Alterations in intestinal microbiota composition are associated with several chronic conditions, including obesity and inflammatory diseases. The microbiota of older people displays greater inter-individual variation than that of younger adults. Here we show that the faecal microbiota composition from 178 elderly subjects formed groups, correlating with residence location in the community, day-hospital, rehabilitation or in long-term residential care. However, clustering of subjects by diet separated them by the same residence location and microbiota groupings. The separation of microbiota composition significantly correlated with measures of frailty, co-morbidity, nutritional status, markers of inflammation and with metabolites in faecal water. The individual microbiota of people in long-stay care was significantly less diverse than that of community dwellers. Loss of community-associated microbiota correlated with increased frailty. Collectively, the data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.

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Gut microbiota composition correlates with diet and health in the elderly

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.

/pdf/novoplasty-de-novo-assembly-of-organelle-genomes-from-whole-2jrfpu42li.pdf

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

We present an in silico approach for the reconstruction of complete mitochondrial genomes of nonmodel organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/ chrishah/MITObim.

/pdf/reconstructing-mitochondrial-genomes-directly-from-genomic-2x03m1bk2z.pdf

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Hypertension 66 (20.3%) 24 (24.2%) 30 (16.3%) NS Diabetes 20 (6.2%) 7 (7.1%) 10 (5.4%) NS Excess weight 78 (24%) 27 (27.3%) 44 (23.9%) NS Smokers 64 (19.7%) 17 (17.2%) 35 (19.0%) NS Age >50 years 137 (42.2%) 54 (54.5%) 67 (36.4%) <0.02 Kidney disease 7 (2.2%) 1 (1%) 5 (2.7%) NS Family history, DM 102 (31.4%) 28 (28.3%) 66 (35.9%) NS

Conflict of interest statement. None declared.

Motivation: This article presents a method for assembling shotgun sequences which primarily uses high confidence regions whilst taking advantage of additional available information such as low confidence regions, quality values or repetitive region tags. Conflict situations are resolved with routines for analysing trace signals. Results: Initial tests with different human and mouse genome projects showed promising results but also demonstrated the need to recognise and handle correctly very long, untagged and nonstandard repeats. Availability: Current versions of the MIRA assembler are available on request at the canonical project homepage as binary for SGI, Intel Linux and SUN Solaris: http://www.dkfz-heidelberg.de/mbp-ased/ Contact: b.chevreux@dkfz-heidelberg.de To whom correspondance should be adressed Introduction Todays large scale genome sequencing efforts produce enormous quantities of data each day. They are now nearly all based on the chain-termination dideoxy method published by Sanger et al. (1977) in one way or another. But the gel or capillary electrophoresis used can determine only about a maximum of 1000 to 1500 bases, the high quality stretch with low error probabilities for the called bases often being around the first 400 to 500 bases. Current sequencing strategies for a contiguous DNA sequence (contig) – ranging anywhere between 20 kilobases (kb) and 200 kb – therefore basically boil down to fragment the given contig in hundreds or thousands of overlapping subclones (Durbin and Dear (1998)), analyse these by electrophoresis and subsequently assemble the subclones back together in one contig. The extensively studied reconstruction of the unknown, correct contiguous DNA sequence by inferring it through the help of a number of representations1 is called the assembly problem. The devil is in the details, however. If the collected readings 1also called fragments, see Myers (1995) (reads) were 100% error free, then a multiplicity of problems would not occur. In reality, the extraction of data by gel electrophoresis is a physical process in which errors due to chemical artifacts like compressions show up quite often. Ewing et al. (1998); Ewing and Green (1998) show that – together with errors occuring in the subsequent signal analysis – current laboratory technologies total an error rate that might be anywhere between 0.1% – for good parts in the middle of a read – and more than 10% in bad parts of a read at the very beginning and at the end. This error rate, combined with the sometimes exacerbating fact that DNA tends to contain highly repetitive stretches with only very few bases differing across different repeat locations, impedes the assembly process in an awesome way. The above mentioned error rates and repetitive properties of DNA lead to the necessity of using fault tolerant and alternatives-seeking algorithms. Wang and Jiang (1994) showed that the assembly problem – even using error free representations (fragments) of the true sequence – is NP complete. This means that the volume of data can only be assembled by approximating strategies, relying on algorithms that are well-behaved in time and space complexity.

Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.

We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.

/pdf/using-the-miraest-assembler-for-reliable-and-automated-mrna-2lyxz50sap.pdf

Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs

Bacillus subtilis is both a model organism for basic research and an industrial workhorse, yet there are major gaps in our understanding of the genomic heritage and provenance of many widely used strains. We analyzed 17 legacy strains dating to the early years of B. subtilis genetics. For three—NCIB 3610T, PY79, and SMY—we performed comparative genome sequencing. For the remainder, we used conventional sequencing to sample genomic regions expected to show sequence heterogeneity. Sequence comparisons showed that 168, its siblings (122, 160, and 166), and the type strains NCIB 3610 and ATCC 6051 are highly similar and are likely descendants of the original Marburg strain, although the 168 lineage shows genetic evidence of early domestication. Strains 23, W23, and W23SR are identical in sequence to each other but only 94.6% identical to the Marburg group in the sequenced regions. Strain 23, the probable W23 parent, likely arose from a contaminant in the mutagenesis experiments that produced 168. The remaining strains are all genomic hybrids, showing one or more “W23 islands” in a 168 genomic backbone. Each traces its origin to transformations of 168 derivatives with DNA from 23 or W23. The common prototrophic lab strain PY79 possesses substantial W23 islands at its trp and sac loci, along with large deletions that have reduced its genome 4.3%. SMY, reputed to be the parent of 168, is actually a 168-W23 hybrid that likely shares a recent ancestor with PY79. These data provide greater insight into the genomic history of these B. subtilis legacy strains.

Bastien Chevreux

Papers

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.

Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs

The origins of 168, W23, and other Bacillus subtilis legacy strains.

MIRA: An Automated Genome and EST Assembler