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Zulfiqar U, Haider FU, Maqsood MF, Mohy-Ud-Din W, Shabaan M, Ahmad M, Kaleem M, Ishfaq M, Aslam Z, Shahzad B. Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil. PLANTS (BASEL, SWITZERLAND) 2023; 12:3147. [PMID: 37687393 PMCID: PMC10490184 DOI: 10.3390/plants12173147] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- University of Chinese Academy of Sciences, Beijing 100039, China
| | | | - Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan;
- Department of Soil and Environmental Sciences, Ghazi University, D. G. Khan 32200, Pakistan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Muhammad Shabaan
- Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan;
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
| | - Muhammad Kaleem
- Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Muhammad Ishfaq
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
- Department of Agriculture, Extension, Azad Jammu & Kashmir, Pakistan
| | - Zoya Aslam
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Babar Shahzad
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
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2
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Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022; 24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [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: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022] Open
Abstract
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
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Affiliation(s)
- Gauri S Navgire
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India
| | - Neha Goel
- Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India
| | - Gifty Sawhney
- Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India
| | - Mohit Sharma
- Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Karkow, Poland
| | | | | | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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3
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Bhanse P, Kumar M, Singh L, Awasthi MK, Qureshi A. Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils: Opportunities, challenges, and prospects. CHEMOSPHERE 2022; 303:134954. [PMID: 35595111 DOI: 10.1016/j.chemosphere.2022.134954] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 05/02/2023]
Abstract
Soil is considered as a vital natural resource equivalent to air and water which supports growth of the plants and provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants' ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants' growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.
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Affiliation(s)
- Poonam Bhanse
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manish Kumar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Luo E, Leu AO, Eppley JM, Karl DM, DeLong EF. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. THE ISME JOURNAL 2022; 16:1627-1635. [PMID: 35236926 PMCID: PMC9122931 DOI: 10.1038/s41396-022-01202-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/15/2022]
Abstract
Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
- Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS 51, Woods Hole MA, 02543, Falmouth, USA.
| | - Andy O Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
- Australia Center for Ecogenomics, University of Queensland, St. Lucia QLD, 4072, Australia
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
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5
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Raj A, Kumar A, Dames JF. Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability. Front Microbiol 2021; 12:791723. [PMID: 35003022 PMCID: PMC8733403 DOI: 10.3389/fmicb.2021.791723] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022] Open
Abstract
Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.
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Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, India
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Joanna Felicity Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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6
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Wu G, Zhao N, Zhang C, Lam YY, Zhao L. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Med 2021; 13:22. [PMID: 33563315 PMCID: PMC7874449 DOI: 10.1186/s13073-021-00840-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.
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Affiliation(s)
- Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Naisi Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Public Health and Community Medicine, School of Medicine, Tufts University, Medford, MA, USA
| | - Chenhong Zhang
- Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA.,State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Y Lam
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA. .,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA. .,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA. .,State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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7
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Zaidi SSA, Kayani MUR, Zhang X, Ouyang Y, Shamsi IH. Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons. BMC Genomics 2021; 22:60. [PMID: 33468056 PMCID: PMC7814594 DOI: 10.1186/s12864-020-07357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/27/2020] [Indexed: 11/10/2022] Open
Abstract
Background Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions. Results In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101). Conclusion With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.
