Summary: The genomic analysis of assemblages of organisms.

Top Publications

  1. Wedemeyer A, Kliemann L, Srivastav A, Schielke C, Reusch T, Rosenstiel P. An improved filtering algorithm for big read datasets and its application to single-cell assembly. BMC Bioinformatics. 2017;18:324 pubmed publisher
    ..Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at . ..
  2. Relton C, Davey Smith G. Epigenetic epidemiology of common complex disease: prospects for prediction, prevention, and treatment. PLoS Med. 2010;7:e1000356 pubmed publisher
  3. Treangen T, Koren S, Sommer D, Liu B, Astrovskaya I, Ondov B, et al. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013;14:R2 pubmed publisher
    ..MetAMOS can be downloaded from: ..
  4. Narum S, Buerkle C, Davey J, Miller M, HOHENLOHE P. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol. 2013;22:2841-7 pubmed publisher
  5. . The Amborella genome and the evolution of flowering plants. Science. 2013;342:1241089 pubmed publisher
    ..Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications. ..
  6. Xu Z, Malmer D, Langille M, Way S, Knight R. Which is more important for classifying microbial communities: who's there or what they can do?. ISME J. 2014;8:2357-9 pubmed publisher
  7. Ai D, Huang R, Wen J, Li C, Zhu J, Xia L. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017;18:1041 pubmed publisher
    ..association between the loss of oral microbiota diversity and the progression of periodontitis, suggesting that metagenomics sequencing and phylogenetic profiling are predictive of early periodontitis, leading to potential therapeutic ..
  8. Nigro O, Jungbluth S, Lin H, Hsieh C, Miranda J, Schvarcz C, et al. Viruses in the Oceanic Basement. MBio. 2017;8: pubmed publisher
    ..These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses. ..
  9. Yinda C, Zell R, Deboutte W, Zeller M, Conceição Neto N, Heylen E, et al. Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats. BMC Genomics. 2017;18:249 pubmed publisher
    ..87 fruit bats (Eidolon helvum and Epomophorus gambianus), were combined into 25 pools and analyzed using viral metagenomics. In total, Picornavirales reads were found in 19 pools, and (near) complete genomes of 11 picorna-like viruses ..

More Information

Publications110 found, 100 shown here

  1. Hao L, Xia Z, Yang H, Wang J, Han M. Ionic liquid-based reagents improve the stability of midterm fecal sample storage. J Microbiol Methods. 2017;139:68-73 pubmed publisher
    ..Thus, this method may have implications in the storage of fecal samples for metagenomic research. ..
  2. Zaza G, Dalla Gassa A, Felis G, Granata S, Torriani S, Lupo A. Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen. PLoS ONE. 2017;12:e0178228 pubmed publisher
    ..However, multicenter studies including healthy controls should be undertaken to better address this objective. ..
  3. Chen H, Peng S, Dai L, Zou Q, Yi B, Yang X, et al. Oral microbial community assembly under the influence of periodontitis. PLoS ONE. 2017;12:e0182259 pubmed publisher
    ..We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation. ..
  4. Relman D. Microbiology: Learning about who we are. Nature. 2012;486:194-5 pubmed publisher
  5. Fang H, Wang H, Cai L, Yu Y. Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey. Environ Sci Technol. 2015;49:1095-104 pubmed
  6. Brito I, Yilmaz S, Huang K, Xu L, Jupiter S, Jenkins A, et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. 2016;535:435-439 pubmed publisher
    ..North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with ..
  7. Schlaberg R, Chiu C, Miller S, Procop G, Weinstock G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Arch Pathol Lab Med. 2017;141:776-786 pubmed publisher
    ..Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked. ..
  8. Crofts T, Gasparrini A, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol. 2017;15:422-434 pubmed publisher
  9. De Mandal S, Chatterjee R, Kumar N. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiol. 2017;17:90 pubmed publisher
    ..These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well. ..
