] Open
Abstract
The microbialization of coral reefs predicts that microbial oxygen consumption will cause reef deoxygenation. Here we tested this hypothesis by analyzing reef microbial and primary producer oxygen metabolisms. Metagenomic data and in vitro incubations of bacteria with primary producer exudates showed that fleshy algae stimulate incomplete carbon oxidation metabolisms in heterotrophic bacteria. These metabolisms lead to increased cell sizes and abundances, resulting in bacteria consuming 10 times more oxygen than in coral incubations. Experiments probing the dissolved and gaseous oxygen with primary producers and bacteria together indicated the loss of oxygen through ebullition caused by heterogenous nucleation on algae surfaces. A model incorporating experimental production and loss rates predicted that microbes and ebullition can cause the loss of up to 67% of gross benthic oxygen production. This study indicates that microbial respiration and ebullition are increasingly relevant to reef deoxygenation as reefs become dominated by fleshy algae. Rising water temperatures, pollution and other factors are increasingly threatening corals and the entire reef ecosystems they build. The potential for corals to resist and recover from the stress these factors cause ultimately depends on their ability to compete against fast-growing fleshy algae that can rapidly take over the reefs. Living on the fleshy algae, the coral and in the surrounding water are communities of bacteria and other microbes that help maintain the health of the coral reef. Both corals and algae modify the chemical and physical environment of the reef to alter the composition of the microbial communities for their own benefit. Algae, for instance, release large amounts of sugars and other molecules of organic carbon into the water. These carbon molecules are then taken up by the bacteria, along with oxygen, to produce chemical energy via a process called respiration. This could cause the levels of oxygen in the water to decrease, potentially damaging the corals and creating more open space for the algae. Previous studies have revealed how communities of microbes on coral reefs use organic carbon, but it remains unclear how they affect the levels of oxygen in the reefs. To address this question, Silveira et al. used an approach called metagenomics to analyze the bacteria in samples of water from 87 reefs across the Pacific and the Caribbean, and also performed experiments with reef bacteria grown in the laboratory. The experiments showed that bacteria growing in the presence of fleshy algae became larger and more abundant than bacteria growing near corals, resulting in the water containing lower levels of oxygen. Furthermore, the fleshy algae produced bubbles of oxygen that were released from the water. Silveira et al. developed a mathematical model that predicted that these bubbles, combined with the respiration of bacteria that live near algae, caused the loss of 67% of the oxygen in the water surrounding the reef. These findings represent a fundamental step towards understanding how changes in the levels of oxygen in water affect the ability of coral reefs to resist and recover from stress.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, United States.,Computational Science Research Center, San Diego State University, San Diego, United States.,Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Ty Nf Roach
- Hawaii Institute of Marine Biology, University of Hawaii at Mānoa, Kāneohe, United States
| | - Helena Villela
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Adam Barno
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, United States
| | - Brandon Reyes
- Department of Biology, San Diego State University, San Diego, United States
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Tram Le
- Department of Biology, San Diego State University, San Diego, United States
| | - Spencer Mead
- Department of Biology, San Diego State University, San Diego, United States
| | - Mark Hatay
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Mark Ja Vermeij
- CARMABI Foundation, Willemstad, Curaçao.,Department of Freshwater and Marine Ecology, Institute for Biodiversity andEcosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Andreas Haas
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Barbara Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
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25
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Nalbantoglu OU, Sayood K. MIMOSA: Algorithms for Microbial Profiling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:2023-2034. [PMID: 29994027 DOI: 10.1109/tcbb.2018.2830324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A significant goal of the study of metagenomes obtained from an environment is to find the microbial diversity and the abundance of each organism in the community. Phylotyping and binning methods which address this problem generally operate using either marker sequences or by classifying each genome fragment individually. However, these approaches might not use all the information contained in the metagenome. We propose an approach based on a Multiple Input Multiple Output (MIMO) communication system model. Results from two different implementations of this approach, one using DNA-DNA hybridization simulations and one using short read mapping are evaluated using simulated and actual metagenomes and compared with other methods of phylotyping. The proposed approaches generally performed better under different scenarios including pathogen detection tasks of community complexity and low and high sequencing coverage while being highly computationally effective. The resulting framework can be integrated to metagenome analysis pipelines for phylogenetic diversity estimation. The approach is modular so that techniques other than hybridization simulations and short read mapping may be integrated. We have observed that even for low coverage samples, the method provides accurate estimates. Therefore, the use of the proposed strategy could enable the task of exploring biodiversity with limited resources.