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Affiliation(s)
- Syed Shujaat Ali Zaidi
- Bioinformatics Division, Beijing National Research Institute for Information Science and Technology (BNRIST), Department of Automation, Tsinghua University, Beijing, 100084, People's Republic of China.,Bioscience Department, COMSATS Institute of Information Technology, Islamabad, 44000, Pakistan.,Center for Innovation in Brain Science, University of Arizona, Tucson, 85719, USA
| | - Masood Ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, People's Republic of China
| | - Xuegong Zhang
- Bioinformatics Division, Beijing National Research Institute for Information Science and Technology (BNRIST), Department of Automation, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Younan Ouyang
- China National Rice Research Institute (CNRRI), 28 Shuidaosuo rd, Fuyang, Hangzhou, 311400, People's Republic of China
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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8
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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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9
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Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME JOURNAL 2020; 14:1304-1315. [PMID: 32060418 PMCID: PMC7174320 DOI: 10.1038/s41396-020-0604-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/17/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses are essential elements of these communities, influencing the productivity, diversity, and evolution of cellular hosts. To further explore the natural history and ecology of open-ocean viruses, we surveyed the spatiotemporal dynamics of double-stranded DNA (dsDNA) viruses in both virioplankton and bacterioplankton size fractions in the North Pacific Subtropical Gyre, one of the largest biomes on the planet. Assembly and clustering of viral genomes revealed a peak in virioplankton diversity at the base of the euphotic zone, where virus populations and host species richness both reached their maxima. Simultaneous characterization of both extracellular and intracellular viruses suggested depth-specific reproductive strategies. In particular, analyses indicated elevated lytic interactions in the mixed layer, more temporally variable temperate phage interactions at the base of the euphotic zone, and increased lysogeny in the mesopelagic ocean. Furthermore, the depth variability of auxiliary metabolic genes suggested habitat-specific strategies for viral influence on light-energy, nitrogen, and phosphorus acquisition during host infection. Most virus populations were temporally persistent over several years in this environment at the 95% nucleic acid identity level. In total, our analyses revealed variable distributional patterns and diverse reproductive and metabolic strategies of virus populations in the open-ocean water column.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Anna E Romano
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA.
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10
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Krishna SBN, Dubey A, Malla MA, Kothari R, Upadhyay CP, Adam JK, Kumar A. Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health. Open Microbiol J 2019. [DOI: 10.2174/1874285801913020330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms. Understanding of this enormous and largely untapped microbial diversity has been the focus of microbial research from the past few decades or so. Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and disease state. In comparison to the human microbiome, plants are also surrounded by a vast diversity of microbes that form complex ecological communities that affect plant growth and health through collective metabolic activities and interactions. This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome. This review primarily focused on the advances and challenges in microbiome research at the interface of plant and human, and role of microbiome at different compartments of the body’s ecosystems along with their correlation to health and diseases. This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.
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11
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Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 2019; 22:178-193. [PMID: 31848574 PMCID: PMC7820839 DOI: 10.1093/bib/bbz155] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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Affiliation(s)
- Richa Bharti
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
| | - Dominik G Grimm
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
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12
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Tamames J, Puente-Sánchez F. SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. Front Microbiol 2019; 9:3349. [PMID: 30733714 PMCID: PMC6353838 DOI: 10.3389/fmicb.2018.03349] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/31/2018] [Indexed: 12/11/2022] Open
Abstract
The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a MySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries. We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins. One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure and in absence of any network connectivity. It is therefore adequate for in situ, real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta.
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Affiliation(s)
- Javier Tamames
- Department of Systems Biology, Spanish Center for Biotechnology, CSIC, Madrid, Spain
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13
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Methods in Metagenomics and Environmental Biotechnology. NANOSCIENCE AND BIOTECHNOLOGY FOR ENVIRONMENTAL APPLICATIONS 2019. [DOI: 10.1007/978-3-319-97922-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3130607. [PMID: 30581850 PMCID: PMC6276491 DOI: 10.1155/2018/3130607] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/10/2018] [Accepted: 11/04/2018] [Indexed: 12/15/2022]
Abstract
Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.
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15
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Pham HL, Ho CL, Wong A, Lee YS, Chang MW. Applying the design-build-test paradigm in microbiome engineering. Curr Opin Biotechnol 2017; 48:85-93. [DOI: 10.1016/j.copbio.2017.03.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/11/2022]
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16
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Abstract
Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.
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17
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Environmental drivers of a microbial genomic transition zone in the ocean's interior. Nat Microbiol 2017; 2:1367-1373. [PMID: 28808230 DOI: 10.1038/s41564-017-0008-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/04/2017] [Indexed: 01/01/2023]
Abstract
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea 1,2 . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain 3-7 . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift. Across a narrow range of increasing depth of just tens of metres, diverse microbial clades trend towards larger genome size, higher genomic GC content, and proteins with higher nitrogen but lower carbon content. These community-wide changes in genome features appear to be driven by gradients in the surrounding environmental energy and nutrient fields. Collectively, our data support hypotheses invoking nutrient limitation as a central driver in the evolution of core bacterial and archaeal genomic and proteomic properties.
