VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

Abstract

BackgroundMetagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge.ResultsWe present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented.ConclusionsVizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-014-0066-1) contains supplementary material, which is available to authorized users.

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

“…The impact of delivery mode and infant feeding history on the gut microbiota may, therefore, be lost after the first years of life, although it is still unclear exactly when (Penders et al ., 2006; Biasucci et al ., 2010). Gut microbiota composition has been reported to begin to converge toward an adult‐like microbiota by the end of the first year of life and fully resemble the adult microbiota by 2.5 years of age (Clemente et al ., 2012), although other studies have shown that the microbiota of children up to 4 years of age differs from that of adults (Kulka et al ., 2013; Hollister et al ., 2015), suggesting that conversion to an ‘adult‐like’ microbiota may be a long and gradual process.…”

“…Although it is recognized that the gut microbiota has the potential to change along with the development of its host, information regarding the structure and function of the microbiome in children remains limited (Hollister et al ., 2015). We hypothesized that an aberrant gut microbiota composition and activity might contribute to the development of childhood obesity.…”

“…Although it has been suggested that the microbiota reaches a relatively stable adult‐like state in the first three years of life, other evidence indicates that it continues to develop through adolescence (Hollister et al ., 2015). As such, childhood may provide unique opportunities for microbiota interventions to promote health or prevent disease.…”

“…As such, childhood may provide unique opportunities for microbiota interventions to promote health or prevent disease. It is, therefore, vital to establish a baseline understanding of pediatric gut microbiota structure and function, as during this period the gastrointestinal tract undergoes a transition from an immature to a mature state (Hollister et al ., 2015). …”

Modulation of the gut microbiota by prebiotic fibres and bacteriocins

“…In addition to the resilience of the gut microbiota, the gut microbiome exhibits functional redundancy, which guarantees that the key functions are maintained for normal gut functioning [28,30]. These key functions are conserved among individuals and this set of genes is normally referred to as a core microbiome [1,31].…”