1901
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Bolaños LM, Rosenblueth M, Castillo-Ramírez S, Figuier-Huttin G, Martínez-Romero E. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota. Environ Microbiol 2015; 18:1364-78. [PMID: 26058415 DOI: 10.1111/1462-2920.12939] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/31/2015] [Indexed: 01/20/2023]
Abstract
Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species.
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Affiliation(s)
- Luis M Bolaños
- Programa de Ecología Genómica y, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Mónica Rosenblueth
- Programa de Ecología Genómica y, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Gilles Figuier-Huttin
- Programa de Ecología Genómica y, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica y, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
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1902
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Abstract
We report the complete mitochondrial genome sequence of the Mediterranean glass sponge Oopsacas minuta. This 19-kb mitochondrial genome has 24 noncoding genes (22 tRNAs and 2 rRNAs) and 14 protein-encoding genes coding for 11 subunits of respiratory chain complexes and 3 ATP synthase subunits.
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1903
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Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL, Banfield JF. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015; 17:4929-41. [DOI: 10.1111/1462-2920.12936] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Rose S. Kantor
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
| | - A. Wynand van Zyl
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Robert P. van Hille
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Brian C. Thomas
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
| | - Susan T. L. Harrison
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
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1904
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Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, Banfield JF. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol 2015; 18:159-73. [DOI: 10.1111/1462-2920.12930] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Laura A. Hug
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Itai Sharon
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | | | - Ritin Sharma
- Oak Ridge National Laboratory; Oak Ridge; TN USA
| | | | - Michael J. Wilkins
- Department of Microbiology; Ohio State University; Columbus OH USA
- School of Earth Sciences; Ohio State University; Columbus OH USA
| | - Kenneth H. Williams
- Department of Geophysics, Division of Earth Sciences; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Andrea Singh
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
- Department of Environmental Science, Policy, and Management; UC Berkeley; Berkeley CA USA
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1905
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Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife 2015. [PMID: 26200428 PMCID: PMC4533152 DOI: 10.7554/elife.08490] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI:http://dx.doi.org/10.7554/eLife.08490.001 Viruses are infectious particles that can only multiply inside the cells of microbes and other organisms. Little is known about the genetic differences between virus particles (so-called ‘genetic diversity’), especially compared to what we know about the diversity of bacteria, archaea, and other single-celled microbes. This lack of knowledge hampers our understanding of the role viruses play in the evolution of microbial communities and their associated ecosystems. Studying the genetics of the viruses in these communities is challenging. There is no single ‘marker’ gene that can be used to identify all viruses in environmental samples. Also, many of the fragments of viral genomes that have been identified have not yet been linked to their host microbes. Many viruses integrate their genome into the DNA of their host cell, and there are computational tools available that exploit this ability to identify viruses and link them to their host. However, other viruses can live and multiply inside cells without integrating their genome into the host's DNA. Earlier in 2015, researchers developed a new computational tool called VirSorter that can predict virus genome sequences within the DNA extracted from microbes. VirSorter identifies viral genome sequences based on the presence of ‘hallmark’ genes that encode for components found in many virus particles, together with a reference database of genomes from many viruses. Now, Roux et al.—including some of the researchers from the earlier work—use VirSorter to predict viral DNA from publicly available bacteria and archaea genome data. The study identifies over 12,000 viral genomes and links them to their microbial hosts. These data increase the number of viral genome sequences that are publically available by a factor of ten and identify the first viruses associated with 13 new types of bacteria, which include species that are abundant in particular environments. It is possible for several different viruses to infect a single cell at the same time. Some viruses are known to be able to exchange DNA, and if this happens frequently in other viruses, it could have a big impact on how viruses evolve. Roux et al.'s findings suggest that although it is common for several different viruses to infect the same cell, it is relatively rare for these viruses to exchange genetic material. Roux et al.'s findings demonstrate the value of searching publicly available microbial genome data for fragments of viral genomes. These new viral genomes will serve as a useful resource for researchers as they explore the communities of viruses and microbes in natural environments, the human body and in industrial processes. DOI:http://dx.doi.org/10.7554/eLife.08490.002
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Affiliation(s)
- Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Tanja Woyke
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
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1906
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Nelson WC, Stegen JC. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Front Microbiol 2015; 6:713. [PMID: 26257709 PMCID: PMC4508563 DOI: 10.3389/fmicb.2015.00713] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/29/2015] [Indexed: 11/21/2022] Open
Abstract
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.
