Showing papers by "Jeroen Raes published in 2017"

Quantitative microbiome profiling links gut community variation to microbial load

Abstract: Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

The resilience of the intestinal microbiota influences health and disease

Abstract: The resilience of the microbiota can protect us from disease, but a resilient dysbiotic microbiota may also cause disease. This Opinion article discusses the concepts and mechanisms of microbial resilience against dietary, antibiotic or bacteriotherapy-induced perturbations and the implications these have for human health. The composition of the intestinal microbiota varies among individuals and throughout development, and is dependent on host and environmental factors. However, although the microbiota is constantly exposed to environmental challenges, its composition and function in an individual are stable against perturbations, as microbial communities are resilient and resistant to change. The maintenance of a beneficial microbiota requires a homeostatic equilibrium within microbial communities, and also between the microorganisms and the intestinal interface of the host. The resilience of the healthy microbiota protects us from dysbiosis-related diseases, such as inflammatory bowel disease (IBD) or metabolic disorder. By contrast, a resilient dysbiotic microbiota may cause disease. In this Opinion article, we propose that microbial resilience has a key role in health and disease. We will discuss the concepts and mechanisms of microbial resilience against dietary, antibiotic or bacteriotherapy-induced perturbations and the implications for human health.

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota.

Abstract: Objective Contrary to the long-standing prerequisite of inducing selective (ie, bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterisation of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (gas chromatography mass spectrometry) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and faecal metabolites profiles. Design Faecal samples collected during a double-blind, randomised, cross-over intervention study set up to assess the effect of inulin consumption on stool frequency in healthy adults with mild constipation were analysed. Faecal microbiota composition and metabolite profiles were linked to the study9s clinical outcome as well as to quality-of-life measurements recorded. Results While faecal metabolite profiles were not significantly altered by inulin consumption, our analyses did detect a modest effect on global microbiota composition and specific inulin-induced changes in relative abundances of Anaerostipes , Bilophila and Bifidobacterium were identified. The observed decrease in Bilophila abundances following inulin consumption was associated with both softer stools and a favourable change in constipation-specific quality-of-life measures. Conclusions Ecosystem-wide analysis of the effect of a dietary intervention with prebiotic inulin-type fructans on the colon microbiota revealed that this effect is specifically associated with three genera, one of which ( Bilophila ) representing a promising novel target for mechanistic research. Trial registration number NCT02548247.

Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis.

Abstract: Objective Dysbiosis of the intestinal microbiota has been widely established in inflammatory bowel disease (IBD). There is significant clinical and genetic overlap between spondyloarthritis (SpA) and IBD, and up to 50% of all patients with SpA exhibit microscopic signs of bowel inflammation, often bearing particular resemblance to early Crohn's disease, a subtype of IBD. This study was undertaken to assess the relationship between intestinal microbial composition, gut histology, and disease activity markers in SpA. Methods Gene analysis by 16S ribosomal RNA amplicon sequencing was used to compare the microbial composition in ileal and colonic biopsy specimens from 27 patients with SpA (14 with microscopic bowel inflammation, 13 without) and 15 healthy control subjects (ileal samples from all 15 subjects and colonic samples from 6). Spearman's rank correlation tests were used to assess correlations of the microbial composition with disease activity measures. Results The intestinal inflammation status (histologically normal versus acute or chronic inflammation) was strongly associated with the mucosal microbiota profile of patients with SpA. In inflamed biopsy tissue, the detected bacterial community composition clustered separately from that in noninflamed biopsy tissue (P < 0.05 by permutational multivariate analysis of variance, using hierarchical clustering on Bray–Curtis distances). Interestingly, abundance of the genus Dialister was found to be positively correlated with the Ankylosing Spondylitis Disease Activity Score (Spearman's rho = 0.62, false discovery rate–corrected q < 0.01). This finding was further supported by the low frequency of Dialister observed in noninflamed ileal and colonic biopsy tissue from patients with SpA and healthy controls. Conclusion These findings demonstrate a significant difference in the intestinal microbial composition in patients with SpA who have microscopic gut inflammation compared to those without microscopic gut inflammation. Moreover, Dialister may represent a potential microbial marker of disease activity in SpA.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

Practical considerations for large-scale gut microbiome studies.

