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Han W, Ye Y. A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019; 24:236-247. [PMID: 30864326 PMCID: PMC6417824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.
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MESH Headings
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/microbiology
- Carcinoma, Non-Small-Cell Lung/therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/microbiology
- Carcinoma, Renal Cell/therapy
- Computational Biology/methods
- Databases, Genetic
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/microbiology
- Genes, Microbial
- Genetic Markers
- Host Microbial Interactions/genetics
- Humans
- Immunotherapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/microbiology
- Kidney Neoplasms/therapy
- Liver Cirrhosis/genetics
- Liver Cirrhosis/microbiology
- Lung Neoplasms/genetics
- Lung Neoplasms/microbiology
- Lung Neoplasms/therapy
- Machine Learning
- Metagenomics/methods
- Metagenomics/statistics & numerical data
- Microbiota/genetics
- Phenotype
- Translational Research, Biomedical
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Affiliation(s)
- Wontack Han
- Computer Science Department, Indiana University, Bloomington, IN 47408, USA
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2
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Cheaib B, Le Boulch M, Mercier PL, Derome N. Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient. Front Microbiol 2018; 9:869. [PMID: 29774016 PMCID: PMC5943556 DOI: 10.3389/fmicb.2018.00869] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 04/16/2018] [Indexed: 11/29/2022] Open
Abstract
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Malo Le Boulch
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.,GenPhySE, Institut National de la Recherche Agronomique, Université de Toulouse, INPT, ENVT, Castanet-Tolosan, France
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
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3
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Gut Dysbiosis and Muscle Aging: Searching for Novel Targets against Sarcopenia. Mediators Inflamm 2018; 2018:7026198. [PMID: 29686533 PMCID: PMC5893006 DOI: 10.1155/2018/7026198] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Advanced age is characterized by several changes, one of which is the impairment of the homeostasis of intestinal microbiota. These alterations critically influence host health and have been associated with morbidity and mortality in older adults. “Inflammaging,” an age-related chronic inflammatory process, is a common trait of several conditions, including sarcopenia. Interestingly, imbalanced intestinal microbial community has been suggested to contribute to inflammaging. Changes in gut microbiota accompanying sarcopenia may be attenuated by supplementation with pre- and probiotics. Although muscle aging has been increasingly recognized as a biomarker of aging, the pathophysiology of sarcopenia is to date only partially appreciated. Due to its development in the context of the age-related inflammatory milieu, several studies favor the hypothesis of a tight connection between sarcopenia and inflammaging. However, conclusive evidence describing the signaling pathways involved has not yet been produced. Here, we review the current knowledge of the changes in intestinal microbiota that occur in advanced age with a special emphasis on findings supporting the idea of a modulation of muscle physiology through alterations in gut microbial composition and activity.
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Fondi M, Karkman A, Tamminen MV, Bosi E, Virta M, Fani R, Alm E, McInerney JO. "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis. Genome Biol Evol 2016; 8:1388-400. [PMID: 27190206 PMCID: PMC4898794 DOI: 10.1093/gbe/evw077] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
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Affiliation(s)
- Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy
| | - Antti Karkman
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Manu V Tamminen
- Department of Environmental Systems Science, ETH Zürich, Switzerland Department of Aquatic Ecology, Eawag, Switzerland
| | - Emanuele Bosi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy
| | - Marko Virta
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy
| | - Eric Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
| | - James O McInerney
- Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland Computational Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, United Kingdom
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5
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Schwende I, Pham TD. Pattern recognition and probabilistic measures in alignment-free sequence analysis. Brief Bioinform 2013; 15:354-68. [PMID: 24096012 DOI: 10.1093/bib/bbt070] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
With the massive production of genomic and proteomic data, the number of available biological sequences in databases has reached a level that is not feasible anymore for exact alignments even when just a fraction of all sequences is used. To overcome this inevitable time complexity, ultrafast alignment-free methods are studied. Within the past two decades, a broad variety of nonalignment methods have been proposed including dissimilarity measures on classical representations of sequences like k-words or Markov models. Furthermore, articles were published that describe distance measures on alternative representations such as compression complexity, spectral time series or chaos game representation. However, alignments are still the standard method for real world applications in biological sequence analysis, and the time efficient alignment-free approaches are usually applied in cases when the accustomed algorithms turn out to fail or be too inconvenient.
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Affiliation(s)
- Isabel Schwende
- PhD, Aizu Research Cluster for Medical Informatics and Engineering (ARC-Medical), Research Center for Advanced Information Science and Technology (CAIST), The University of Aizu, Aizuwakamatsu, Fukushima 965-8580, Japan.
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Aminov RI. Horizontal gene exchange in environmental microbiota. Front Microbiol 2011; 2:158. [PMID: 21845185 PMCID: PMC3145257 DOI: 10.3389/fmicb.2011.00158] [Citation(s) in RCA: 351] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/11/2011] [Indexed: 01/21/2023] Open
Abstract
Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.