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Affiliation(s)
- William C Nelson
- Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - James C Stegen
- Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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1907
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Kim Y, Aw TG, Teal TK, Rose JB. Metagenomic Investigation of Viral Communities in Ballast Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:8396-407. [PMID: 26107908 DOI: 10.1021/acs.est.5b01633] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.
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Affiliation(s)
- Yiseul Kim
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tiong Gim Aw
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tracy K Teal
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joan B Rose
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
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1908
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Aguado MT, Glasby CJ, Schroeder PC, Weigert A, Bleidorn C. The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata. Sci Rep 2015; 5:12072. [PMID: 26183383 PMCID: PMC4505326 DOI: 10.1038/srep12072] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/12/2015] [Indexed: 12/13/2022] Open
Abstract
Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis.
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Affiliation(s)
- M. Teresa Aguado
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Christopher J. Glasby
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, N.T., Australia
| | - Paul C. Schroeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99163-4236, USA
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
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1909
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Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L. Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children. EBioMedicine 2015; 2:968-84. [PMID: 26425705 PMCID: PMC4563136 DOI: 10.1016/j.ebiom.2015.07.007] [Citation(s) in RCA: 287] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation. RESEARCH IN CONTEXT Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader-Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.
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Affiliation(s)
- Chenhong Zhang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aihua Yin
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Hongde Li
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruirui Wang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guojun Wu
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Shen
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaping Hou
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Haimei Ouyang
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yan Zhang
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yinan Zheng
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jicheng Wang
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Xiaofei Lv
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Zhang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Wenxia Li
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Feiyan Yan
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yufeng Zhao
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaqing Fu
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Chen
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Naisi Zhao
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bruce R Hamaker
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ; Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Laura C Bridgewater
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ; Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - David Weinkove
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Karine Clement
- Institut of cardiometabolism and Nutrition, Pitié-Salpêtrière, Paris, France
| | - Joel Dore
- Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Elaine Holmes
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Huasheng Xiao
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Shang Biochip Company, Shanghai 201203, China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Shang Biochip Company, Shanghai 201203, China
| | - Shengli Yang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jeremy K Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Huiru Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaozhuang Zhang
- Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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1910
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Metagenomic Assembly and Draft Genome Sequence of an Uncharacterized Prevotella sp. from Nelore Rumen. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00723-15. [PMID: 26159527 PMCID: PMC4498113 DOI: 10.1128/genomea.00723-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore. We report the draft genome sequence of Prevotella sp., comprising 2,971,040 bp, obtained using the Illumina sequencing platform. This genome includes 127 contigs and presents a low 48% GC.
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1911
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Kinjo Y, Saitoh S, Tokuda G. An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. Microbes Environ 2015; 30:208-20. [PMID: 26156552 PMCID: PMC4567559 DOI: 10.1264/jsme2.me14153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Whole-genome sequencing has emerged as one of the most effective means to elucidate the biological roles and molecular features of obligate intracellular symbionts (endosymbionts). However, the de novo assembly of an endosymbiont genome remains a challenge when host and/or mitochondrial DNA sequences are present in a dataset and hinder the assembly of the genome. By focusing on the traits of genome evolution in endosymbionts, we herein developed and investigated a genome-assembly strategy that consisted of two consecutive procedures: the selection of endosymbiont contigs from an output obtained from a de novo assembly performed using a TBLASTX search against a reference genome, named TBLASTX Contig Selection and Filtering (TCSF), and the iterative reassembling of the genome from reads mapped on the selected contigs, named Iterative Mapping and ReAssembling (IMRA), to merge the contigs. In order to validate this approach, we sequenced two strains of the cockroach endosymbiont Blattabacterium cuenoti and applied this strategy to the datasets. TCSF was determined to be highly accurate and sensitive in contig selection even when the genome of a distantly related free-living bacterium was used as a reference genome. Furthermore, the use of IMRA markedly improved sequence assemblies: the genomic sequence of an endosymbiont was almost completed from a dataset containing only 3% of the sequences of the endosymbiont’s genome. The efficiency of our strategy may facilitate further studies on endosymbionts.
