Somak 🥼💻✨️

Sorry meant 0.1%. A lot of tinkering at db level might be needed before the illumina v4-v5 could be analysed.

Would it make sense to create otu bins till 99% at 1% increments and gather a representative sequence? The repset could be made into a strain blast db or bowtie index. No. Of mapped reads to strain db divided by total reads should give strain level relative abundance from v4 regions.

Full length 16S data is from Sanger seq or extracted from wgs denovo assembly?

Rookie scientists make research teams more innovative Papers from research teams with a substantial number of beginners are highly disruptive and innovative, study shows.

Papers from research teams with a substantial number of beginners are highly disruptive and innovative

go.nature.com/4nrEvqg

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes | Philosophical Transactions of the Royal Society B: Biological Sciences Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or can...

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes

Phil. Trans. R. Soc. B by @annecmg.bsky.social et al
with @fbaumdicker.bsky.social

royalsocietypublishing.org/doi/10.1098/...

Welcome to #bluesky team CEH shoutout to Tim from India this time!

Vacancy — Assistant Professor in Microbiome Imaging and Functional Analysis Are you pioneering molecular tools and applying advanced imaging strategies to uncover how microbial communities are organized and interact in space and time? If so, we invite you to join The Swammerd...

Assistant Professor position in the Microbiome Engineering group (Prof Sahar El Aidy) at University of Amsterdam

Assistant Professor in Microbiome Imaging and Functional Analysis
werkenbij.uva.nl/en/vacancies...

Great to see our Review "The gut microbiome connects nutrition and human health" making the cover of this month's @natrevgastrohep.nature.com

@patrickveiga.bsky.social @eranelinav.bsky.social
www.nature.com/articles/s41...

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Hi #microbiome folks, Do you have a custom recipe that is used for anaerobic faecal sample preservation during collection and transport at room temp? Need it for samples whose fate is culturomics.
#gutmicrobiome

Hi #microbiome folks, Do you have a custom recipe that is used for anaerobic faecal sample preservation during collection and transport at room temp? Need it for samples whose fate is culturomics.
#gutmicrobiome

Keeping it behind a landing page with necessary forms and authentication is also reasonable as long as wait times are not too long imho.

There is no problem in wanting to know how many times and by whom data has been accessed. But if no personal identity info is part of the data then i see no reason why in the age of figshare, sra and other open repos intent to share is hiding behind this tactic.

Data not shared = science didnt happen.

Journals should do a test request and then send notice why such papers shouldn’t be retracted.

🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria

-in BMC Microbiome

microbiomejournal.biomedcentral.com/articles/10....

If bclconvert is done then output of that too passed to multiqc for a detailed summary

Fastqc with fastp summarized using multiqc when sample numbers are very large.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

I think this is a paper every microbiome scientist should read:
www.nature.com/articles/s41...

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation Abstract. Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in

We're happy to announce that the #antiSMASH v8 paper is out in @narjournal.bsky.social: academic.oup.com/nar/advance-...
Many thanks to @kblin.bsky.social, @marnixmedema.bsky.social and many international collaborators!

Your periodic reminder that one way to think about privilege is: who's allowed to make mistakes?

Now in airport vending machines.
The evidence that it does anything to promote one's health does not exist.

Most bacterial gene families are biased toward specific chromosomal positions The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...

I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/

A chemical radar allows bacteria to detect and kill predators Pseudomonas syringae can detect and kill microbial predators via a chemical radar (Cra), which also allows the bacterium to infect plants despite predation pressure.

📜 A chemical radar allows bacteria to detect and kill predators

🧑‍🔬 Shuaibing Zhang, Pierre Stallforth, et al.

📔 @cellpress.bsky.social

🔗 www.cell.com/cell/fulltex...

#️⃣ #PlantImmunity #Microbiology #ChemicalEcology #SocialAmoebae #Pseudomonas

DTU IT is tracking some network issues that seem to also affect the #antiSMASH servers. I'll post an update once I know more.

A chemical radar allows bacteria to detect and kill predators Pseudomonas syringae can detect and kill microbial predators via a chemical radar (Cra), which also allows the bacterium to infect plants despite predation pressure.

chemical crosstalk at a distance of 𝘗𝘴𝘦𝘶𝘥𝘰𝘮𝘰𝘯𝘢𝘴 𝘴𝘺𝘳𝘪𝘯𝘨𝘢𝘦 with 𝘗𝘰𝘭𝘺𝘴𝘱𝘩𝘰𝘯𝘥𝘺𝘭𝘪𝘶𝘮 𝘱𝘢𝘭𝘭𝘪𝘥𝘶𝘮 amoebae. oh nos, this does not end well for the amoebas...

www.cell.com/cell/fulltex...
#MicroSky

Radar_paper This is "Radar_paper" by somak chowdhury on Vimeo, the home for high quality videos and the people who love them.

Hot of the Press 🎙️ : "A chemical radar allows bacteria to detect and kill predators"

Very glad to have been a part of this study from Stallforth lab published in journal @cellpress.bsky.social .

Link to the paper 🔗 : shorturl.at/4DWPp

Here is an explainer of the study🎙️. vimeo.com/1072064686

If you are interested in a postdoc opportunity in Europe, I'd suggest you to consider the EU Marie Curie Postdoctoral Fellowship:

ec.europa.eu/info/funding...

If you are into marine microbial ecology and evolution, I'd love to support your application (see more at merenlab.org).

E-MAIL ME NOW! :)