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How to assemble a beneficial microbiome in three easy steps.

ABSTRACT: There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of Pseudonocardia bacteria, which (somehow) evolve new compounds in arms-race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non-coevolved actinobacterial genera from the soil, enabling a 'multi-drug' strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic-producing (and -resistant) bacteria. This partner-choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in disease-suppressive soils.

SUBMITTER: Scheuring I

PROVIDER: S-EPMC3507015 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature

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How to assemble a beneficial microbiome in three easy steps.

Scheuring István I Yu Douglas W DW

Ecology letters 20120822 11

There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of Pseudono ...[more]

PMID: 22913725

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Project description:BackgroundThe rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills.ResultsHere we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP.ConclusionsThis EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.

Project description:BackgroundWhile scoliosis has, for a long time, been defined as a three-dimensional (3D) deformity, morphological classifications are confined to the two dimensions of radiographic assessments. The actually existing 3-D classification proposals have been developed in research laboratories and appear difficult to be understood by clinicians.Aim of the studyThe aim of this study was to use the results of a 3D evaluation to obtain a simple and clinically oriented morphological classification (3-DEMO) that might make it possible to distinguish among different populations of scoliotic patients.MethodWe used a large database of evaluations obtained through an optoelectronic system (AUSCAN) that gives a 3D reconstruction of the spine. The horizontal view was used, with a spinal reference system (Top View). An expert clinician evaluated the morphological reconstruction of 149 pathological spines in order to find parameters that could be used for classificatory ends. These were verified in a mathematical way and through computer simulations: some parameters had to be excluded. Pathological data were compared with those of 20 normal volunteers.ResultsWe found three classificatory parameters, which are fully described and discussed in this paper: Direction, the angle between spinal pathological and normal AP axis; Shift, the co-ordinates of the barycentre of the Top View ; Phase, the parameter describing the spatial evolution of the curve. Using these parameters it was possible to distinguish normal and pathological spines, to classify our population and to differentiate scoliotic patients with identical AP classification but different 3D behaviors.ConclusionThe 3-DEMO classification offers a new and simple way of viewing the spine through an auxiliary plane using a spinal reference system. Further studies are currently under way to compare this new system with the existing 3-D classifications, to obtain it using everyday clinical and x-rays data, and to develop a triage for clinical use.

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How to assemble a beneficial microbiome in three easy steps.

Publications

How to assemble a beneficial microbiome in three easy steps.

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