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Affiliation(s)
- Yukihiro Kinjo
- Tropical Biosphere Research Center, University of the Ryukyus
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1912
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Bolduc B, Wirth JF, Mazurie A, Young MJ. Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis. ISME JOURNAL 2015; 9:2162-77. [PMID: 26125684 DOI: 10.1038/ismej.2015.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 12/29/2014] [Accepted: 01/12/2015] [Indexed: 01/31/2023]
Abstract
Understanding of viral assemblage structure in natural environments remains a daunting task. Total viral assemblage sequencing (for example, viral metagenomics) provides a tractable approach. However, even with the availability of next-generation sequencing technology it is usually only possible to obtain a fragmented view of viral assemblages in natural ecosystems. In this study, we applied a network-based approach in combination with viral metagenomics to investigate viral assemblage structure in the high temperature, acidic hot springs of Yellowstone National Park, USA. Our results show that this approach can identify distinct viral groups and provide insights into the viral assemblage structure. We identified 110 viral groups in the hot springs environment, with each viral group likely representing a viral family at the sub-family taxonomic level. Most of these viral groups are previously unknown DNA viruses likely infecting archaeal hosts. Overall, this study demonstrates the utility of combining viral assemblage sequencing approaches with network analysis to gain insights into viral assemblage structure in natural ecosystems.
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Affiliation(s)
- Benjamin Bolduc
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA.,Department of Plant Sciences and Plant Pathology and, Montana State University, Bozeman, MT, USA
| | - Jennifer F Wirth
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA.,Department of Plant Sciences and Plant Pathology and, Montana State University, Bozeman, MT, USA
| | - Aurélien Mazurie
- Bioinformatics Core Facility, Montana State University, Bozeman, MT, USA
| | - Mark J Young
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA.,Department of Plant Sciences and Plant Pathology and, Montana State University, Bozeman, MT, USA
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1913
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Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJC, Chiu KP. Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy. PLoS One 2015; 10:e0130673. [PMID: 26125617 PMCID: PMC4488429 DOI: 10.1371/journal.pone.0130673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/24/2015] [Indexed: 11/18/2022] Open
Abstract
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.
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Affiliation(s)
- Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
| | - Mohit Midha
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Tai Wang
- National Center for High-Performance Computing, Hsinchu, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, United States of America
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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1914
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Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015; 24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
Abstract
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
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Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern, 3005, Switzerland
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Timothee Cezard
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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1915
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Alkema W, Boekhorst J, Wels M, van Hijum SAFT. Microbial bioinformatics for food safety and production. Brief Bioinform 2015; 17:283-92. [PMID: 26082168 PMCID: PMC4793891 DOI: 10.1093/bib/bbv034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
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1916
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Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 2015; 523:208-11. [PMID: 26083755 DOI: 10.1038/nature14486] [Citation(s) in RCA: 727] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/10/2015] [Indexed: 02/04/2023]
Abstract
A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.
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1917
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Bikel S, Valdez-Lara A, Cornejo-Granados F, Rico K, Canizales-Quinteros S, Soberón X, Del Pozo-Yauner L, Ochoa-Leyva A. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J 2015; 13:390-401. [PMID: 26137199 PMCID: PMC4484546 DOI: 10.1016/j.csbj.2015.06.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/07/2023] Open
Abstract
The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.
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Affiliation(s)
- Shirley Bikel
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Alejandra Valdez-Lara
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Fernanda Cornejo-Granados
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Karina Rico
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., Mexico
| | | | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
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1918
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Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Curr Microbiol 2015; 71:296-302. [PMID: 26044993 PMCID: PMC4486115 DOI: 10.1007/s00284-015-0846-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022]
Abstract
Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases.
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1919
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Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME JOURNAL 2015; 10:225-39. [PMID: 26046257 DOI: 10.1038/ismej.2015.81] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/05/2015] [Accepted: 04/09/2015] [Indexed: 11/08/2022]
Abstract
Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.
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1920
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Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00585-15. [PMID: 26044431 PMCID: PMC4457068 DOI: 10.1128/genomea.00585-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve as sources of future industrial enzymes.
