Meta-analysis of human gut microbiome case-control studies

In this paper, Duvallet et al. present an effective way to conduct meta-analyses of 16S-based case-control studies of human-gut associated diseases. By reprocessing the datasets with a common bioinformatic pipeline and collapsing to the genus level, significant associations can be compared across studies for the same disease and across multiple studies of different diseases.
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Quantitative microbiome profiling

...relative abundance data cannot be used to determine directional changes in taxa abundance or the biological relevance of these shifts. Vandeputte et al., attempt to solve this issue by measuring absolute bacterial loads of samples in combination with relative abundance information from 16S profiling to create quantitative microbiome profiles.
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Autism in mice linked to maternal microbiome

...evidence that MIA-mediated abnormal behavioural phenotypes requires both the presence of segmented filamentous bacteria (SBF) and viral immune activation during pregnancy in mice. These two factors induce the differentiation of IL-17-producing T helper 17 (TH17) cells in pregnant mothers. Their offspring display behavioural abnormalities, which are associated with the presence of cortical patches in the somatosensory cortex of the brain.
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Comparative metagenomics of Blastocystis

This paper is a great example of data-mining available shotgun metagenomics sequencing (MGS) datasets for novel inference. They focus on Blastocystis, a genus of unicellular eukaryotic microorganisms in the Stramenopile phylum. Morphologically strains are similar, but genetically can be extremely different.
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