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Affiliation(s)
- Rustam I Aminov
- Rowett Institute of Nutrition and Health, University of Aberdeen Aberdeen, UK
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Liu X, Wan L, Li J, Reinert G, Waterman MS, Sun F. New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J Theor Biol 2011; 284:106-16. [PMID: 21723298 DOI: 10.1016/j.jtbi.2011.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 05/30/2011] [Accepted: 06/17/2011] [Indexed: 12/15/2022]
Abstract
Alignment-free sequence comparison is widely used for comparing gene regulatory regions and for identifying horizontally transferred genes. Recent studies on the power of a widely used alignment-free comparison statistic D2 and its variants D*2 and D(s)2 showed that their power approximates a limit smaller than 1 as the sequence length tends to infinity under a pattern transfer model. We develop new alignment-free statistics based on D2, D*2 and D(s)2 by comparing local sequence pairs and then summing over all the local sequence pairs of certain length. We show that the new statistics are much more powerful than the corresponding statistics and the power tends to 1 as the sequence length tends to infinity under the pattern transfer model.
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Affiliation(s)
- Xuemei Liu
- School of Physics, South China University of Technology, Guangzhou, PR China
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8
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Silveira CB, Vieira RP, Cardoso AM, Paranhos R, Albano RM, Martins OB. Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean. PLoS One 2011; 6:e17789. [PMID: 21408023 PMCID: PMC3052384 DOI: 10.1371/journal.pone.0017789] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 02/09/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. CONCLUSIONS/SIGNIFICANCE Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.
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Affiliation(s)
- Cynthia B. Silveira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo P. Vieira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexander M. Cardoso
- Instituto Nacional de Metrologia
Normalização e Qualidade Industrial, Rio de Janeiro,
Brazil
- * E-mail:
| | - Rodolfo Paranhos
- Instituto de Biologia, Universidade Federal do
Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica,
Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando B. Martins
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Weng FC, Su CH, Hsu MT, Wang TY, Tsai HK, Wang D. Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency. BMC Bioinformatics 2010; 11:565. [PMID: 21083935 PMCID: PMC3098102 DOI: 10.1186/1471-2105-11-565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 11/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies. RESULTS Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach. CONCLUSIONS Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.
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Affiliation(s)
- Francis C Weng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A. Environmental distribution of prokaryotic taxa. BMC Microbiol 2010; 10:85. [PMID: 20307274 PMCID: PMC2850351 DOI: 10.1186/1471-2180-10-85] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/22/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. RESULTS We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. CONCLUSIONS This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.
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Affiliation(s)
- Javier Tamames
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
- Centro Nacional de Biotecnología (CNB-CSIC). C/Darwin 3, 28049 Madrid, Spain
| | - Juan José Abellán
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Miguel Pignatelli
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Antonio Camacho
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva y Departamento de Microbiología y Ecología Universidad de Valencia. C/Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
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Impacts of Forest Conversion to Agriculture on Microbial Communities and Microbial Function. SOIL BIOLOGY 2010. [DOI: 10.1007/978-3-642-05076-3_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A 2009; 107:127-32. [PMID: 20007769 DOI: 10.1073/pnas.0908978107] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA flows between chromosomes and mobile elements, following rules that are poorly understood. This limited knowledge is partly explained by the limits of current approaches to study the structure and evolution of genetic diversity. Network analyses of 119,381 homologous DNA families, sampled from 111 cellular genomes and from 165,529 phage, plasmid, and environmental virome sequences, offer challenging insights. Our results support a disconnected yet highly structured network of genetic diversity, revealing the existence of multiple "genetic worlds." These divides define multiple isolated groups of DNA vehicles drawing on distinct gene pools. Mathematical studies of the centralities of these worlds' subnetworks demonstrate that plasmids, not viruses, were key vectors of genetic exchange between bacterial chromosomes, both recently and in the past. Furthermore, network methodology introduces new ways of quantifying current sampling of genetic diversity.
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Hooper SD, Mavromatis K, Kyrpides NC. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol 2009; 10:R45. [PMID: 19393086 PMCID: PMC2688936 DOI: 10.1186/gb-2009-10-4-r45] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 04/01/2009] [Accepted: 04/24/2009] [Indexed: 01/10/2023] Open
Abstract
Interactions between microbial communities are revealed using a network of lateral gene transfer events. Background Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with? Results All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections. Conclusions We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.
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Affiliation(s)
- Sean D Hooper
- Department of Energy Joint Genome Institute, Genome Biology Program, Mitchell Drive, Walnut Creek, CA 94598, USA.
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Wooley JC, Ye Y. Metagenomics: Facts and Artifacts, and Computational Challenges*. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 2009; 25:71-81. [PMID: 20648230 PMCID: PMC2905821 DOI: 10.1007/s11390-010-9306-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.
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Affiliation(s)
- John C. Wooley
- Center for Research on BioSystems, Calit2, UC San Diego, La Jolla CA 92093
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408
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15
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