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1921
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Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. Lifestyle evolution in cyanobacterial symbionts of sponges. mBio 2015; 6:e00391-15. [PMID: 26037118 PMCID: PMC4453008 DOI: 10.1128/mbio.00391-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/30/2015] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED The "Candidatus Synechococcus spongiarum" group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a "Ca. Synechococcus spongiarum" group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, "Ca. Synechococcus spongiarum" includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of "Ca. Synechococcus spongiarum," each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of "Ca. Synechococcus spongiarum" members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the "Ca. Synechococcus spongiarum" group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack. IMPORTANCE While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world's oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, "Candidatus Synechococcus spongiarum," was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt "Ca. Synechococcus spongiarum" to its life within the sponge host.
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Affiliation(s)
- Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Beate M Slaby
- Department of Botany II, Julius-von-Sachs Institute for Biosciences, University of Würzburg, Würzburg, Germany
| | - Kim M Handley
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jochen Blom
- Bioinformatics and System Biology Justus-Liebig-University, Giessen, Giessen, Germany
| | - Christopher W Marshall
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, Illinois, USA
| | | | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biosciences, University of Würzburg, Würzburg, Germany
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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1922
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Al Rwahnih M, Daubert S, Golino D, Islas C, Rowhani A. Comparison of Next-Generation Sequencing Versus Biological Indexing for the Optimal Detection of Viral Pathogens in Grapevine. PHYTOPATHOLOGY 2015; 105:758-63. [PMID: 25689518 DOI: 10.1094/phyto-06-14-0165-r] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A bioassay is routinely used to determine the viral phytosanitary status of commercial grapevine propagation material in many countries around the world. That test is based on the symptoms developed in the field by specific indicator host plants that are graft-inoculated from the vines being tested. We compared the bioassay against next-generation sequencing (NGS) analysis of grapevine material. NGS is a laboratory procedure that catalogs the genomic sequences of the viruses and other pathogens extracted as DNA and RNA from infected vines. NGS analysis was found to be superior to the standard bioassay in detection of viruses of agronomic significance, including virus infections at low titers. NGS was also found to be superior to the bioassay in its comprehensiveness, the speed of its analysis, and for the discovery of novel, uncharacterized viruses.
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Affiliation(s)
- Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis 95616
| | - Steve Daubert
- Department of Plant Pathology, University of California, Davis 95616
| | - Deborah Golino
- Department of Plant Pathology, University of California, Davis 95616
| | - Christina Islas
- Department of Plant Pathology, University of California, Davis 95616
| | - Adib Rowhani
- Department of Plant Pathology, University of California, Davis 95616
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1923
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Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PSG, Huang LN, Shu WS. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. THE ISME JOURNAL 2015; 9:1280-94. [PMID: 25361395 PMCID: PMC4438317 DOI: 10.1038/ismej.2014.212] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 07/21/2014] [Accepted: 09/21/2014] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Yu-Jiao Han
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Lin-Xing Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Min Hu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Sheng-Jin Li
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Jia-Liang Kuang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Patrick SG Chain
- Metagenomics Applications Team, Genome Science Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
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1924
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Aguirre de Cárcer D, López-Bueno A, Pearce DA, Alcamí A. Biodiversity and distribution of polar freshwater DNA viruses. SCIENCE ADVANCES 2015; 1:e1400127. [PMID: 26601189 PMCID: PMC4640604 DOI: 10.1126/sciadv.1400127] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 05/05/2015] [Indexed: 05/29/2023]
Abstract
Viruses constitute the most abundant biological entities and a large reservoir of genetic diversity on Earth. Despite the recent surge in their study, our knowledge on their actual biodiversity and distribution remains sparse. We report the first metagenomic analysis of Arctic freshwater viral DNA communities and a comparative analysis with other freshwater environments. Arctic viromes are dominated by unknown and single-stranded DNA viruses with no close relatives in the database. These unique viral DNA communities mostly relate to each other and present some minor genetic overlap with other environments studied, including an Arctic Ocean virome. Despite common environmental conditions in polar ecosystems, the Arctic and Antarctic DNA viromes differ at the fine-grain genetic level while sharing a similar taxonomic composition. The study uncovers some viral lineages with a bipolar distribution, suggesting a global dispersal capacity for viruses, and seemingly indicates that viruses do not follow the latitudinal diversity gradient known for macroorganisms. Our study sheds light into the global biogeography and connectivity of viral communities.
