Today’s digest features a 30-color colorblind friendly color palette and functions for mapping color to hierarchical/nested data, ecosystem-specific reference databases, stoma samples for a very effective way of small intestinal microbiome characterization, and a reminder that 16S rRNA gene sequencing is NOT metagenomics. Happy Friday!

Join the next #MVIF when Sarah Lebeer will talk about citizen science and vaginal microbiome!!

It's Monday!
…and #MVIF 13 program is out! 🤩
Looking forward to hearing all these talks!

⭐️Keynote: @SarahLebeer
⭐️Selected talks: @MikeNeug @Josiane63293249 @_YHuang

⭐️Highlights: @HuiminYe4 Chloe Mirzayi
@samueldgamboa

Registstratino:https://t.co/kQMf0mXqSz pic.twitter.com/rdhuyRJh5j

— Microbiome Virtual International Forum (@MicrobiomeVIF) October 31, 2022

Global resistome

Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome

Host-microbiome interactions: Gut-Liver axis and its connection with other organs – Swadha Anand & Sharmila S. Mande – npj Biofilms and Microbiomes

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment – Alice Chen-Liaw – bioRxiv

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut – Katrine Lekang – Plos One

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons – Joseph J. Bruckner – Plos Biology

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants – Lauren C. Beck – Nature Microbiology

*Plasticity of the adult human small intestinal stoma microbiota – Bahtiyar Yilmaz – Cell Host & Microbe

Happy to share our latest study published @cellhostmicrobe. We used stoma samples which provide a very effective way of small intestinal microbiome characterization with deep genetic sequencing without any purgatives. https://t.co/3iznKsQCIp pic.twitter.com/TL2tKdyfKU

— Bahtiyar Yilmaz (@bahti_yil) October 31, 2022

Bioinformatics

MIDAS2: Metagenomic Intra-species Diversity Analysis System – Chunyu Zhao – Bioinformatics

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data – Matteo Ciciani – Nature Communications

*microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data – Erin M. Dahl – Microbiology Resource Announcements

*Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling – Christina Karmisholt Overgaard – Frontiers in Microbiology

"shotgun and 16S metagenomics data"

16S metagenomics is a misnomer – a wrong or inaccurate use of a name or term

TL;DR 16S rRNA gene sequencing is NOT metagenomics

Well if you are still in doubt, you should read the thread below.
1/5 pic.twitter.com/DcVaCwzEH5

— Svetlana U. Perović (@svetlana_up) May 18, 2021