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18
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Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ. A geographically-diverse collection of 418 human gut microbiome pathway genome databases. Sci Data 2017; 4:170035. [PMID: 28398290 PMCID: PMC5387927 DOI: 10.1038/sdata.2017.35] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/10/2017] [Indexed: 01/16/2023] Open
Abstract
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.
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Affiliation(s)
- Aria S Hahn
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA
| | - Tomer Altman
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California 94305, USA.,Whole Biome, Inc., 953 Indiana Street, San Francisco, California 94107, USA
| | - Kishori M Konwar
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Niels W Hanson
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Dongjae Kim
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA.,Ecosystem Services, Commercialization and Entrepreneurship (ECOSCOPE), University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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19
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Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Transl Res 2017; 179:7-23. [PMID: 27513210 PMCID: PMC5164958 DOI: 10.1016/j.trsl.2016.07.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 12/29/2022]
Abstract
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA
- Santa Fe Institute, Santa Fe, NM
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20
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Abstract
AbstractOwing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis.We review here the contribution of machine learning techniques for the field of metagenomics, by presenting known successful approaches in a unified framework. This review focuses on five important metagenomic problems:OTU-clustering, binning, taxonomic proffiing and assignment, comparative metagenomics and gene prediction. For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods.We conclude our review looking further ahead at the challenge posed by the analysis of interactions within microbial communities and different environments, in a field one could call “integrative metagenomics”.
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21
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Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016; 535:376-81. [PMID: 27409811 DOI: 10.1038/nature18646] [Citation(s) in RCA: 1251] [Impact Index Per Article: 156.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/14/2016] [Indexed: 02/07/2023]
Abstract
Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus are identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.
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22
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Abstract
Type 1 diabetes mellitus (T1DM) is a chronic immune-mediated disease with a subclinical prodromal period, characterized by selective loss of insulin-producing-β cells in the pancreatic islets of genetically susceptible individuals. The incidence of T1DM has increased several fold in most developed countries since World War II, in conjunction with other immune-mediated diseases. Rapid environmental changes and modern lifestyles are probably the driving factors that underlie this increase. These effects might be mediated by changes in the human microbiota, particularly the intestinal microbiota. Research on the gut microbiome of individuals at risk of developing T1DM and in patients with established disease is still in its infancy, but initial findings indicate that the intestinal microbiome of individuals with prediabetes or diabetes mellitus is different to that of healthy individuals. The gut microbiota in individuals with preclinical T1DM is characterized by Bacteroidetes dominating at the phylum level, a dearth of butyrate-producing bacteria, reduced bacterial and functional diversity and low community stability. However, these changes seem to emerge after the appearance of autoantibodies that are predictive of T1DM, which suggests that the intestinal microbiota might be involved in the progression from β-cell autoimmunity to clinical disease rather than in the initiation of the disease process.
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Affiliation(s)
- Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, PO Box 22, FI-00014 Helsinki, Finland
| | - Heli Siljander
- Children's Hospital, University of Helsinki and Helsinki University Hospital, PO Box 22, FI-00014 Helsinki, Finland
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23
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Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015; 528:262-266. [PMID: 26633628 PMCID: PMC4681099 DOI: 10.1038/nature15766] [Citation(s) in RCA: 1352] [Impact Index Per Article: 150.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Kristoffer Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gwen Falony
- Center for the Biology of Disease, VIB, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Emmanuelle Le Chatelier
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Edi Prifti
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Sara Vieira-Silva
- Center for the Biology of Disease, VIB, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Valborg Gudmundsdottir
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helle K Pedersen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Anita Yvonne Voigt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit , University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajna Hercog
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Paul Igor Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jens Roat Kultima
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - Florence Levenez
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Joël Dore
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - H Bjørn Nielsen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeroen Raes
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Jun Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China.,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong
| | - S Dusko Ehrlich
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, United Kingdom
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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24
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Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol 2015; 11:e1004573. [PMID: 26565399 PMCID: PMC4643905 DOI: 10.1371/journal.pcbi.1004573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/29/2015] [Indexed: 12/30/2022] Open
Abstract
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. Microbial communities perform a wide variety of functions, from marine photosynthesis to aiding digestion in the human gut. Shotgun “metagenomic” sequencing can be used to sample millions of short DNA sequences from such communities directly, without needing to first culture its constituents in the laboratory. Using these data, researchers can survey which functions are encoded by mapping these short sequences to known protein families and pathways. Several tools for this annotation already exist. But, annotation is a multi-step process that includes identification of genes in a metagenome and determination of the type of protein each gene encodes. We currently know little about how different choices of parameters during annotation influences the final results. In this work, we systematically test how several key decisions affect the accuracy and speed of annotation, and based on these results, develop new software for annotation, which we named ShotMAP. We then use ShotMAP to functionally characterize marine communities and gut communities in a clinical cohort of inflammatory bowel disease. We find several functions are differentially represented in the gut microbiome of Crohn’s disease patients, which could be candidates for biomarkers and could also offer insight into the pathophysiology of Crohn’s. ShotMAP is freely available (https://github.com/sharpton/shotmap).