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Affiliation(s)
- Daniel Aguirre de Cárcer
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - David A. Pearce
- British Antarctic Survey, Natural Environment Research Council, Cambridge CB3 0ET, UK
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne NE1 8ST, UK
- University Centre in Svalbard, Longyearbyen N-9171, Norway
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas–Universidad Autónoma de Madrid, Madrid 28049, Spain
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1925
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Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ 2015; 3:e985. [PMID: 26038737 PMCID: PMC4451026 DOI: 10.7717/peerj.985] [Citation(s) in RCA: 729] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona , USA
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand , France ; CNRS UMR 6023, LMGE , Aubière , France
| | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona , USA
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1926
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Abstract
Single-cell sequencing (SCS) has emerged as a powerful new set of technologies for studying rare cells and delineating complex populations. Over the past 5 years, SCS methods for DNA and RNA have had a broad impact on many diverse fields of biology, including microbiology, neurobiology, development, tissue mosaicism, immunology, and cancer research. In this review, we will discuss SCS technologies and applications, as well as translational applications in the clinic.
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Affiliation(s)
- Yong Wang
- Department of Genetics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas E Navin
- Department of Genetics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.
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1927
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Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00490-15. [PMID: 25999577 PMCID: PMC4440957 DOI: 10.1128/genomea.00490-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Anoxybacillus thermarum AF/04T was isolated from the Euganean hot springs in Abano Terme, Italy. The present work reports a high-quality draft genome sequence of strain AF/04T. This work also provides useful insights into glycoside hydrolases, glycoside transferases, and sugar transporters that may be involved in cellular carbohydrate metabolism.
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1928
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Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. Bioinformatics 2015; 31:2972-80. [PMID: 25995232 DOI: 10.1093/bioinformatics/btv311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/13/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. RESULTS We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. AVAILABILITY AND IMPLEMENTATION Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs CONTACT stelo@cs.ucr.edu or timothy.close@ucr.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefano Lonardi
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Hamid Mirebrahim
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Steve Wanamaker
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Alpert
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Gianfranco Ciardo
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Denisa Duma
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy J Close
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
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1929
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Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00457-15. [PMID: 25977433 PMCID: PMC4432339 DOI: 10.1128/genomea.00457-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium.
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1930
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Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015; 32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Matthew L Gimmel
- Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic
| | | | - Timothy D Cockerill
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chey Vun Khen
- Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
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1931
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Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights 2015; 9:75-88. [PMID: 25983555 PMCID: PMC4426941 DOI: 10.4137/bbi.s12462] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 12/14/2022] Open
Abstract
Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.
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Affiliation(s)
- Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
- Department of Biology, University of Ghent, Ghent, Belgium
- Department of Microbial Ecophysiology, University of Bremen, Bremen, Germany
| | - Paraskevi Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Georgios A Pavlopoulos
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
| | - Nikolas Papanikolaou
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ioannis Iliopoulos
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
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1932
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Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res 2015; 43:5331-9. [PMID: 25940625 PMCID: PMC4477656 DOI: 10.1093/nar/gkv424] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres’ tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms.
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Affiliation(s)
- Nelle Varoquaux
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré 77300 Fontainebleau, France Institut Curie, Paris, F-75248, France U900, INSERM, Paris, F-75248, France
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Joshua N Burton
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Jean-Philippe Vert
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré 77300 Fontainebleau, France Institut Curie, Paris, F-75248, France U900, INSERM, Paris, F-75248, France
| | - William S Noble
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
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1933
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Metagenome sequencing of a coastal marine microbial community from monterey bay, california. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00341-15. [PMID: 25931598 PMCID: PMC4417694 DOI: 10.1128/genomea.00341-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. We present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.