  10. Costea P, Munch R, Coelho L, Paoli L, Sunagawa S, Bork P. metaSNV: A tool for metagenomic strain level analysis. PLoS ONE. 2017;12:e0182392 pubmed publisher
    ..The implementation of metaSNV is available at: ..
  11. Li Y, Khalafalla A, Paden C, Yusof M, Eltahir Y, Al Hammadi Z, et al. Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates. PLoS ONE. 2017;12:e0184718 pubmed publisher
    ..6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population. ..
  12. Mourani P, Sontag M. Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm. Pediatr Clin North Am. 2017;64:1039-1056 pubmed publisher
    ..As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment. ..
  13. Harris E. Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes. Evol Anthropol. 2017;26:228-241 pubmed publisher
    ..I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age...
  14. Woyke T, Doud D, Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods. 2017;14:1045-1054 pubmed publisher
    ..samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies...
  15. Wichmann F, Udiković Kolić N, Andrew S, Handelsman J. Diverse antibiotic resistance genes in dairy cow manure. MBio. 2014;5:e01017 pubmed publisher
    ..Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance ..
  16. Yang P, Su X, Ou Yang L, Chua H, Li X, Ning K. Microbial community pattern detection in human body habitats via ensemble clustering framework. BMC Syst Biol. 2014;8 Suppl 4:S7 pubmed publisher
    ..Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome. ..
  17. McAllister T, Meale S, Valle E, Guan L, Zhou M, Kelly W, et al. RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis. J Anim Sci. 2015;93:1431-49 pubmed publisher
    ..b>Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how ..
  18. Gong Y, Yang S, Chen G, Chen Y, Huang Y, Ning H, et al. A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach. Arch Virol. 2017;162:2003-2012 pubmed publisher
    ..These results demonstrate that this NGS pipeline allows to detect viruses which were not identified by routine diagnostic assays, directly from clinical samples. ..
  19. Kim D, Hofstaedter C, Zhao C, Mattei L, Tanes C, Clarke E, et al. Optimizing methods and dodging pitfalls in microbiome research. Microbiome. 2017;5:52 pubmed publisher
    ..We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors. ..
  20. Lewandowska D, Schreiber P, Schuurmans M, Ruehe B, Zagordi O, Bayard C, et al. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PLoS ONE. 2017;12:e0177340 pubmed publisher
    ..This study highlights the potential of metagenomic sequencing for virus diagnostics in cases with previously unknown etiology of infection and in complex diagnostic situations such as in immunocompromised hosts. ..
  21. Chrząstek K, Lee D, Smith D, Sharma P, Suarez D, Pantin Jackwood M, et al. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology. 2017;509:159-166 pubmed publisher
    Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples...
  22. Claesson M, Clooney A, O Toole P. A clinician's guide to microbiome analysis. Nat Rev Gastroenterol Hepatol. 2017;14:585-595 pubmed publisher
    ..We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications. ..
  23. Brady A, Salzberg S. PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods. 2011;8:367 pubmed publisher
  24. Delwart E. A roadmap to the human virome. PLoS Pathog. 2013;9:e1003146 pubmed publisher
  25. Pawlowski J. The new micro-kingdoms of eukaryotes. BMC Biol. 2013;11:40 pubmed publisher
  26. Lin Y, Hsieh C, Chen J, Lu X, Kao J, Chen P, et al. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. BMC Bioinformatics. 2017;18:223 pubmed publisher
    ..assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for ..
  27. Chitrala K, Guan H, Singh N, Busbee B, Gandy A, Mehrpouya Bahrami P, et al. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur J Immunol. 2017;47:1188-1199 pubmed publisher
    ..Furthermore, our studies also demonstrate that the phenotype of gene knock-out animals may be shaped by gut microbiota. ..
  28. Hirai J, Nagai S, Hidaka K. Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454. PLoS ONE. 2017;12:e0181452 pubmed publisher
    ..Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality. ..
  29. Deck J, Gaither M, Ewing R, Bird C, Davies N, Meyer C, et al. The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biol. 2017;15:e2002925 pubmed publisher
    ..By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science. ..