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26
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von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol 2019; 20:217. [PMID: 31640809 PMCID: PMC6805573 DOI: 10.1186/s13059-019-1817-x] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/10/2019] [Indexed: 01/08/2023] Open
Abstract
Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.
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Affiliation(s)
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Diego D Cambuy
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Felipe H Coutinho
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Present Address: Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, 03550, Alicante, Spain
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.
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27
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von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol 2019; 20:217. [PMID: 31640809 DOI: 10.1101/530188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/10/2019] [Indexed: 05/23/2023] Open
Abstract
Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.
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Affiliation(s)
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Diego D Cambuy
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Felipe H Coutinho
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Present Address: Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, 03550, Alicante, Spain
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.
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28
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de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. Front Microbiol 2019; 10:1680. [PMID: 31417506 PMCID: PMC6682628 DOI: 10.3389/fmicb.2019.01680] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.
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Affiliation(s)
- Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Raffaella Rossetto
- São Paulo's Agency for Agribusiness Technology APTA-SAA, Piracicaba, Brazil
| | - Robert Alan Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, United States
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Environmental Sciences, Federal University of São Carlos, Sorocaba, Brazil
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29
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Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q. Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. Brief Bioinform 2019; 19:1415-1429. [PMID: 28481971 DOI: 10.1093/bib/bbx051] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 12/12/2022] Open
Abstract
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- Sheng-Yong Niu
- Department of Biochemical Science and Technology, National Taiwan University, Taiwan
| | - Jinyu Yang
- Department of Mathematics and Statistics at South Dakota State University, Brookings, SD, USA
| | - Adam McDermaid
- Department of Mathematics and Statistics at South Dakota State University, Brookings, SD, USA
| | - Jing Zhao
- Department of Internal Medicine at University of South Dakota Sanford School of Medicine
| | - Yu Kang
- Beijing Institute of Genomics of Chinese Academy of Sciences
| | - Qin Ma
- Department of Mathematics and Statistics at South Dakota State University and BioSNTR, SD, USA
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30
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Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D. Assessing taxonomic metagenome profilers with OPAL. Genome Biol 2019; 20:51. [PMID: 30832730 PMCID: PMC6398228 DOI: 10.1186/s13059-019-1646-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/31/2019] [Indexed: 12/25/2022] Open
Abstract
The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. OPAL is freely available at https://github.com/CAMI-challenge/OPAL .
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Affiliation(s)
- Fernando Meyer
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Bremges
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Peter Belmann
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Stefan Janssen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
| | - Alice C McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.
| | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, OR, USA.
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Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution. QUANTITATIVE BIOLOGY 2018. [DOI: 10.1007/s40484-018-0142-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Andreote APD, Dini-Andreote F, Rigonato J, Machineski GS, Souza BCE, Barbiero L, Rezende-Filho AT, Fiore MF. Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom. Front Microbiol 2018; 9:244. [PMID: 29520256 PMCID: PMC5827094 DOI: 10.3389/fmicb.2018.00244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/31/2018] [Indexed: 11/29/2022] Open
Abstract
Soda lakes have high levels of sodium carbonates and are characterized by salinity and elevated pH. These ecosystems are found across Africa, Europe, Asia, Australia, North, Central, and South America. Particularly in Brazil, the Pantanal region has a series of hundreds of shallow soda lakes (ca. 600) potentially colonized by a diverse haloalkaliphilic microbial community. Biological information of these systems is still elusive, in particular data on the description of the main taxa involved in the biogeochemical cycling of life-important elements. Here, we used metagenomic sequencing to contrast the composition and functional patterns of the microbial communities of two distinct soda lakes from the sub-region Nhecolândia, state of Mato Grosso do Sul, Brazil. These two lakes differ by permanent cyanobacterial blooms (Salina Verde, green-water lake) and by no record of cyanobacterial blooms (Salina Preta, black-water lake). The dominant bacterial species in the Salina Verde bloom was Anabaenopsis elenkinii. This cyanobacterium altered local abiotic parameters such as pH, turbidity, and dissolved oxygen and consequently the overall structure of the microbial community. In Salina Preta, the microbial community had a more structured taxonomic profile. Therefore, the distribution of metabolic functions in Salina Preta community encompassed a large number of taxa, whereas, in Salina Verde, the functional potential was restrained across a specific set of taxa. Distinct signatures in the abundance of genes associated with the cycling of carbon, nitrogen, and sulfur were found. Interestingly, genes linked to arsenic resistance metabolism were present at higher abundance in Salina Verde and they were associated with the cyanobacterial bloom. Collectively, this study advances fundamental knowledge on the composition and genetic potential of microbial communities inhabiting tropical soda lakes.
