Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls

BACKGROUND: As little is known of association(s) between gut microbiota profiles and host immunological markers, we explored these in children with and without multiple sclerosis (MS). METHODS: Children ≤18 years provided stool and blood. MS cases were within 2-years of onset. Fecal 16S rRNA gene profiles were generated on an Illumina Miseq platform. Peripheral blood mononuclear cells were isolated, and Treg (CD4(+)CD25(hi)CD127(low)FoxP3(+)) frequency and CD4(+) T-cell intracellular cytokine production evaluated by flow cytometry. Associations between microbiota diversity, phylum-level abundances and immune markers were explored using Pearson’s correlation and adjusted linear regression. RESULTS: Twenty-four children (15 relapsing-remitting, nine controls), averaging 12.6 years were included. Seven were on a disease-modifying drug (DMD) at sample collection. Although immune markers (e.g. Th2, Th17, Tregs) did not differ between cases and controls (p > 0.05), divergent gut microbiota associations occurred; richness correlated positively with Th17 for cases (r = +0.665, p = 0.018), not controls (r = −0.644, p = 0.061). Bacteroidetes inversely associated with Th17 for cases (r = −0.719, p = 0.008), not controls (r = +0.320, p = 0.401). Fusobacteria correlated with Tregs for controls (r = +0.829, p = 0.006), not cases (r = −0.069, p = 0.808). CONCLUSIONS: Our observations motivate further exploration to understand disruption of the microbiota-immune balance so early in the MS course. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12883-016-0703-3) contains supplementary material, which is available to authorized users

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

Abstract Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets

Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion

Purpose: Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes within and upon them. We analyzed the microbiomes of these underground organs from both an important crop plant (Medicago sativa) and a related legume (M. polymorpha) using metagenomic and culture-based techniques to identify the main cultivatable contributors to plant growth enhancement. Methods: Using high-throughput sequencing, culturing, and in planta techniques, we identified and analyzed a broad population of the bacterial taxa within Medicago nodules and the surrounding soil. Results: Fifty-one distinct bacterial strains were isolated and characterized from nodules of both Medicago species and their growth-promoting activities were studied. Sequencing of 16S rRNA gene amplicons showed that in addition to Ensifer, the dominant genus, a large number of Gram-positive bacteria belonging to the Firmicutes and Actinobacteria were also present. After performing ecological and plant growth-promoting trait analyses, selecting the most promising strains, and then performing in planta assays, we found that strains of Bacillus and Micromonospora among others could play important roles in supporting the growth, health, and productivity of the host plant. Conclusion: To our knowledge, the comparison of the biodiversity of the microbiota of undomesticated vs. cultivated Medicago roots and nodules is novel and shows the range of potential Plant Growth-Promoting Bacteria that could be used for plants of agricultural interest. These and other nodule-isolated microbes could also serve as inoculants with rhizobia with the goal of replacing synthetic fertilizers and pesticides for sustainable agriculture