  30. Sharon I, Banfield J. Microbiology. Genomes from metagenomics. Science. 2013;342:1057-8 pubmed publisher
  31. von Wintersdorff C, Penders J, Stobberingh E, Oude Lashof A, Hoebe C, Savelkoul P, et al. High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerg Infect Dis. 2014;20:649-57 pubmed publisher
    ..305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance. ..
  32. Lee M, Song J, Jung M, Lee S, Chang J. Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation. Food Microbiol. 2017;66:173-183 pubmed publisher
    ..Analyses of changes in bacterial ecology during fermentation will improve our understanding of the biological properties of kimchi, as well as the relationships between these properties and the microbiota of kimchi. ..
  33. Nabizadeh E, Jazani N, Bagheri M, Shahabi S. Association of altered gut microbiota composition with chronic urticaria. Ann Allergy Asthma Immunol. 2017;119:48-53 pubmed publisher
    ..This is the first study, to our knowledge, to show the change of microbiota composition in patients with CU. ..
  34. Wang Y, Leung H, Yiu S, Chin F. MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning. BMC Genomics. 2014;15 Suppl 1:S12 pubmed publisher
    ..MetaCluster-TA can outperform widely-used MEGAN4 and can annotate more reads with higher accuracy and higher efficiency. It also outperforms MetaCluster 5.0 as a binning tool. ..
  35. Wood D, Salzberg S. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46 pubmed publisher
    ..1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at ..
  36. Orellana L, Rodriguez R L, Konstantinidis K. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res. 2017;45:e14 pubmed publisher
    ..Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes. ..
  37. Alanko J, Cunial F, Belazzougui D, Mäkinen V. A framework for space-efficient read clustering in metagenomic samples. BMC Bioinformatics. 2017;18:59 pubmed publisher
    ..Our experimental results show that our algorithms are practical, they can exploit multiple cores by a parallel traversal of the suffix-link tree, and they are competitive both in space and in time with the state of the art. ..
  38. Petersen T, Lukjancenko O, Thomsen M, Maddalena Sperotto M, Lund O, Møller Aarestrup F, et al. MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS ONE. 2017;12:e0176469 pubmed publisher
    ..gene identification studies rely on the use of next generation sequence analysis of either single isolate or metagenomics samples...
  39. Weng F, Yang Y, Wang D. Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. BMC Genomics. 2016;17:1024 pubmed publisher
    ..We infer that artificial hibernation may impose potential effects on primary immunodeficiency and increase the risk of bacterial infections in the brown tree frog. ..
  40. Truong D, Franzosa E, Tickle T, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12:902-3 pubmed publisher
  41. Mahana D, Trent C, Kurtz Z, Bokulich N, Battaglia T, Chung J, et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med. 2016;8:48 pubmed
    ..These studies form the basis for new models of type 2 diabetes and NAFLD that involve microbiome perturbation. ..
  42. Lakiotaki K, Kanterakis A, Kartsaki E, Katsila T, Patrinos G, Potamias G. Exploring public genomics data for population pharmacogenomics. PLoS ONE. 2017;12:e0182138 pubmed publisher
    ..Herein, we exploit ePGA, a web-based electronic Pharmacogenomics Assistant and publicly available genetic data from the 1000 Genomes Project to explore genotype to phenotype associations among the 1000 Genomes Project populations. ..
  43. Jayasundara D, Saeed I, Chang B, Tang S, Halgamuge S. Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness. BMC Bioinformatics. 2015;16 Suppl 18:S3 pubmed publisher
    .. ..
  44. Liang C, Tseng H, Chen H, Wang W, Chiu C, Chang J, et al. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics. 2017;18:932 pubmed publisher
    ..We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. ..
  45. Ludington W, Seher T, Applegate O, Li X, Kliegman J, Langelier C, et al. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS ONE. 2017;12:e0174930 pubmed publisher
    ..Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae ..
