I did not do justice to the great work of @bcoltman.bsky.social on MetaCoOc in this thread. A manuscript describing the tool fully, and a stable release of the code, are in preparation.

In the meantime, the code can be found here: github.com/bcoltman/met...

In addition, the environmental metadata is included in the amino acid sequence toolkit (AASTK) SQL database, and can be directly accessed using the Meta command. Thus, any dataset of GlobDB derived AA sequences can be annotated with their primary environments.

More on this here: globdb.org/aastk

Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories

We now provide environmental metadata for the GlobDB genomes!
🖥️🧬🦠

More info here:
globdb.org/news

🧵

Our new preprint introduces #kineochelins, a new group of #siderophores produced by the Antarctic soil actinomycete 🦠🔬🧫 #Actinokineospora sp. UV203

Kudos to the amazing Stanislava Králová & a fantastic team of collaborators 🤩
#microbiomesky

www.biorxiv.org/content/10.6...

Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard!
With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution.

Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado

www.biorxiv.org/content/10.6...

Associations of dietary intake for gut microbiota with frailty risk and mortality in older adults - Journal of Translational Medicine Journal of Translational Medicine - The associations between a diet that associated with a healthy gut microbiota and the risk of frailty, as well as mortality in older adults with frailty, remains...

A diet enriched in microbiome-fermentable substrates (more fruits and veggies) was shown to be associated with lower frailty and lower mortality risk in an older cohort (N>6000; 65+ y/o), with inflammation markers significantly mediating the dietary effect. link.springer.com/article/10.1...

Fresh from our group, a new role for oxygen production in ammonia-oxidizing archaea:

Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea

Congrats to Thomas Pribasnig for this great work!

Check it out here:
www.biorxiv.org/content/10.6...

Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬

Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!

doi.org/10.1093/isme...

Cosmopolitan marine bacteria facilitate a vast phytoplankton-derived sulfonate-based carbon flow through sulfoquinovosidases www.nature.com/articles/s41... #jcampubs 🌊

The Microflora Danica atlas of Danish environmental microbiomes - Nature Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...

Still a good deal in deed :)

That is an insane depth for 70 dollars, if DNA extraction and library prep are calculated in the cost. Would be curious to know how many samples one needs to multiplex to get costs this liw. Like, really - definitely sth I'd like to look into implementing.

The annual increase in number of dereplicated species representative genomes in GTDB or GlobDB shows how undersampled. And reference based MG profiling works best at species level, but not so great at higher phylogenetic distance.
Anyways, what I want to say is amplicon sequencing ain't dead (yet)

Agreed, our amp system pays of most if done high throughput and standardized, as we do.
How many MG reads do you get for 70 CAD?
Shallow MGs are wonderful, if you work in well sampled environments (i.e. human gut). However, the majority of habitats is still very undersampled.

JMF | Joint Microbiome Facility JMF | Joint Microbiome Facility

Jup :)
jmf.univie.ac.at

But if you sequence loads, anyone can set the system up in house and adjust turnaround time. 10.3389/fmicb.2021.669776
Or depth per samples (which affect price only a bit, majorityof cost is PCR, not seq), but more depth does you no good (less is OK for most samples, but that's a different topic).

5-15k reads of any amplicon per sample. Turnaround time depends on other workload, since we are researcher lab and not a company ;) 5 weeks for 1000 samples inc DNA extraction and data analysis.

You got the point. The V4EXT can become the platinum standard ;)

Also allows you to assess better how deep your MGs need to be. If you are working in an underexplored or highly variable habitat, it's hard to tell otherwise. Better 12€ and a few weeks for amplicons, than hundreds of € for depth you didn't need.

With the amount of contaminated and mixed up samples, or experiment gone wrong I've seen over 7 years and literally over 1000 amplicon sequencing projects I personally inspected for data quality, trust me, it's money well spent and responsible grant money handling to amplicon screen first.

While I see where the idea comes from, running a microbiome sequencing facility clearly shows it isn't. The overwhelming majority of projects is amplicon sequencing.
Also, genuinely, with our approach running amplicons before metagenomes costs 12€.

This nice summary by @michiwagner4.bsky.social makes it easy to fit my post in a few characters.
Amplicon sequencing is still an affordable and quick way to get good insights into who lives in your samples. Our new primers make sure your vision is 20/20.
Try em, and contact me if you have questions!

Organizer Thilo Hofmann @cemess.bsky.social, contributions from 30+ @univie.ac.at scientists, incl @michiwagner4.bsky.social, @christinakaiser.bsky.social, Stephan Krämer, @jillianmpetersen.bsky.social, @ppjevac.bsky.social, @andreasrichter.bsky.social, and @loutsi.bsky.social from our cluster.

Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity academic.oup.com/ismej/advanc... #jcampubs

Metabolic biochemical models of N2 fixation for sulfide oxidizers, methanogens, and methanotrophs journals.asm.org/doi/full/10.... #jcampubs

Struc­tures of meth­ane-ac­tiv­at­ing en­zyme in elu­sive ar­chaea

@mariecmueller.bsky.social @cuwelte.bsky.social @mpimarinemicrobio.bsky.social

#methane #ANME #archaea #MCR #microbiology #biochemistry #StructuralBiology

mpi-bremen.de/en/Structure...

✈️ Calling all grad students & postdocs in microbial ecology!
Want to work, train, or collaborate abroad? ISME’s Scholar Mobility Fund can help you get there.
📅 Apply by 1 October
🌍 Open to applicants worldwide (esp. outside NA & Europe!)
Details: isme-microbes.org/isme-scholar...
#MicrobialEcology

We are hiring: Full Professor of Soil Ecosystems and Global Change Soil ecosystems form the foundation of planetary health and play a critical role in climate feedback mechanisms. However, they are also vulnerable to the impacts of global change.

One week to go! Apply by Sept 17 for the Full Professor position in Soil Ecosystems and Global Change at #CeMESS at the University of Vienna.

More info: 🔗 ter.univie.ac.at/news-talks/n...

@univie.ac.at #SoilEcosystems #WeAreHiring

We are hiring: Full Professor of Environmental Biogeochemistry of Metals Human activities are driving rapid environmental change on a global scale, with pollutants playing a critical role in pushing planetary systems beyond safe limits. These changes have profound conseque...

Deadline approaching on Sept 17! We are hiring a Full Professor of Environmental Biogeochemistry of Metals at #CeMESS at the University of Vienna.

Learn more: 🔗 edge.univie.ac.at/news-talks/n...

@edge-vienna.bsky.social @univie.ac.at #EnvironmentalBiochemistry

Trans rights are, in fact, human rights. Pass it on. 🏳️‍⚧️🫂