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Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice.

TL;DR: This is the first study suggesting that the poor stroke recovery in aged mice can be reversed via poststroke bacteriotherapy following the replenishment of youthful gut microbiome via modulation of immunologic, microbial, and metabolomic profiles in the host.
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Gut microbial molecules in behavioural and neurodegenerative conditions.

TL;DR: Bacterial metabolites with known or suspected neuromodulatory activity are described, mechanisms of signalling pathways from the gut microbiota to the brain are defined and direct effects that gut bacterial molecules are likely exerting on specific brain cells are discussed.
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Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease

TL;DR: This paper found that the immature phenotype of microglia from germ-free (GF) mice is epigenetically imprinted by H3K4me3 and H3k9ac on metabolic genes associated with substantial functional alterations including increased mitochondrial mass and specific respiratory chain dysfunctions.
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Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes

TL;DR: Dysbiosis of SCFAs‐producing bacteria andSCFAs in AIS patients increased the subsequent risk for poor functional outcomes, indicating that SCFas could be potential prognostic markers and therapeutic targets for stroke.
References
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Journal ArticleDOI

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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STAR: ultrafast universal RNA-seq aligner

TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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Cutadapt removes adapter sequences from high-throughput sequencing reads

TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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