Showing papers by "Jeroen Raes published in 2014"

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Abstract: Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Abstract: Summary Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mitags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mitags may provide more realistic estimates of community richness and evenness than amplicon 454tags. In addition, mitags can capture expected beta diversity patterns. Using mitags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.

LotuS: an efficient and user-friendly OTU processing pipeline

Abstract: Background 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools.

A20 controls intestinal homeostasis through cell-specific activities

Abstract: The transcription factor NF-κB is indispensable for intestinal immune homeostasis, but contributes to chronic inflammation and inflammatory bowel disease (IBD). A20, an inhibitor of both NF-κB and apoptotic signalling, was identified as a susceptibility gene for multiple inflammatory diseases, including IBD. Despite absence of spontaneous intestinal inflammation in intestinal epithelial cell (IEC) specific A20 knockout mice, we found additional myeloid-specific A20 deletion to synergistically drive intestinal pathology through cell-specific mechanisms. A20 ensures intestinal barrier stability by preventing cytokine-induced IEC apoptosis, while A20 prevents excessive cytokine production in myeloid cells. Combining IEC and myeloid A20 deletion induces ileitis and severe colitis, characterized by IEC apoptosis, Paneth and goblet cell loss, epithelial hyperproliferation and intestinal microbiota dysbiosis. Continuous epithelial cell death and regeneration in an inflammatory environment sensitizes cells for neoplastic transformation and the development of colorectal tumours in aged mice.

Addendum: Enterotypes of the human gut microbiome

Abstract: This corrects the article DOI: 10.1038/nature09944

Relationship between genome and epigenome - challenges and requirements for future research

Abstract: Understanding the links between genetic, epigenetic and non-genetic factors throughout the lifespan and across generations and their role in disease susceptibility and disease progression offer entirely new avenues and solutions to major problems in our society. To overcome the numerous challenges, we have come up with nine major conclusions to set the vision for future policies and research agendas at the European level.

The skin microbiome of caspase‐14‐deficient mice shows mild dysbiosis

Abstract: Caspase-14, an important proteinase involved in filaggrin catabolism, is mainly active in terminally differentiating keratinocytes, where it is required for the generation of skin natural moisturizing factors (NMFs). Consequently, caspase-14 deficient epidermis is characterized by reduced levels of NMFs such as urocanic acid and 2-pyrrolidone-5-carboxylic acid. Patients suffering from filaggrin deficiency are prone to develop atopic dermatitis, which is accompanied with increased microbial burden. Among several reasons, this effect could be due to a decrease in filaggrin breakdown products. In this study, we found that caspase-14(-/-) mice show enhanced antibacterial response compared to wild-type mice when challenged with bacteria. Therefore, we compared the microbial communities between wild-type and caspase-14(-/-) mice by sequencing of bacterial 16S ribosomal RNA genes. We observed that caspase-14 ablation leads to an increase in bacterial richness and diversity during steadystate conditions. Although both wild-type and caspase-14(-/-) skin were dominated by the Firmicutes phylum, the Staphylococcaceae family was reduced in caspase-14(-/-) mice. Altogether, our data demonstrated that caspase-14 deficiency causes the imbalance of the skin-resident bacterial communities.

Analysis of the draft genome of Pseudomonas fluorescens ATCC17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines

Abstract: All fluorescent pseudomonads (Pseudomonas aeruginosa, P. putida, P. fluorescens, P. syringae and others) are known to produce the high-affinity peptidic yellow-green fluorescent siderophore pyoverdine. These siderophores have peptide chains that are quite diverse and more than 50 pyoverdine structures have been elucidated. In the majority of the cases, a Pseudomonas species is also able to produce a second siderophore of lower affinity for iron. Pseudomonas fluorescens ATCC 17400 has been shown to produce a unique second siderophore, (thio)quinolobactin, which has an antimicrobial activity against the phytopathogenic Oomycete Pythium debaryanum. We show that this strain has the capacity to utilize 16 different pyoverdines, suggesting the presence of several ferripyoverdine receptors. Analysis of the draft genome of P. fluorescens ATCC 17400 confirmed the presence of 55 TonB-dependent receptors, the largest so far for Pseudomonas, among which 15 are predicted to be ferripyoverdine receptors (Fpv). Phylogenetic analysis revealed the presence of two different clades containing ferripyoverdine receptors, with sequences similar to the P. aeruginosa type II FpvA forming a separate cluster. Among the other receptors we confirmed the presence of the QbsI (thio)quinolobactin receptor, an ferri-achromobactin and an ornicorrugatin receptor, several catecholate and four putative heme receptors. Twenty five of the receptors genes were found to be associated with genes encoding extracytoplasmic sigma factors (ECF σ) and transmembrane anti-σ sensors.

The gut microbiome - a new target for understanding, diagnosing and treating disease

Abstract: The functioning of the human body constitutes a complex interplay of human processes and ‘services’ rendered to us by the 1000 trillion microbial cells we carry. Disruption of this natural microbial flora is linked to infection, autoimmune diseases and cancer, but detailed knowledge about our microbial component remains scarce [1]. Recent technological advances such as metagenomics and next-generation sequencing permit the study of the various microbiota of the human body at a previously unseen scale. These advances have allowed the initiation of the International Human Microbiome Project, aiming at genomically characterizing the totality of human-associated microorganisms (the “microbiome”) [2]. Here, I will present our work on characterizing the human intestinal flora based upon the analysis of high-throughput meta-omics (metagenomics, metatranscriptomics, metaproteomics) data. I will show how the healthy gut flora can be classified “enterotypes” that are independent from host nationality, age, BMI and gender, but linked to nutrition [3]. I will also show how metagenome-wide association studies (MGWAS) can lead to the detection of diagnostic markers for host properties and disease (e.g. in IBD, diabetes and obesity), and aid in further understanding on how the gut flora disturbances contribute to these pathologies. Finally, I will illustrate how gut microbiota-based treatment strategies are emerging, for example through Faecal Microbiota Transplantation (FMT).

Transplantatie van fecale microbiota : oude wijn in nieuwe zakken?

Abstract: The intestinal microbiota play an important role in the homeostasis of the human body. A dis- ruption of this delicate balance (commonly called „dysbiosis”) is known to be involved in various gastrointestinal and systemic diseases such as antibiotic-associated diarrhea, inflam- matory bowel disease and obesity. A restoration of this balance could exert therapeutic effects. Probiotics have been tried extensively, but fail to alter the gastrointestinal microbiota significantly. A fecal microbiota trans- plantation (FMT), in which healthy donor feces are transferred, remains a promising technique which could prove to be the answer. In this manuscript, the practical considerations of FMT are discussed and the current indications reviewed, most evidence being available for relapsing infections with Clostridium difficile.