  46. Heinz E, Domman D. Reshaping the tree of life. Nat Rev Microbiol. 2017;15:322 pubmed publisher
    This month's Genome Watch highlights how metagenomics is continuing to reveal the diversity of microorganisms in the environment and how it is challenging and expanding our understanding of how life evolved on Earth.
  47. Balvociute M, Huson D. SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?. BMC Genomics. 2017;18:114 pubmed publisher
    ..While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic. ..
  48. Iliev I, Yahubyan G, Marhova M, Apostolova E, Gozmanova M, Gecheva G, et al. Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs. J Basic Microbiol. 2017;57:669-679 pubmed publisher
    ..The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments. ..
  49. Bovo S, Mazzoni G, Ribani A, Utzeri V, Bertolini F, Schiavo G, et al. A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections. PLoS ONE. 2017;12:e0179462 pubmed publisher
    ..This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.
  50. Elderman M, Sovran B, Hugenholtz F, Graversen K, Huijskes M, Houtsma E, et al. The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice. PLoS ONE. 2017;12:e0184274 pubmed publisher
    ..Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups. ..
  51. Zhang S, Jin X, Zhang T. Gene Prediction in Metagenomic Fragments with Deep Learning. Biomed Res Int. 2017;2017:4740354 pubmed publisher
    Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species...
  52. Beckmann N, Karri S, Fang G, Bashir A. Detecting epigenetic motifs in low coverage and metagenomics settings. BMC Bioinformatics. 2014;15 Suppl 9:S16 pubmed publisher
    ..Lastly, we show that these motifs can provide an alternative source of information by which to cluster metagenomics contigs and that iterative refinement on these clustered contigs can further improve both sensitivity and ..
  53. Páez Espino D, Eloe Fadrosh E, Pavlopoulos G, Thomas A, Huntemann M, Mikhailova N, et al. Uncovering Earth's virome. Nature. 2016;536:425-30 pubmed
    ..Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions. ..
  54. Xie C, Goi C, Huson D, Little P, Williams R. RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. BMC Bioinformatics. 2016;17:508 pubmed publisher
    ..The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs. ..
  55. Jenkins T, Rathnayaka Y, Perera P, Peachey L, Nolan M, Krause L, et al. Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition. PLoS ONE. 2017;12:e0184719 pubmed publisher
  56. Ismail W, Ye Y, Tang H. Gene finding in metatranscriptomic sequences. BMC Bioinformatics. 2014;15 Suppl 9:S8 pubmed publisher
    ..TransGeneScan is available as open-source software on SourceForge at ..
  57. Buttó L, Haller D. Functional relevance of microbiome signatures: The correlation era requires tools for consolidation. J Allergy Clin Immunol. 2017;139:1092-1098 pubmed publisher
  58. Ahlgren N, Chen Y, Needham D, Parada A, Sachdeva R, Trinh V, et al. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environ Microbiol. 2017;19:2434-2452 pubmed publisher
    ..This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes. ..
  59. Yarygin K, Tyakht A, Larin A, Kostryukova E, Kolchenko S, Bitner V, et al. Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PLoS ONE. 2017;12:e0176154 pubmed publisher
    ..The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions...
  60. Lau P, Cordey S, Brito F, Tirefort D, Petty T, Turin L, et al. Metagenomics analysis of red blood cell and fresh-frozen plasma units. Transfusion. 2017;57:1787-1800 pubmed publisher
    ..This study demonstrates that HTS is a promising tool for detecting common and less frequent infectious pathogens in blood products. ..
  61. Dai Q, Moshitch Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, et al. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nat Methods. 2017;14:695-698 pubmed publisher
    ..Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles...
  62. Festa S, Coppotelli B, Madueño L, Loviso C, Macchi M, Neme Tauil R, et al. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches. PLoS ONE. 2017;12:e0184505 pubmed publisher ..
  63. Cox M, Cookson W, Moffatt M. Sequencing the human microbiome in health and disease. Hum Mol Genet. 2013;22:R88-94 pubmed publisher
    ..In particular, 16S rRNA sequencing, whole microbial genome sequencing and metagenomics are revealing the extraordinary diversity of microorganisms on Earth and their vast genetic and metabolic ..