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Affiliation(s)
- Stephen Nayfach
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Patrick H. Bradley
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Stacia K. Wyman
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Timothy J. Laurent
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Alex Williams
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, UC Davis Genome Center, University of California, Davis, Davis, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (TJS)
| | - Thomas J. Sharpton
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail: (KSP); (TJS)
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25
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Thangam M, Gopal RK. CRCDA--Comprehensive resources for cancer NGS data analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav092. [PMID: 26450948 PMCID: PMC4597977 DOI: 10.1093/database/bav092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/31/2015] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL: http://bioinfo.au-kbc.org.in/ngs/ngshome.html.
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Affiliation(s)
- Manonanthini Thangam
- AU-KBC Research Centre, MIT Campus of Anna University, Chromepet, Chennai, India
| | - Ramesh Kumar Gopal
- AU-KBC Research Centre, MIT Campus of Anna University, Chromepet, Chennai, India
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Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348:1261359. [PMID: 25999513 DOI: 10.1126/science.1261359] [Citation(s) in RCA: 1376] [Impact Index Per Article: 152.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Affiliation(s)
- Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Karine Labadie
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Bardya Djahanschiri
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel R Mende
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adriana Alberti
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France
| | - Stefan Engelen
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Florian Kokoszka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France
| | - Cyrille Lepoivre
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Julie Poulain
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Hugo Sarmento
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Céline Dimier
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Jean Weissenbach
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Patrick Wincker
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
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27
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Mandal RS, Saha S, Das S. Metagenomic surveys of gut microbiota. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:148-58. [PMID: 26184859 PMCID: PMC4563348 DOI: 10.1016/j.gpb.2015.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 01/21/2023]
Abstract
Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.
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Affiliation(s)
- Rahul Shubhra Mandal
- Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
| | - Santasabuj Das
- Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India; Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India.
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28
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Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. Temporal and technical variability of human gut metagenomes. Genome Biol 2015; 16:73. [PMID: 25888008 PMCID: PMC4416267 DOI: 10.1186/s13059-015-0639-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject. RESULTS We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods. CONCLUSIONS Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.
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Affiliation(s)
- Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany.
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Simone S Li
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, Australia.
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, 13125, Berlin, Germany.
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29
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Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10:766. [PMID: 25432777 PMCID: PMC4299606 DOI: 10.15252/msb.20145645] [Citation(s) in RCA: 710] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.
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Affiliation(s)
- Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julien Tap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aurélien Amiot
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jürgen Böhm
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Brunetti
- Department of Surgery, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajna Hercog
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Koch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Alain Luciani
- Department of Radiology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Daniel R Mende
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin A Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christophe Tournigand
- Department of Medical Oncology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jeanne Tran Van Nhieu
- Department of Pathology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Takuji Yamada
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Jürgen Zimmermann
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Iradj Sobhani
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany
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Ladoukakis E, Kolisis FN, Chatziioannou AA. Integrative workflows for metagenomic analysis. Front Cell Dev Biol 2014; 2:70. [PMID: 25478562 PMCID: PMC4237130 DOI: 10.3389/fcell.2014.00070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/05/2014] [Indexed: 01/22/2023] Open
Abstract
The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e., Sanger). From a bioinformatic perspective, this boils down to many GB of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control, and annotation of metagenomic data, embracing various, major sequencing technologies and applications.
