📢 New release of AncientMetagenomeDir (v23.09: Historic Centre of Cienfuegos) by the @spaam_community !

https://github.com/SPAAM-community/AncientMetagenomeDir/releases/tag/v23.09.0

💀 #AncientMetagenomeDir is a community curated resource of standardised lists of #metadata of >2000 shotgun-sequenced and publicly available #AncientMetagenome or ancient microbial genome-level enriched samples and >5000 libraries.

Release stats in the thread below 👇

#AncientDNA #palaeogenomics #aDNA #SPAAM #metagenomics

There are obviously limitations such as an inability to quantify supplements or very processed foods with little or no DNA, but overall it seems to work quite well and will combine well with marker gene and metabolomics approaches since they are very complementary.
https://www.pnas.org/doi/full/10.1073/pnas.2304441120
https://www.nature.com/articles/s41587-022-01368-1

Many thanks to @gibbological and the ISB for the patience with this long-running project.

Food genomic material was detected only in about half of infant stool samples but increased at the onset of solid food consumption and was ubiquitous in adult stool samples.

We also ran a proof-of-concept identifying foods and nutrients that were associated with the onset of metabolic disease in an adult cohort.

Building a comprehensive genomic database for as many foods in FOODB as possible we could connect individual genomes to nutrient content. For now we can match 77% of all foods in FOODB with taxonomic information and the next version of the database will push this to 90%.

Using a decoy-aware mapping approach with additional consistency filtering we could show good sensitivity and specificity in simulated sequencing samples with a false positive rate around 1-10 reads per million.

Happy to announce that my last preprint from the Gibbons Lab at ISB is now out at https://www.biorxiv.org/content/10.1101/2024.02.02.578701v1 . In the end it took us almost 5 years to make this work well.

Dietary intake is major factor in many studies but is not easy to measure on a fine-grained level. Our idea was to use metagenomic shotgun sequencing of fecal samples to detect and quantify food-derived DNA.

Thrilled to congratulate #MathiasGotsmy on a stellar defense! 🥳

Grateful for the opportunity to have guided you through the start of your academic journey, proud to witness your achievements & excited for a bright future ahead

Huge congrats! 🙌

#phdlife #proudPI #univienna

🐈 ← 💼 Some personal news: Early 2024 I will be joining the faculty of the @medunigraz. It's definitely a bitter-sweet moment leaving the amazing @gibbological lab at ISB, but I am very excited for what comes next and can't wait to work with the great research community in Graz (and Europe). https://www.cdiener.com/posts/meduni-graz/

Disease-specific loss of microbial cross-feeding interactions in the human gut https://www.nature.com/articles/s41467-023-42112-w

Do I get a trophy now? #compbio #bioinformatics #nextflow #microbiome

The final day of the 2023 ISB Microbiome series will start in 30m. Today we have a symposium packed with amazing speakers, so be there or be ▣. 🦠+💻=💕 Session 1 will feature @cecilia and Lisa Maier. #ISBMicro23 #microbiome @isbsci

We will start day 2 of the Virtual ISB Microbiome course 2023 in 1h. Today, we will learn how to predict strain engraftment using metabolic modeling. https://isbscience.org/microbiome2023

The course will be based on Alex's preprint: https://doi.org/10.1101/2023.04.28.538771. 🦠+💻=💕

#microbiome #ISBMicro23

Only 45 minutes left until we start our Virtual ISB Microbiome course 2023. Can't wait to meet all the participants and chat with you about the course. 🦠+💻=💕. https://isbscience.org/microbiome2023 #microbiome #ISBMicro23

Better training for non-academic careers https://www.nature.com/articles/s41564-023-01499-4

A relational framework for microbiome research with Indigenous communities https://www.nature.com/articles/s41564-023-01471-2 #jcampubs

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes https://www.nature.com/articles/s41467-023-41424-1 #jcampubs

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle https://www.cell.com/cell/fulltext/S0092-8674(23)00906-6 #jcampubs

I'm excited to announce that the 2023 ISB Virtual Microbiome Series registration site is live!

We will host a 2-day bioinformatic course and a 1-day symposium Oct. 11-13.

This year's theme is 'how the ecology of our guts protects us from pathogens'

https://isbscience.org/microbiome2023/

If you are drafting figures for a scientific paper or presentation, remember that https://scidraw.io/ exists: a repository of free SVG cartoons for science.

#SciDraw is supported by the Sainsbury Wellcome Centre – @SWC_Neuro

All content on SciDraw is shared under creative commons license (CC-BY) unless stated otherwise.

#inkscape #SVG #science

Nennt mir einen wenig bekannten Fakt, der euch total vom Hocker gehauen hat, als ihr von ihm erfahren habt. 👇

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03028-2