Abstract: First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.

The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.

Abstract: Biological psychiatry research has long focused on the brain in elucidating the neurobiological mechanisms of anxiety- and trauma-related disorders. This review challenges this assumption and suggests that the gut microbiome and its interactome also deserve attention to understand brain disorders and develop innovative treatments and diagnostics in the 21st century. The recent, in-depth characterization of the human microbiome spurred a paradigm shift in human health and disease. Animal models strongly suggest a role for the gut microbiome in anxiety- and trauma-related disorders. The microbiota–gut–brain (MGB) axis sits at the epicenter of this new approach to mental health. The microbiome plays an important role in the programming of the hypothalamic–pituitary–adrenal (HPA) axis early in life, and stress reactivity over the life span. In this review, we highlight emerging findings of microbiome research in psychiatric disorders, focusing on anxiety- and trauma-related disorders specifically, an...

Multi-stability and the origin of microbial community types

Abstract: The study of host-associated microbial community composition has suggested the presence of alternative community types. We discuss three mechanisms that could explain these observations. The most commonly invoked mechanism links community types to a response to environmental change; alternatively, community types were shown to emerge from interactions between members of local communities sampled from a metacommunity. Here, we emphasize multi-stability as a third mechanism, giving rise to different community types in the same environmental conditions. We illustrate with a toy model how multi-stability can generate community types and discuss the consequences of multi-stability for data interpretation.

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

Abstract: High-throughput sequencing technologies have recently made it possible to interrogate the phylogenetic diversity of soils at considerable depth. This ability has led to the development of many computational tools to infer interaction networks from environmental samples. Although such tools have widely been used, they have more often served as a visual means to compare microbial communities across environmental gradients than as a means to appreciate microbial interactions associated with certain ecological processes. Previous studies have often regarded a subnetwork (module) as a functional unit but its functionality in ecological context has never been evidenced. To make better use of these tools in appreciating microbial interactions, we propose the combinational use of different inference tools. This ensemble approach permits the use of more independent predictors and the removal of tool-specific predictions in order to increase prediction accuracy. The purpose of the present study is to identify ecologically meaningful bacterial associations using multi-tool approach. Soil samples were collected in time series from experimental paddy rice plots. Bacterial communities were characterized by high-throughput tag sequencing of 16S rRNA gene fragments. We used three tools, Co-occurrence Network inference (CoNet), Molecular Ecological Network Analysis (MENA) and extended Local Similarity Analysis (eLSA), to infer networks from abundance profiles, partitioned the networks into modules, screened for the modules with ≥50% of genus-/species-level nodes, captured the modules that were derived from different tools and shared ≥ 50% of order-level nodes (tool-agreed modules) and tested their robustness against the changes in the tool parameters. By these procedures, two three-tool-agreed modules were found. One represented a guild that is phenotypically associated with aerobic respiration and fermentation and the other represented a guild phenotypically associated with metal/sulphur cycles, all of which are essential processes of water-submerged paddy soils that are mediated by bacteria. These data suggested that the linked members in a module were functionally associated taxa that work together to achieve a distinct function or an ecological process, and thus were ecologically meaningful to the environment. We selected three linked species from a three-tool-agreed module and validated their interactions using co-culture methods. Results showed that the interaction type between Janthinobacterium lividum and Leuconostoc lactis in the two-species mixture was validated to be ambivalent, positive for one partner and negative for the other. However, this type of interaction was not retained when a third party Lactococcus piscium was introduced, signifying the complexity of multi-species interactions. Validation results suggested that the selected species were interacting partners in laboratory but the validated interaction types were different from those inferred. By multi-tool approach, we also found that highly linked nodes, which are often referred to as “keystone species” and are frequently interpreted as the species playing important roles in soils, are tool dependent. Among top ten highly linked nodes, only four are conserved across three tools. These results suggest more research is required on the ecological significance of degree-based identification of keystone species. Overall, the present study highlights the potential utility of combined use of inference tools to identify ecologically meaningful bacterial associations in soils and other environmental samples. It is interesting to see what type of ecologically meaningful bacterial associations can be found in other soils.

Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating

Abstract: We read with interest the work by Halmos et al 1 in which they describe the effects of dietary FODMAP (Fermentable Oligo-, Di- and Mono- saccharides And Polyols) restriction in patients with IBS on the intestinal microbiota. They showed that low FODMAP intake was associated with reduced total bacterial and lower relative abundance of butyrate-producing Clostridium cluster XIVa, changes that are generally considered unfavourable.2 Therefore, they discourage long-term dietary FODMAP restriction, a suggestion also supported by the recent work of McIntosh and colleagues who noticed unfavourable changes in both microbiota and metabolome of patients with IBS who were on a low FODMAP diet.3 Although low FODMAP intake reduces GI symptoms in almost 75% of patients with IBS, the effects of this diet on the intestinal microbiota might be disadvantageous in the long run. Combining these observations with the important role for the intestinal microbiota in IBS pathogenesis,4 we report here faecal microbiota transplantation (FMT) as an alternative to FODMAP restriction in patients with IBS. We applied FMT in 12 refractory IBS patients (Rome III criteria) with intermittent diarrhoea and severe bloating, …

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.

Abstract: The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors, and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS, and USEARCH. Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate, and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines. The newly introduced pipeline translates Illumina MiSeq amplicon sequencing data into high-quality and reliable OTUs, with improved performance and accuracy compared to the currently existing pipelines.

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Abstract: Nature 528, 262–266 (2015); doi:10.1038/nature15766 In the Supplementary Information to this Letter, data from two previous studies were used in the meta-analysis. However, the unit conversions used to make the data comparable were inconsistent for two of the included phenotype measures. Although this error does not affect the data used to generate the conclusions of the Letter, it might affect follow-up studies using the glycated haemoglobin (HbA1c) and serum insulin phenotypes.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

Abstract: Summary Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. This article is protected by copyright. All rights reserved.

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine

Abstract: Chronic inflammatory diseases (CIDs), including Crohn’s disease and ulcerative colitis (inflammatory bowel diseases, IBD), rheumatoid arthritis, psoriasis, psoriatic arthritis, spondyloarthritides, hidradenitis suppurativa, and immune-mediated uveitis, are treated with biologics targeting the pro-inflammatory molecule tumour necrosis factor-α (TNF) (i.e., TNF inhibitors). Approximately one-third of the patients do not respond to the treatment. Genetics and lifestyle may affect the treatment results. The aims of this multidisciplinary collaboration are to identify (1) molecular signatures of prognostic value to help tailor treatment decisions to an individual likely to initiate TNF inhibitor therapy, followed by (2) lifestyle factors that support achievement of optimised treatment outcome. This report describes the establishment of a cohort that aims to obtain this information. Clinical data including lifestyle and treatment response and biological specimens (blood, faeces, urine, and, in IBD patients, intestinal biopsies) are sampled prior to and while on TNF inhibitor therapy. Both hypothesis-driven and data-driven analyses will be performed according to pre-specified protocols including pathway analyses resulting from candidate gene expression analyses and global approaches (e.g., metabolomics, metagenomics, proteomics). The final purpose is to improve the lives of patients suffering from CIDs, by providing tools facilitating treatment selection and dietary recommendations likely to improve the clinical outcome.

Water activity does not shape the microbiota in the human colon

Abstract: We recently reported an association between stool consistency as measured by the Bristol Stool Scale (BSS) and major markers of the gut ecosystem, including microbial richness, enterotypes and bacterial growth rates in 53 healthy women.1 Meanwhile, the link between stool consistency and colon microbiota composition has been confirmed in two large-scale (n>1000) cohorts including individuals of both sexes, different age and varying health statuses.2 ,3 In our original manuscript, we hypothesised on mechanisms that would explain the associations observed. Two potential mechanisms were put forward, namely colon ecosystem differentiation through passage rate variation and reduction of water availability. While the impact of passage rate on ecosystem composition has recently been shown to partially account for BSS-associated microbiota variation,4 the potential correlation with water availability remains unexplored. Water activity (aw) is a dimensionless variable that reflects …

Microbiology: Crowdsourcing Earth's microbes.

Abstract: A large-scale study has been assessing microbial diversity by analysing DNA sequences from samples submitted by scientists around the globe. The initial results are now being used to create an open-access resource. See Article p.457