Taxonomic metagenome sequence assignment with structured output models

Patil, Kaustubh R.; Haider, Peter; Pope, Phillip B.; Turnbaugh, Peter J.; Morrison, Mark; Scheffer, Tobias; McHardy, Alice C.

doi:10.1038/nmeth0311-191

Cited by 116 publications

(136 citation statements)

References 6 publications

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“…However, incorporation of CheckM into a complete quality control and annotation pipeline where plasmids (Jørgensen et al 2014), genomic islands (Langille et al 2010), phage (Akhter et al 2012), and other genomic elements are automatically identified and screened will likely improve the quality and characterization of recovered genomes. Use of taxonomic assignment methods (Patil et al 2011;Dröge et al 2014) would also be of benefit within a complete quality control pipeline in order to identify genomes exhibiting clear chimerism and sources of contamination within single-cell and isolate genomes. The estimates for highly incomplete or highly contaminated genomes must be interpreted with regard to the observed systematic bias, which arises from marker genes from foreign genomes being misinterpreted as an indication of additional completeness (Supplemental Fig.…”

Section: Discussionmentioning

confidence: 99%

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

et al. 2015

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Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene-and genome-centric analyses of microbial communities.

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Section: Discussionmentioning

confidence: 99%

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

et al. 2015

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“…Binning of metagenomes was performed using Metawatt version 1.7 (Strous et al, 2012), PhylopythiaS (Patil et al, 2011) and an emergent self-organizing maps (ESOM) procedure (Dick et al, 2009). For Metawatt, binning was performed using medium sensitivity with a taxonomic database containing SAG data from Rinke et al (2013) and Dodsworth et al (2013), as well as all complete bacterial and archaeal genomes (n = 2535) downloaded from http://ftp.ncbi.nlm.nih.gov/genomes/Bacteria on 9 July 2013.…”

Section: Metagenome Binningmentioning

confidence: 99%

“…Contig fragments in distinct regions of the ESOM were selected by manual inspection, and corresponding contigs were included in the bin if 450% of their length was represented by these fragments. ClaMS (Patil et al, 2011) was also used for binning of the Etoliko Lagoon metagenome. Other homology-based binning methods such as BLASTN and BLASTP (Altschul et al, 1997) were used on the TA biofilm and Sakinaw Lake metagenomes for comparison.…”

Section: Metagenome Binningmentioning

confidence: 99%

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

et al. 2015

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The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species-to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

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“…Por isso, o uso de técnicas metagenômicas supera a necessidade de culturas e tornou-se uma ferramenta importante para a compreensão do potencial genomico que reside no microbioma ruminal. Esta técnica aliada ao desenvolvimento de algoritmos em bioinformáticas, tem mostrado substancial precisão e tem melhorado os estudos de uma única espécie microbiana (PATIL et al, 2011 As enzimas responsáveis pela degradação da celulose são pertencentes às famílias 5 e 9 das glicosil hidrolases (GH), incluindo as endoglucanases, exoglucanases e beta-glucanase (VOCADLO;DAVIES, 2008). A exo-celobiohidrolases estão envolvidas no ataque inicial da celulose em frações cristalinas e regiões amorfas.…”

Section: 2%unclassified

Dinâmica do microbioma ruminal de ovinos (<i>Ovis aries</i>) e sua relação com a degradação de biomassa

Romagnoli¹

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Dynamics of the sheep (Ovis aries) rumen microbiome and its relationship with the degradation of biomassConsidering the diet as a modulator of ruminal microbiome, this work aimed to investigate the impact of sugarcane bagasse on the composition and function of microbial species residents in the sheep (Ovis aries) rumen. Six cannulated male animals were used in the experiment, where three individuals were fed on a diet consisting of 70% forage and 30% concentrate (control treatment), and three were fed on a similar diet, but with sugarcane bagasse replacing 14% of the forage portion (bagasse treatment). The ruminal content (i.e., liquid and fiber) were sampled every two weeks during 60 days. From these samples, the structure and composition of the microbial community were assessed by total DNA extraction and amplification of V3 and V6-V7 regions of 16S rRNA gene from bacteria and the fungal intergenic region (ITS2). Furthermore, metagenomics and metatranscriptomics approaches were used to evaluate the enrichment of specific members of the microbial community in the ruminal fiber and genes related to lignocellulolytic enzymes. The liquid and fiber fractions of the O. aries rumen revealed a microbial community dominated mainly by Firmicutes and Bacteroidetes throughout the experimental period. The genera Prevotella and Ruminococcus accounted for 20% and 4% of the bacterial community of rumen, respectively. In the fungal community, the phylum Neocallimastigomycota accounted for 91% of sequences and its main genera adhered on the ruminal fiber were Piromyces, Neocallimastix, Orpinomyces, Anaeromyces, Caecomyces, and Cyllamyces. The genus Caecomyces was significantly more abundant in the ruminal fiber in animals fed on sugarcane bagasse. Furthermore, there was a significant increase in the frequency of enzymes, such as α-1,4-glucan, α-galactosidase, endo-1,4-β-xylanase, β-xylosidase, xylose isomerase, cellobiose phosphorylase and α-Narabinofuranosidase in the bagasse treatment. Considering that the recovery of enzymes from ecosystems naturally evolved for degradation of biomass is a promising strategy to overcome the current inefficient enzymatic action in industrial production of biofuels, the results of this study bring great possibilities to increase the discovery and or recovery of enzymes from ruminants, as well as the possibility of the ruminal microbiome structure manipulation to be used as source of an enriched inoculum for biomass degradation in industrial processes.

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Taxonomic metagenome sequence assignment with structured output models

Cited by 116 publications

References 6 publications

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

Dinâmica do microbioma ruminal de ovinos (<i>Ovis aries</i>) e sua relação com a degradação de biomassa

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