Host-Microbe Interactions

microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data #Microbiome #Rstats #metagenomics journals.asm.org/doi/10.1128/mr…

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases #microbiome #metagenomics #bioinformatics #Rstats academic.oup.com/bib/article/26…

Bifidobacteria support optimal infant vaccine responses | Nature #microbiome #science #microbology nature.com/articles/s4158…

Free scientific illustrations for biologists! 😍 @NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations! all freely available in the public domain. Retweet and spread the message! bioart.niaid.nih.gov

BTW I’m not trying to dunk on this. Genuinely trying to learn. I might have misunderstood sometime. I mean it’s a Cell paper so obviously super impressive.

What do others think of this? I’m sceptical of any universal #microbiome signature. In this case they focus on genomes which “were detectable in more than 75% of the samples”. This seems very high to me but they found hundreds of genomes which met this threshold?

A core microbiome signature as an indicator of health | Cell Metagenomics on a high-fiber dietary intervention plus reanalysis of 26 case-control studies. Identified a set of stably correlated genome pairs perturbed by interventions and diseases cell.com/cell/fulltext/…

Classifying compounds as prebiotics — scientific perspectives and recommendations | Nature Reviews Gastroenterology & Hepatology #microbiome #research nature.com/articles/s4157…

The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions | FEBS Journal. Comprehensive Review, summarizes evidence & highlights potential mechanisms. #Immunology #microbiome febs.onlinelibrary.wiley.com/doi/full/10.11…

Haven’t used this account in months. I come back and somehow I’m verified 😳

Exercise mitigates a gut microbiota-mediated reduction in adult hippocampal neurogenesis and associated behaviours in rats Great to see this out - Congrats @_Sarah_Nicolas @yvonnemnolan and all nature.com/articles/s4139…

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system | Nature Immunology Review which critically assess underlying assumptions and limitations of these technologies in #immunology. nature.com/articles/s4159…

Utilization of the microbiome in personalized medicine | Nature Reviews Microbiology nature.com/articles/s4157…

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition | Cell Must read. Great example of why we shouldn't just look at bacteria in the gut microbiome. cell.com/cell/fulltext/…

Infant gut DNA bacteriophage strain persistence during the first 3 years of life | Cell Host & Microbe Analysed viral contigs assembled from 819 metagenomic samples collected from 52 infants. #microbiome #microbiota #virome sciencedirect.com/science/articl…

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients | Microbiome Compares ITS vs Metagen + demonstrates how to enrich for fungi using centrifugation. #microbiome microbiomejournal.biomedcentral.com/articles/10.11…

Microbiome diversity protects against pathogens by nutrient blocking | Science I don't think this will be surprising to anyone in the field but nice to see it demonstrated in using a combination of in vitro and in vivo gnotobiotic experiments. science.org/doi/10.1126/sc…

Spatial host–microbiome sequencing reveals niches in the mouse gut | Nature Biotechnology SHM-seq - an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue nature.com/articles/s4158…

Are people considering any other platforms for keeping up with the literature? I’m finding it increasingly difficult to justify being on here but I enjoy doing this

Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra | Nature Microbiology Resource based upon analysis of 2,229 HMP genomes. Identified candidates in-siliso and validated in-vitro. nature.com/articles/s4156…