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Affiliation(s)
- Efthymios Ladoukakis
- Laboratory of Biotechnology, Department of Chemical Engineering, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, Department of Chemical Engineering, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Aristotelis A Chatziioannou
- Metabolic Engineering and Bioinformatics Program, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
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31
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An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014; 32:834-41. [DOI: 10.1038/nbt.2942] [Citation(s) in RCA: 1217] [Impact Index Per Article: 121.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/03/2014] [Indexed: 02/08/2023]
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32
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Morgan XC, Huttenhower C. Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology 2014; 146:1437-1448.e1. [PMID: 24486053 DOI: 10.1053/j.gastro.2014.01.049] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 12/16/2022]
Abstract
Nucleotide sequencing has become increasingly common and affordable, and is now a vital tool for studies of the human microbiome. Comprehensive microbial community surveys such as MetaHit and the Human Microbiome Project have described the composition and molecular functional profile of the healthy (normal) intestinal microbiome. This knowledge will increase our ability to analyze host and microbial DNA (genome) and RNA (transcriptome) sequences. Bioinformatic and statistical tools then can be used to identify dysbioses that might cause disease, and potential treatments. Analyses that identify perturbations in specific molecules can leverage thousands of culture-based isolate genomes to contextualize culture-independent sequences, or may integrate sequence data with whole-community functional assays such as metaproteomic or metabolomic analyses. We review the state of available systems-level models for studies of the intestinal microbiome, along with analytic techniques and tools that can be used to determine its functional capabilities in healthy and unhealthy individuals.
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Affiliation(s)
- Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts.
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Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME JOURNAL 2014; 8:1391-402. [PMID: 24621522 DOI: 10.1038/ismej.2014.30] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, 'Group 936 lactococcal phages' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage-host network of the human gut was established and includes numerous novel host-phage associations.
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Affiliation(s)
- Alison S Waller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Takuji Yamada
- Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama, Japan
| | - David M Kristensen
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eugene V Koonin
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Sharpton TJ. An introduction to the analysis of shotgun metagenomic data. FRONTIERS IN PLANT SCIENCE 2014; 5:209. [PMID: 24982662 PMCID: PMC4059276 DOI: 10.3389/fpls.2014.00209] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/29/2014] [Indexed: 05/19/2023]
Abstract
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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Affiliation(s)
- Thomas J. Sharpton
- *Correspondence: Thomas J. Sharpton, Department of Microbiology and Department of Statistics, Oregon State University, 220 Nash Hall, Corvallis, OR 97331, USA e-mail:
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Abstract
Recent findings have demonstrated that the gut microbiome complements our human genome with at least 100-fold more genes. In contrast to our Homo sapiens-derived genes, the microbiome is much more plastic, and its composition changes with age and diet, among other factors. An altered gut microbiota has been associated with several diseases, including obesity and diabetes, but the mechanisms involved remain elusive. Here we discuss factors that affect the gut microbiome, how the gut microbiome may contribute to metabolic diseases, and how to study the gut microbiome. Next-generation sequencing and development of software packages have led to the development of large-scale sequencing efforts to catalog the human microbiome. Furthermore, the use of genetically engineered gnotobiotic mouse models may increase our understanding of mechanisms by which the gut microbiome modulates host metabolism. A combination of classical microbiology, sequencing, and animal experiments may provide further insights into how the gut microbiota affect host metabolism and physiology.