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Affiliation(s)
- Ana P. D. Andreote
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Francisco Dini-Andreote
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Bruno C. E. Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Laurent Barbiero
- Observatoire Midi-Pyrénées, Géosciences Environnement Toulouse, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Ary T. Rezende-Filho
- Faculty of Engineering, Architecture and Urbanism and Geography, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Marli F. Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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33
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Jeffries TC, Rayu S, Nielsen UN, Lai K, Ijaz A, Nazaries L, Singh BK. Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils. Front Microbiol 2018. [PMID: 29515526 PMCID: PMC5826299 DOI: 10.3389/fmicb.2018.00147] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.
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Affiliation(s)
- Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Smriti Rayu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Kaitao Lai
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, Australia
| | - Ali Ijaz
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Loic Nazaries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
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34
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Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA. Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. BMC Genomics 2017; 18:915. [PMID: 29183281 PMCID: PMC5706307 DOI: 10.1186/s12864-017-4294-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/13/2017] [Indexed: 11/12/2022] Open
Abstract
Background Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools. Methods We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification. Results We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1.49), low species richness (4.91 ± 0.66), and higher genome completeness (40.92 ± 1.75) across all projects. MetaBat extracted 115 bins from the 4 projects of which 66 bins were identified as reconstructed metagenome-assembled genomes with sequences belonging to a specific genus. We identified 13 novel genomes, some of which were 100% complete, but show low similarity to genomes within databases. Conclusions In conclusion, we present a set of biologically relevant parameters for evaluation to select for optimal assembly and binning tools. For the tools we tested, SPAdes assembler and MetaBat binning tools reconstructed quality metagenome-assembled genomes for the four projects. We also conclude that metagenomes from microbial communities that have high coverage of phylogenetically distinct, and low taxonomic diversity results in highest quality metagenome-assembled genomes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4294-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bhavya Papudeshi
- Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA.,National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana, USA
| | - J Matthew Haggerty
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92115, California, USA
| | - Michael Doane
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92115, California, USA
| | - Megan M Morris
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92115, California, USA
| | - Kevin Walsh
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92115, California, USA
| | - Douglas T Beattie
- Department of Biology, University of New South Wales, Sydney, New South Wales, Australia
| | - Dnyanada Pande
- Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Parisa Zaeri
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Genivaldo G Z Silva
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California, USA
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92115, California, USA.
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35
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Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods 2017; 14:1063-1071. [PMID: 28967888 DOI: 10.1101/099127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/25/2017] [Indexed: 05/25/2023]
Abstract
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
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Affiliation(s)
- Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Peter Hofmann
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Peter Belmann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, Oregon, USA
| | - Stefan Janssen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Department of Pediatrics, University of California, San Diego, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - Johannes Dröge
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ivan Gregor
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Stephan Majda
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
| | - Jessika Fiedler
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Eik Dahms
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Bremges
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ruben Garrido-Oter
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Matthew Z DeMaere
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rayan Chikhi
- Department of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, France
- National Centre of the Scientific Research (CNRS), Rennes, France
| | - Niranjan Nagarajan
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Christopher Quince
- Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fernando Meyer
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Monika Balvočiūtė
- Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Søren J Sørensen
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Burton K H Chia
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Bertrand Denis
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Jeff L Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Zhong Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Robert Egan
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Dongwan Don Kang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Charles Deltel
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Claire Lemaitre
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Pierre Peterlongo
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Guillaume Rizk
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
- Algorizk-IT consulting and software systems, Paris, France
| | - Dominique Lavenier
- National Centre of the Scientific Research (CNRS), Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, California, USA
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chirag Jain
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marc Strous
- Energy Engineering and Geomicrobiology, University of Calgary, Calgary, Alberta, Canada
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael D Barton
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hsin-Hung Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | | | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, New York, New York, USA
| | - Vitor C Piro
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
- Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alice C McHardy
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
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36
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Zielezinski A, Vinga S, Almeida J, Karlowski WM. Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol 2017; 18:186. [PMID: 28974235 PMCID: PMC5627421 DOI: 10.1186/s13059-017-1319-7] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Susana Vinga
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
| | - Jonas Almeida
- Stony Brook University (SUNY), 101 Nicolls Road, Stony Brook, NY, 11794, USA
| | - Wojciech M Karlowski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
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37
