IDBA-UD: a <i>de novo</i> assembler for single-cell and metagenomic sequencing data with highly uneven depth

The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM). Analysis of intra-and inter-individual variation demonstrates that family membership has a pronounced effect on the structural and functional composition of the gastrointestinal microbiome. In the context of T1DM, consistent taxonomic differences were absent across families, but certain human exocrine pancreatic proteins were found at lower levels. The associated microbial functional signatures were linked to metabolic traits in distinct taxa. The methodologies and results provide a foundation for future large-scale integrated multi-omic analyses of the gastrointestinal microbiome in the context of host-microbe interactions in human health and disease.

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“…64). IDBA-UD was then run using its pre-error-correction step for correcting reads (idba_ud -pre_correction).…”

Section: Methodsmentioning

confidence: 99%

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

et al. 2016

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“…Quality control was carried out using FastQC (Babraham Bioinformatics (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)). High-quality reads from each sample were assembled into scaftigs using IDBA-UD (Peng et al, 2012) with default parameters. High-quality reads of each sample have been submitted to MG-RAST using the 'join fastqformatted paired-reads' option retaining the nonoverlapping reads.…”

Section: Methodsmentioning

confidence: 99%

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

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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“…The sequences were assembled using IDBA_ud v. 1.1.0 (ref. 59) with a kmer range of 40-70 and step size of 15. To improve recovery of the most abundant Verrucomicrobia, the genome was selectively re-assembled using Velvet with a kmer size of 59 and expected kmer coverage of 11.5 (range 7.5-15.5).…”

Section: Methodsmentioning

confidence: 99%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

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Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘Candidatus Udaeobacter copiosus’. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

Abstract: The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud

Cited by 2,761 publications

References 21 publications

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

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

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

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