Literature highlights 04/04/2022

My favorite recent cover goes to the Biram et al. article in Immunity which found that germinal centre formation can be disrupted when infected with a second pathogen.

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Cell Host & Microbe

Host-fungi interactions are clearly very important but have long been ignored so happy to see some mechanisms being profiled. This article demonstrates that sensing fungi can lead to altered neutrophil activity. I wonder does this extend to fungi in the microbiome (The authors here used a Candida model). 

Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones– Immunity

I’m always a sucker for a multi-omics paper. The biology here is obviously very cool for studying HIV infection but from a methods point of view it’s pretty amazing that they can get surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell.

Bioinformatic methods corner

cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies – Nature Communications

An implementation of popular batch correction technique COMBAT for cytometry data. This is potentially a game changer for large flow cytometry or other datasets. COMBAT is so useful for RNASeq, and I’m pretty excited to try this out! Find more info at their Github

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation – Microbiome

Reports on development of SameStr, a tool for identifying shared strains across metagenomes through SNVs in marker genes. Seems like a useful tool (although I’d love one that doesn’t need a reference db :D). Not sure I’ve ever seen someone related strains from metagenomics to a host phenotype in a systematic way but this gives me an idea. 

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Microbiome

Some love for viral metagenomes. This tools looks useful. Seems to go beyond just implementing command line things in a user-friendly way. The macro- and micro-diversity estimates look interesting, not sure I’ve seen that in a viral metagenome paper (Although I’ve been out of that game for ~4 years now).


Viewing Bacterial Colonization through the Lens of Systems Biology – mSystems

Carbohydrate-active enzymes (CAZymes) in the gut microbiome – Nature Reviews Microbiology

Other papers that caught my eye recently

Unifying the known and unknown microbial coding sequence space – eLife

Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort – Genome Medicine

Immunisation with the BCG and DTPw vaccines induces different programs of trained immunity in mice – Vaccine

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