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MESH Headings
- Animals
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/microbiology
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/microbiology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/microbiology
- Diet
- Disease Models, Animal
- Female
- Gastrointestinal Tract/metabolism
- Gastrointestinal Tract/microbiology
- Genetic Variation
- Germ-Free Life
- Humans
- Male
- Mice
- Microbiota/genetics
- Microbiota/physiology
- Obesity/genetics
- Obesity/metabolism
- Obesity/microbiology
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, RNA/methods
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Affiliation(s)
- Fredrik Karlsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valentina Tremaroli
- The Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Corresponding author: Fredrik Bäckhed,
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Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods 2013; 95:401-14. [PMID: 24029734 DOI: 10.1016/j.mimet.2013.08.011] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023]
Abstract
High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms. We also discuss commonly used and recently developed bioinformatic tools applied to microbiomes, including analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences. This field is relatively new and rapidly evolving, thus we hope that this review will provide a baseline for understanding these methods of microbiome analyses. Additionally, we seek to stimulate others to solve the many problems that still exist with the sensitivity, specificity and interpretation of high throughput microbiome sequence analysis.
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Affiliation(s)
- Julia M Di Bella
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
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37
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Accurate and universal delineation of prokaryotic species. Nat Methods 2013; 10:881-4. [PMID: 23892899 DOI: 10.1038/nmeth.2575] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/24/2013] [Indexed: 11/09/2022]
Abstract
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.
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Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol 2013; 9:666. [PMID: 23670539 PMCID: PMC4039370 DOI: 10.1038/msb.2013.22] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/03/2013] [Indexed: 12/16/2022] Open
Abstract
Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.
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Affiliation(s)
- Nicola Segata
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- Present address: Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Daniela Boernigen
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy L Tickle
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xochitl C Morgan
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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van Hijum SAFT, Vaughan EE, Vogel RF. Application of state-of-art sequencing technologies to indigenous food fermentations. Curr Opin Biotechnol 2013; 24:178-86. [DOI: 10.1016/j.copbio.2012.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/21/2022]
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40
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Sanli K, Karlsson FH, Nookaew I, Nielsen J. FANTOM: Functional and taxonomic analysis of metagenomes. BMC Bioinformatics 2013; 14:38. [PMID: 23375020 PMCID: PMC3566963 DOI: 10.1186/1471-2105-14-38] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/29/2013] [Indexed: 01/18/2023] Open
Abstract
Background Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. Results Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases. Conclusions The software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.
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Affiliation(s)
- Kemal Sanli
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE 412 96, Sweden
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41
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Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol 2013; 14:R2. [PMID: 23320958 PMCID: PMC4053804 DOI: 10.1186/gb-2013-14-1-r2] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 01/15/2013] [Indexed: 12/31/2022] Open
Abstract
We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS.
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42
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Desai DK, Schunck H, Löser JW, Laroche J. Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes. ACTA ACUST UNITED AC 2013; 29:790-1. [PMID: 23303511 DOI: 10.1093/bioinformatics/bts721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The sheer scale of the metagenomic and metatranscriptomic datasets that are now available warrants the development of automated protocols for organizing, annotating and comparing the samples in terms of their metabolic profiles. We describe a user-friendly java program FROMP (Fragment Recruitment on Metabolic Pathways) for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores, their relative Activity Scores or enzyme enrichment odds ratios. This program along with our fully configurable PERL-based annotation organization pipeline Meta2Pro (METAbolic PROfiling of META-omic data) offers a quick and accurate standalone solution for metabolic profiling of environmental samples or cultures from different treatments. Apart from pictorial comparisons, FROMP can also generate score matrices for multiple meta-omics samples, which can be used directly by other statistical programs.
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Affiliation(s)
- Dhwani K Desai
- Helmholtz Centre for Ocean Research Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel 24105, Germany.
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43
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Starovoitova SA. REVIEW OF INTERNATIONAL PROJECTS IN А FIELD OF HUMAN MICROBIAL ECOLOGY AND CONSTRUCTION OF PROBIOTICS. BIOTECHNOLOGIA ACTA 2013. [DOI: 10.15407/biotech6.03.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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44
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Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, Pavlenko AV, Kostryukova ES, Selezneva OV, Larin AK, Karpova IY, Alexeev DG. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. SOURCE CODE FOR BIOLOGY AND MEDICINE 2012; 7:13. [PMID: 23216677 PMCID: PMC3599743 DOI: 10.1186/1751-0473-7-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/27/2012] [Indexed: 11/10/2022]
Abstract
MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors’ knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from
http://hmpdacc.org). MALINA is made freely available on the web at
http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine of Russian Federal Medico-Biological Agency (RIPCM), Malaya Pirogovskaya 1a, Moscow, 119435, Russia.