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Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods 2017; 14:1063-1071. [PMID: 28967888 DOI: 10.1038/nmeth.4458] [Citation(s) in RCA: 430] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/25/2017] [Indexed: 12/12/2022]
Abstract
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
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Affiliation(s)
- Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Peter Hofmann
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Peter Belmann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, Oregon, USA
| | - Stefan Janssen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Department of Pediatrics, University of California, San Diego, California, USA.,Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - Johannes Dröge
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ivan Gregor
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Stephan Majda
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
| | - Jessika Fiedler
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Eik Dahms
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Bremges
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ruben Garrido-Oter
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark.,Department of Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Matthew Z DeMaere
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rayan Chikhi
- Department of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, France.,National Centre of the Scientific Research (CNRS), Rennes, France
| | - Niranjan Nagarajan
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Christopher Quince
- Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fernando Meyer
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Monika Balvočiūtė
- Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Søren J Sørensen
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Burton K H Chia
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Bertrand Denis
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Jeff L Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Zhong Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Robert Egan
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Dongwan Don Kang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Charles Deltel
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Claire Lemaitre
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Pierre Peterlongo
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Guillaume Rizk
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France.,Algorizk-IT consulting and software systems, Paris, France
| | - Dominique Lavenier
- National Centre of the Scientific Research (CNRS), Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, California, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chirag Jain
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marc Strous
- Energy Engineering and Geomicrobiology, University of Calgary, Calgary, Alberta, Canada
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael D Barton
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hsin-Hung Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | | | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, New York, New York, USA
| | - Vitor C Piro
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany.,Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.,Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alice C McHardy
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
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38
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Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun 2017; 8:15955. [PMID: 28677677 PMCID: PMC5504273 DOI: 10.1038/ncomms15955] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.
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Affiliation(s)
- Felipe H. Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Cynthia B. Silveira
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Gustavo B. Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Baixada Santista 11070100, Brazil
| | - Cristiane C. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
| | - Robert A. Edwards
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Corina P. D. Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, PO Box 59, 1790 AB Den Burg Texel, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Bas E. Dutilh
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Fabiano L. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ)/COPPE/SAGE, Rio de Janeiro 21941950, Brazil
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39
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Campeão ME, Reis L, Leomil L, de Oliveira L, Otsuki K, Gardinali P, Pelz O, Valle R, Thompson FL, Thompson CC. The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation. Front Microbiol 2017; 8:1019. [PMID: 28659874 PMCID: PMC5468453 DOI: 10.3389/fmicb.2017.01019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/22/2017] [Indexed: 12/05/2022] Open
Abstract
One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.
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Affiliation(s)
- Mariana E Campeão
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Luciana Reis
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Luciana Leomil
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Louisi de Oliveira
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Koko Otsuki
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Piero Gardinali
- Department of Chemistry, Florida International University, MiamiFL, United States
| | - Oliver Pelz
- BP Exploration & Production Inc., HoustonTX, United States
| | - Rogerio Valle
- SAGE/COPPE, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil.,SAGE/COPPE, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
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40
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Silveira CB, Gregoracci GB, Coutinho FH, Silva GGZ, Haggerty JM, de Oliveira LS, Cabral AS, Rezende CE, Thompson CC, Francini-Filho RB, Edwards RA, Dinsdale EA, Thompson FL. Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle. Front Microbiol 2017; 8:784. [PMID: 28588555 PMCID: PMC5438984 DOI: 10.3389/fmicb.2017.00784] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 04/18/2017] [Indexed: 11/13/2022] Open
Abstract
Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the coral's surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.
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Affiliation(s)
- Cynthia B Silveira
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Department of Biology, San Diego State UniversitySan Diego, CA, USA
| | | | - Felipe H Coutinho
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CentreNijmegen, Netherlands
| | - Genivaldo G Z Silva
- Department of Computational Science, San Diego State UniversitySan Diego, CA, USA
| | - John M Haggerty
- Department of Biology, San Diego State UniversitySan Diego, CA, USA
| | - Louisi S de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Anderson S Cabral
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Carlos E Rezende
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | | | - Robert A Edwards
- Department of Computational Science, San Diego State UniversitySan Diego, CA, USA
| | - Elizabeth A Dinsdale
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Laboratório de Sistemas Avançados de Gestão da Produção, COPPE, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
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41
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Alvarenga DO, Fiore MF, Varani AM. A Metagenomic Approach to Cyanobacterial Genomics. Front Microbiol 2017; 8:809. [PMID: 28536564 PMCID: PMC5422444 DOI: 10.3389/fmicb.2017.00809] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023] Open
Abstract
Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria.