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1934
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Flot JF, Marie-Nelly H, Koszul R. Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Lett 2015; 589:2966-74. [PMID: 25935414 DOI: 10.1016/j.febslet.2015.04.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 12/12/2022]
Abstract
High-throughput DNA sequencing technologies are fuelling an accelerating trend to assemble de novo or resequence the genomes of numerous species as well as to complete unfinished assemblies. While current DNA sequencing technologies remain limited to reading stretches of a few hundreds or thousands of base pairs, experimental and computational methods are continuously improving with the goal of assembling entire genomes from large numbers of short DNA sequences. However, the algorithms that piece together DNA strands face important limitations due, notably, to the presence of repeated sequences or of multiple haplotypes within one genome, thus leaving many assemblies incomplete. Recently, the realization that the physical contacts experienced by a portion of a DNA molecule could be used as a robust and quantitative assay to determine its genomic position has led to the emerging field of contact genomics, which promises to revolutionize current genome assembly approaches by exploiting the flexible polymer properties of chromosomes. Here we review the current applications of contact genomics to genome scaffolding, haplotyping and metagenomic assembly, then outline the future developments we envision.
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Affiliation(s)
- Jean-François Flot
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Hervé Marie-Nelly
- Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France.
| | - Romain Koszul
- Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France.
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1935
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Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME JOURNAL 2015; 9:2697-711. [PMID: 25918833 DOI: 10.1038/ismej.2015.66] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects.
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1936
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Urbieta MS, Donati ER, Chan KG, Shahar S, Sin LL, Goh KM. Thermophiles in the genomic era: Biodiversity, science, and applications. Biotechnol Adv 2015; 33:633-47. [PMID: 25911946 DOI: 10.1016/j.biotechadv.2015.04.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/18/2014] [Accepted: 04/14/2015] [Indexed: 01/30/2023]
Abstract
Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.
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Affiliation(s)
- M Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Edgardo R Donati
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saleha Shahar
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Lee Li Sin
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia.
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1937
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Abstract
The current genomic revolution was made possible by joint advances in genome sequencing technologies and computational approaches for analyzing sequence data. The close interaction between biologists and computational scientists is perhaps most apparent in the development of approaches for sequencing entire genomes, a feat that would not be possible without sophisticated computational tools called genome assemblers (short for genome sequence assemblers). Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago.
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Affiliation(s)
- Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
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1938
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Abstract
UNLABELLED Many bacteria rely on CRISPR-Cas systems to provide adaptive immunity against phages, predation by which can shape the ecology and functioning of microbial communities. To characterize the impact of CRISPR immunization on phage genome evolution, we performed long-term bacterium-phage (Streptococcus thermophilus-phage 2972) coevolution experiments. We found that in this species, CRISPR immunity drives fixation of single nucleotide polymorphisms that accumulate exclusively in phage genome regions targeted by CRISPR. Mutation rates in phage genomes highly exceed those of the host. The presence of multiple phages increased phage persistence by enabling recombination-based formation of chimeric phage genomes in which sequences heavily targeted by CRISPR were replaced. Collectively, our results establish CRISPR-Cas adaptive immunity as a key driver of phage genome evolution under the conditions studied and highlight the importance of multiple coexisting phages for persistence in natural systems. IMPORTANCE Phages remain an enigmatic part of the biosphere. As predators, they challenge the survival of host bacteria and archaea and set off an "arms race" involving host immunization countered by phage mutation. The CRISPR-Cas system is adaptive: by capturing fragments of a phage genome upon exposure, the host is positioned to counteract future infections. To investigate this process, we initiated massive deep-sequencing experiments with a host and infective phage and tracked the coevolution of both populations over hundreds of days. In the present study, we found that CRISPR immunity drives the accumulation of phage genome rearrangements (which enable longer phage survival) and escape mutations, establishing CRISPR as one of the fundamental drivers of phage evolution.
