PhyloSift: phylogenetic analysis of genomes and metagenomes

Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric; Matsen, F. A.; Bik, Holly M.; Eisen, Jonathan A.

doi:10.7717/peerj.243

Cited by 584 publications

(573 citation statements)

References 69 publications

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“…CGs that contained at least 75% of the single-copy genes were further analyzed. Genomes were identified to appropriate taxonomic levels based on two approaches: (i) A set of 107 essential single-copy genes were blasted (BLASTP, Eo 1e À 5 ) against the NCBI-nr database with follow-up analysis in MEGAN (Huson and Weber, 2013) to identify the lowest common ancestor of the blast output, (ii) using the standard settings of PhyloSift (Darling et al, 2014). A taxon was assigned when at least 75% of the identified essential single-copy genes resulted in a concordant taxonomy.…”

Section: Methodsmentioning

confidence: 99%

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

et al. 2016

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Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.

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Section: Methodsmentioning

confidence: 99%

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

et al. 2016

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“…Testing of taxonomic congruency was performed as described in Soo et al (2014). The final set of 43 phylogenetically informative marker genes (Supplemental Table S5) consists primarily of ribosomal proteins and RNA polymerase domains, and is similar to the universal marker sets used by PhyloSift (Darling et al 2014; Supplemental Table S6 …”

Section: Genome Tree Inferencementioning

confidence: 99%

“…Using lineage-specific marker sets, 2190 (96%) of these genomes were estimated to be ≥95% complete with ≤5% contamination (Supplemental Table S13) making them excellent reference genomes for analyses such as assigning taxonomy to anonymous genome fragments (Brady and Salzberg, 2009;Parks et al 220 2011) or characterizing metagenomic samples using marker genes (Darling et al 2014). The remaining 91 (4%) genomes were found to be <95% complete or >5% contaminated making them poor reference genomes for some analyses.…”

mentioning

confidence: 99%

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

Parks

Imelfort

Skennerton

et al. 2014

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560

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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. While 25 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 30 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 along with 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 35 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. CheckM is open 40 source software available at http://ecogenomics.github.io/CheckM.

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“…The reference data sets were derived from the Phylosift database (Darling et al, 2014), with additional sets from the Joint Genomic Institute IMG database . The presence of all 16 genes was not seen in the majority of sequences.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Seitz¹,

et al. 2016

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Marine and estuary sediments contain a variety of uncultured archaea whose metabolic and ecological roles are unknown. De novo assembly and binning of high-throughput metagenomic sequences from the sulfate-methane transition zone in estuary sediments resulted in the reconstruction of three partial to near-complete (2.4-3.9 Mb) genomes belonging to a previously unrecognized archaeal group. Phylogenetic analyses of ribosomal RNA genes and ribosomal proteins revealed that this group is distinct from any previously characterized archaea. For this group, found in the White Oak River estuary, and previously registered in sedimentary samples, we propose the name 'Thorarchaeota'. The Thorarchaeota appear to be capable of acetate production from the degradation of proteins. Interestingly, they also have elemental sulfur and thiosulfate reduction genes suggesting they have an important role in intermediate sulfur cycling. The reconstruction of these genomes from a deeply branched, widespread group expands our understanding of sediment biogeochemistry and the evolutionary history of Archaea.

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PhyloSift: phylogenetic analysis of genomes and metagenomes

Cited by 584 publications

References 69 publications

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

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

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

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