My shout out to an amazing cover goes to Glass et al. Cell Reports. An acrylic painting representing their study of human B cell diversity of IL-10+ B cell states.
Environmental factors shaping the gut microbiome in a Dutch population – Nature
This represents a significant resource for studying the human gut microbiome.
- Metagenomics of >8,000 people from >2000 families + meta data on 241 host and environmental factors, including diet.
- Found the microbiome is shaped primarily by the environment and cohabitation.
- Less than 7% of taxa are heritable,
- Almost half of variation is explained by cohabitation.
Reporting on the development of a novel spatial omics platform for studying host-microbe interactions. The authors use this approach to investigate bacterial colonization of crypts
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections – Nature Microbiology
Fascinating study combining 16S data with RNASeq & data collected on early life viral infections. Integrating 16S and RNASeq data is growing more and more common but not sure I’ve ever seen it integrated with data on viral infections like this. Also have to hand it to the authors for their presentation of the data in this study. Simple yet highly effective visualisations that don’t sacrifice style. Figure 5A is particularly pretty.
Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation – Science Immunology.
- A major mechanistic study demonstrating how the gut virome directly shapes the immune system.
- Mice humanized with non-IBD colon tissue viromes were protected from intestinal inflammation, whereas IBD virome mice exhibited exacerbated inflammation in a nucleic acid sensing–dependent fashion
- There’s been several association studies of the virome and IBD, nice to see it a more causative mechanistic investigation.
Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – PLOS Biology
I love microbiome meta analyses and this is no exception. I think this quote sums up the main findings nicely:
“>90% of published findings for type 1 diabetes (T1D) and type 2 diabetes (T2D) were particularly nonrobust”
Reviews
- Targeting the gut and tumor microbiota in cancer – Nature Medicine
- “Molding” immunity—modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease – Mucosal Immunology
- Role of the gut–brain axis in energy and glucose metabolism – Experimental & Molecular Medicine
- Holo-omics for deciphering plant-microbiome interactions – Microbiome.
- Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression? – Nature Reviews Gastroenterology and hepatology
Other articles to highlight
- ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs – Nature. (Really going to need to start collecting data on secretor status in our microbiome studies)
- Consumer-grade wearables identify changes in multiple physiological systems during COVID-19 disease progression – Cell Reports Medicine.
- Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa – Plos Computational Biology
- Impact of gene annotation choice on the quantification of RNA-seq data – BMC Bioinformatics
- Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis – eLife
- Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants – Kaelin et al. Nature Microbiology
Host - Microbe interactions literature 