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1939
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Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 2015; 6:mBio.00231-15. [PMID: 25873374 PMCID: PMC4453556 DOI: 10.1128/mbio.00231-15] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A mechanistic understanding of the purported health benefits conferred by consumption of probiotic bacteria has been limited by our knowledge of the resident gut microbiota and its interaction with the host. Here, we detail the impact of a single-organism probiotic, Lactobacillus rhamnosus GG ATCC 53103 (LGG), on the structure and functional dynamics (gene expression) of the gut microbiota in a study of 12 healthy individuals, 65 to 80 years old. The analysis revealed that while the overall community composition was stable as assessed by 16S rRNA profiling, the transcriptional response of the gut microbiota was modulated by probiotic treatment. Comparison of transcriptional profiles based on taxonomic composition yielded three distinct transcriptome groups that displayed considerable differences in functional dynamics. The transcriptional profile of LGG in vivo was remarkably concordant across study subjects despite the considerable interindividual nature of the gut microbiota. However, we identified genes involved in flagellar motility, chemotaxis, and adhesion from Bifidobacterium and the dominant butyrate producers Roseburia and Eubacterium whose expression was increased during probiotic consumption, suggesting that LGG may promote interactions between key constituents of the microbiota and the host epithelium. These results provide evidence for the discrete functional effects imparted by a specific single-organism probiotic and challenge the prevailing notion that probiotics substantially modify the resident microbiota within nondiseased individuals in an appreciable fashion. Probiotic bacteria have been used for over a century to promote digestive health. Many individuals report that probiotics alleviate a number of digestive issues, yet little evidence links how probiotic microbes influence human health. Here, we show how the resident microbes that inhabit the healthy human gut respond to a probiotic. The well-studied probiotic Lactobacillus rhamnosus GG ATCC 53103 (LGG) was administered in a clinical trial, and a suite of measurements of the resident microbes were taken to evaluate potential changes over the course of probiotic consumption. We found that LGG transiently enriches for functions to potentially promote anti-inflammatory pathways in the resident microbes.
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1940
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Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol 2015; 18:1686-703. [DOI: 10.1111/1462-2920.12817] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne B. Emerson
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Walter Alvarez
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
- Department of Environmental Science, Policy, and Management; University of California, Berkeley; Berkeley CA 94720-4767 USA
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1941
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Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 2015; 25:534-43. [PMID: 25665577 PMCID: PMC4381525 DOI: 10.1101/gr.183012.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/06/2015] [Indexed: 01/18/2023]
Abstract
Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.
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Affiliation(s)
- Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Michael Kertesz
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Laura A Hug
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Dmitry Pushkarev
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | | | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Mojgan Amirebrahimi
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Susannah G Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA; Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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1942
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Chandler JA, Liu RM, Bennett SN. RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi. Front Microbiol 2015; 6:185. [PMID: 25852655 PMCID: PMC4371751 DOI: 10.3389/fmicb.2015.00185] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/19/2015] [Indexed: 01/09/2023] Open
Abstract
Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS) approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis) collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host-group specificity among disparate viral taxa. Interestingly, we identified a Narnavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with a specific host.
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Affiliation(s)
- James Angus Chandler
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
| | - Rachel M Liu
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
| | - Shannon N Bennett
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
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1943
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Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00132-15. [PMID: 25792053 PMCID: PMC4395064 DOI: 10.1128/genomea.00132-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.
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1944
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Roux S, Enault F, Ravet V, Pereira O, Sullivan MB. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Front Microbiol 2015; 6:199. [PMID: 25852662 PMCID: PMC4360716 DOI: 10.3389/fmicb.2015.00199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics (viromics) is a tremendous tool to reveal viral taxonomic and functional diversity across ecosystems ranging from the human gut to the world's oceans. As with microbes however, there appear vast swaths of “dark matter” yet to be documented for viruses, even among relatively well-studied viral types. Here, we use viromics to explore the “Far-T4 phages” sequence space, a neighbor clade from the well-studied T4-like phages that was first detected through PCR study in seawater and subsequently identified in freshwater lakes through 454-sequenced viromes. To advance the description of these viruses beyond this single marker gene, we explore Far-T4 genome fragments assembled from two deeply-sequenced freshwater viromes. Single gene phylogenetic trees confirm that the Far-T4 phages are divergent from the T4-like phages, genome fragments reveal largely collinear genome organizations, and both data led to the delineation of five Far-T4 clades. Three-dimensional models of major capsid proteins are consistent with a T4-like structure, and highlight a highly conserved core flanked by variable insertions. Finally, we contextualize these now better characterized Far-T4 phages by re-analyzing 196 previously published viromes. These suggest that Far-T4 are common in freshwater and seawater as only four of 82 aquatic viromes lacked Far-T4-like sequences. Variability in representation across the five newly identified clades suggests clade-specific niche differentiation may be occurring across the different biomes, though the underlying mechanism remains unidentified. While complete genome assembly from complex communities and the lack of host linkage information still bottleneck virus discovery through viromes, these findings exemplify the power of metagenomics approaches to assess the diversity, evolutionary history, and genomic characteristics of novel uncultivated phages.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - François Enault
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
| | - Viviane Ravet
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
| | - Olivier Pereira
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
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1945
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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1946
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 03/26/2024] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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1947
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Chan CS, Chan KG, Tay YL, Chua YH, Goh KM. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front Microbiol 2015; 6:177. [PMID: 25798135 PMCID: PMC4350410 DOI: 10.3389/fmicb.2015.00177] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 02/04/2023] Open
Abstract
The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.