  64. Hjort K, Presti I, Elväng A, Marinelli F, Sjöling S. Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics. Appl Microbiol Biotechnol. 2014;98:2819-28 pubmed
    ..In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome...
  65. Mizuno C, Rodriguez Valera F, Ghai R. Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. MBio. 2015;6: pubmed publisher
    ..This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans. ..
  66. Oliveira J, Araújo W, Lopes Sales A, Brito Guerra A, Silva Araújo S, de Vasconcelos A, et al. BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. Database (Oxford). 2015;2015: pubmed publisher
    ..Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/..
  67. Guo L, Hua X, Zhang W, Yang S, Shen Q, Hu H, et al. Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae. Virol Sin. 2017;32:130-138 pubmed publisher
    ..Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy ..
  68. Legoff J, Resche Rigon M, Bouquet J, Robin M, Naccache S, Mercier Delarue S, et al. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease. Nat Med. 2017;23:1080-1085 pubmed publisher
    ..Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of ..
  69. Brouchkov A, Kabilov M, Filippova S, Baturina O, Rogov V, Galchenko V, et al. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia). Gene. 2017;636:48-53 pubmed publisher
    ..Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. ..
  70. Cruz F, Brennan A, Gonzalez Voyer A, Muñoz Fuentes V, Eaaswarkhanth M, Roques S, et al. Genetics and genomics in wildlife studies: implications for ecology, evolution, and conservation biology. Bioessays. 2012;34:245-6 pubmed publisher
  71. Warnke J, Ali H. An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads. BMC Bioinformatics. 2013;14 Suppl 11:S7 pubmed publisher
    ..Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. ..
  72. Bougouffa S, Radovanovic A, Essack M, Bajic V. DEOP: a database on osmoprotectants and associated pathways. Database (Oxford). 2014;2014: pubmed publisher
    ..Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: ..
  73. Maritz J, Sullivan S, Prill R, Aksoy E, Scheid P, Carlton J. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City. PLoS ONE. 2017;12:e0175527 pubmed publisher
    ..Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea...
  74. Alshawaqfeh M, Bashaireh A, Serpedin E, Suchodolski J. Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm. BMC Bioinformatics. 2017;18:328 pubmed publisher
    ..Due to the recent advances in high throughput sequencing technologies, an increased number of metagenomics studies have suggested the dysbiosis in microbial communities as potential biomarker for certain diseases...
  75. Bowers R, Kyrpides N, Stepanauskas R, Harmon Smith M, Doud D, Reddy T, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725-731 pubmed publisher
    ..Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity. ..
  76. Quince C, Walker A, Simpson J, Loman N, Segata N. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2017;35:833-844 pubmed publisher
    ..High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology...
  77. . A framework for human microbiome research. Nature. 2012;486:215-21 pubmed publisher
    ..Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies. ..
  78. Deatherage Kaiser B, Li J, Sanford J, Kim Y, Kronewitter S, Jones M, et al. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. PLoS ONE. 2013;8:e67155 pubmed publisher
    ..We used a multi-omics "systems" approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar ..
  79. Nayfach S, Pollard K. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16:51 pubmed publisher
    ..Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes. ..
  80. Schokker D, Jansman A, Veninga G, de Bruin N, Vastenhouw S, de Bree F, et al. Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development. BMC Genomics. 2017;18:241 pubmed publisher
  81. Ballenghien M, Faivre N, Galtier N. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol. 2017;15:25 pubmed publisher
    ..Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis. ..
  82. Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, et al. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods. 2017;14:1063-1071 pubmed publisher
    ..The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions...
  83. Martorell Marugan J, Toro Dominguez D, Alarcon Riquelme M, Carmona Saez P. MetaGenyo: a web tool for meta-analysis of genetic association studies. BMC Bioinformatics. 2017;18:563 pubmed publisher
    ..MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at . ..
  84. . Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14 pubmed publisher
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