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45
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Lawley B, Tannock GW. Nucleic acid-based methods to assess the composition and function of the bowel microbiota. Gastroenterol Clin North Am 2012; 41:855-68. [PMID: 23101691 DOI: 10.1016/j.gtc.2012.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This article describes nucleic acid-based methods to assess the composition and function of the bowel microbiota. The methods range from the relatively simple (polymerase chain reaction) to the technically sophisticated (metatranscriptomics). Not all are accessible to the majority of laboratories, but a core of validated (used in more than 1 study) tools is readily available to most researchers. Reliance on a single methodology per human study is not recommended. Generally, a study could commence with a screening of samples to determine whether it will be worthwhile expending further time and money on an in-depth analysis.
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Affiliation(s)
- Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Prakash T, Taylor TD. Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 2012; 13:711-27. [PMID: 22772835 PMCID: PMC3504928 DOI: 10.1093/bib/bbs033] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/26/2012] [Indexed: 12/14/2022] Open
Abstract
Metagenomic sequencing provides a unique opportunity to explore earth's limitless environments harboring scores of yet unknown and mostly unculturable microbes and other organisms. Functional analysis of the metagenomic data plays a central role in projects aiming to explore the most essential questions in microbiology, namely 'In a given environment, among the microbes present, what are they doing, and how are they doing it?' Toward this goal, several large-scale metagenomic projects have recently been conducted or are currently underway. Functional analysis of metagenomic data mainly suffers from the vast amount of data generated in these projects. The shear amount of data requires much computational time and storage space. These problems are compounded by other factors potentially affecting the functional analysis, including, sample preparation, sequencing method and average genome size of the metagenomic samples. In addition, the read-lengths generated during sequencing influence sequence assembly, gene prediction and subsequently the functional analysis. The level of confidence for functional predictions increases with increasing read-length. Usually, the most reliable functional annotations for metagenomic sequences are achieved using homology-based approaches against publicly available reference sequence databases. Here, we present an overview of the current state of functional analysis of metagenomic sequence data, bottlenecks frequently encountered and possible solutions in light of currently available resources and tools. Finally, we provide some examples of applications from recent metagenomic studies which have been successfully conducted in spite of the known difficulties.
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MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS One 2012; 7:e47656. [PMID: 23082188 PMCID: PMC3474746 DOI: 10.1371/journal.pone.0047656] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/13/2012] [Indexed: 11/30/2022] Open
Abstract
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.
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Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H. Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches. J Microbiol Methods 2012; 91:106-13. [DOI: 10.1016/j.mimet.2012.07.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 07/19/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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49
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Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert J, Meyer F. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics 2012; 13:183. [PMID: 22839106 PMCID: PMC3526449 DOI: 10.1186/1471-2105-13-183] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/13/2012] [Indexed: 11/17/2022] Open
Abstract
Background Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp) fragments containing sequence error from previously published artificial data and “real” metagenomic datasets. Results While gene prediction tools have similar accuracies predicting genes on error-free fragments, in the presence of sequencing errors considerable differences between tools become evident. For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal. This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50%) specificity and overprediction of genes in noncoding regions. Conclusions Ab initio gene callers offer a significant reduction in the computational burden of annotating individual nucleic acid reads and are used in many metagenomic annotation systems. For predicting reading frames on raw reads, we find the hidden Markov model approach in FragGeneScan is more sensitive than other gene prediction tools, while Prodigal, MGA, and MGM are better suited for higher-quality sequences such as assembled contigs.
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Affiliation(s)
- William L Trimble
- Computation Institute, University of Chicago, Chicago, IL 60637, USA.
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50
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Illeghems K, De Vuyst L, Papalexandratou Z, Weckx S. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity. PLoS One 2012; 7:e38040. [PMID: 22666442 PMCID: PMC3362557 DOI: 10.1371/journal.pone.0038040] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/01/2012] [Indexed: 01/08/2023] Open
Abstract
This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.
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Affiliation(s)
- Koen Illeghems
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Zoi Papalexandratou
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- * E-mail:
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