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Affiliation(s)
- Danillo O Alvarenga
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil.,Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Marli F Fiore
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Alessandro M Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil
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42
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Pham DT, Gao S, Phan V. An accurate and fast alignment-free method for profiling microbial communities. J Bioinform Comput Biol 2017; 15:1740001. [PMID: 28345370 DOI: 10.1142/s0219720017400017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Although homology-based methods are popular, they have shown to be computationally expensive due to the alignment of tens of millions of reads from metagenomic samples to reference genomes of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers (GSM). We compared our method against popular alignment-free and homology-based methods. Without contamination, our method was more accurate than other alignment-free methods while being much faster than a homology-based method. In more realistic settings where samples were contaminated with human DNA, our method was the most accurate method in predicting abundance at varying levels of contamination. We achieve higher accuracy than both alignment-free and homology-based methods.
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Affiliation(s)
- Diem-Trang Pham
- 1 Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA
| | - Shanshan Gao
- 1 Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA
| | - Vinhthuy Phan
- 1 Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA
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43
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Heck K, Machineski GS, Alvarenga DO, Vaz MGMV, Varani ADM, Fiore MF. Evaluating methods for purifying cyanobacterial cultures by qPCR and high-throughput Illumina sequencing. J Microbiol Methods 2016; 129:55-60. [PMID: 27476485 DOI: 10.1016/j.mimet.2016.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/27/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
Abstract
Cyanobacteria are commonly found in association with other microorganisms, which constitutes a great challenge during the isolation of cyanobacterial strains. Although several methods have been published for obtaining axenic cyanobacterial cultures, their efficiency is usually evaluated by observing the growth of non-cyanobacteria in culture media. In order to verify whether uncultured bacteria should be a concern during cyanobacterial isolation, this work aimed to detect by molecular methods sequences from cyanobacteria and other bacteria present before and after a technique for obtaining axenic cultures from plating and exposure of Fischerella sp. CENA161 akinetes to the Extran detergent and sodium hypochlorite. Solutions containing 0.5, 1, and 2% sodium hypochlorite were able to remove contaminant bacterial CFUs from the culture. However, qPCR pointed that the quantity of sequences amplified with universal bacteria primers was higher than the number of cyanobacteria-specific sequences before and after treatments. The presence of uncultured bacteria in post-hypochlorite cultures was confirmed by high-throughput Illumina sequencing. These results suggest that culturing may overlook the presence of uncultured bacteria associated to cyanobacterial strains and is not sufficient for monitoring the success of cyanobacterial isolation by itself. Molecular methods such as qPCR could be employed as an additional measure for evaluating axenity in cyanobacterial strains.
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Affiliation(s)
- Karina Heck
- University of São Paulo, Center for Nuclear Energy in Agriculture, Piracicaba, São Paulo, Brazil
| | | | | | | | - Alessandro de Mello Varani
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Marli Fátima Fiore
- University of São Paulo, Center for Nuclear Energy in Agriculture, Piracicaba, São Paulo, Brazil.
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44
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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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Zhang Y, Ji P, Wang J, Zhao F. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Res 2016; 44:e99. [PMID: 26984526 PMCID: PMC4889936 DOI: 10.1093/nar/gkw165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/16/2016] [Accepted: 03/02/2016] [Indexed: 12/30/2022] Open
Abstract
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities.
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Affiliation(s)
- Yanming Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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Lytic to temperate switching of viral communities. Nature 2016; 531:466-70. [PMID: 26982729 DOI: 10.1038/nature17193] [Citation(s) in RCA: 302] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 02/03/2016] [Indexed: 12/17/2022]
Abstract
Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus 'more microbes, fewer viruses'.
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Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ 2016; 4:e1603. [PMID: 26870609 PMCID: PMC4748697 DOI: 10.7717/peerj.1603] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022] Open
Abstract
Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability.PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.
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Affiliation(s)
- Ivan Gregor
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Johannes Dröge
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Melanie Schirmer
- The Broad Institute of MIT and Harvard , Cambridge, MA , United States
| | | | - Alice C McHardy
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
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Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG. Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. BMC Bioinformatics 2016; 17:38. [PMID: 26774270 PMCID: PMC4715287 DOI: 10.1186/s12859-015-0875-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/14/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study. RESULTS We developed a method for calculating pairwise dissimilarity (beta-diversity) of "shotgun" metagenomes based on short k-mer spectra (5 ≤ k ≤ 11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified. CONCLUSIONS Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.
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Affiliation(s)
- Veronika B Dubinkina
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry S Ischenko
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | | | - Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry G Alexeev
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
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Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev 2015; 40:258-72. [PMID: 26657537 PMCID: PMC5831537 DOI: 10.1093/femsre/fuv048] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 01/21/2023] Open
Abstract
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
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Affiliation(s)
- Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bas E Dutilh
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
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