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Affiliation(s)
- Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | | | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
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1948
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Grandjean F, Tan MH, Gan HY, Gan HM, Austin CM. The complete mitogenome of the endangered white-clawed freshwater crayfish Austropotamobius pallipes (Lereboullet, 1858) (Crustacea: Decapoda: Astacidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3329-30. [DOI: 10.3109/19401736.2015.1018207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Poitiers Cedex, France,
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Huan You Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Christopher M. Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
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1949
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Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 2015; 4. [PMID: 25735037 PMCID: PMC4384745 DOI: 10.7554/elife.05477] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 12/11/2022] Open
Abstract
Premature infants are highly vulnerable to aberrant gastrointestinal tract
colonization, a process that may lead to diseases like necrotizing enterocolitis.
Thus, spread of potential pathogens among hospitalized infants is of great concern.
Here, we reconstructed hundreds of high-quality genomes of microorganisms that
colonized co-hospitalized premature infants, assessed their metabolic potential, and
tracked them over time to evaluate bacterial strain dispersal among infants. We
compared microbial communities in infants who did and did not develop necrotizing
enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same
species colonized many infants, our genome-resolved analysis revealed that strains
colonizing each baby were typically distinct. In particular, no strain was common to
all infants who developed necrotizing enterocolitis. The paucity of shared gut
colonizers suggests the existence of significant barriers to the spread of bacteria
among infants. Importantly, we demonstrate that strain-resolved comprehensive
community analysis can be accomplished on potentially medically relevant time
scales. DOI:http://dx.doi.org/10.7554/eLife.05477.001 The spread of potentially harmful bacteria is a major source of disease in patients
staying in hospitals. Premature babies—born before 37 weeks of
pregnancy—can be particularly vulnerable to these infections because their
organs may not yet be fully developed. Also, young babies do not have the fully
established populations of beneficial microbes that help to protect us from dangerous
bacteria. Necrotizing enterocolitis—a life-threatening disease that can cause portions
of the bowel to die—is mostly seen in extremely premature babies. Although it
is not known what causes this serious condition, research has suggested that a
contagious microbe may be responsible. The development of methods that can sequence DNA from whole communities of microbes,
known as metagenomics, allows researchers to identify the presence of individual
strains of bacteria within these communities. This makes it possible to compare and
contrast the strains of bacteria present in both diseased and healthy individuals, to
help identify the bacteria responsible for a disease. Here, Raveh-Sadka et al. used a metagenomics approach to study the communities of
microbes present in premature babies in a hospital unit during an outbreak of
necrotizing enterocolitis. The study found that very few bacterial strains were
present in more than one baby, suggesting that bacterial strains are not readily
transferred between the babies while they are in the hospital. Furthermore,
Raveh-Sadka et al. reveal that no single bacterial strain was shared among all the
babies who developed necrotizing enterocolitis. These findings indicate that necrotizing enterocolitis is not caused by a single
strain of bacterium. Instead, if bacteria do contribute to the disease, it maybe that
it is caused by a variety of potentially harmful bacteria colonizing the gut at the
cost of beneficial bacteria. In future, better understanding of the barriers that
limit the transfer of bacteria between premature babies could help inform efforts to
reduce the spread of infections between patients in hospitals. DOI:http://dx.doi.org/10.7554/eLife.05477.002
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Affiliation(s)
- Tali Raveh-Sadka
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Brandon Brooks
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States
| | - Misty Good
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
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1950
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Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism. Appl Environ Microbiol 2015; 81:3142-56. [PMID: 25724961 DOI: 10.1128/aem.00039-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.
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