Dr.Somak Chowdhury 🥼💻✨️

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! :)

How a PhD student’s lab size affects their chance of future academic success Trainees in big research groups tend to go on to greater academic success than their small-group counterparts ― but are more likely to quit academia altogether.

How a PhD student’s lab size affects their chance of future academic success - perhaps not very surprising but still fascinating
🧪 #AcademicSky

Original work www.nature.com/articles/s41...
@naturehumbehav.bsky.social
@nature.com
www.nature.com/articles/d41...

Absolutely! Dm’d you my details. Looking forward…

Any plans to visit Bengaluru?

We are looking for a bioinformatician with expertise in microbiome data analysis join our team at the University of Lausanne. The successful candidate will lead and support research projects within nccr-microbiomes.ch. More details here: shorturl.at/mC46o . Please share with potential candidates.

Page shown when one deactivates / leaves twitter

Quote by Elie Wiesl asking to take sides as neutrality favours the oppressor!

Not sorry to leave! F**k Elon! ✊🏽

Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses - Nature Microbiology Hexa-acylated lipopolysaccharides from the gut microbiota are associated with efficacy in patients with cancer receiving anti-PD-1 and stimulate host immune activation for enhanced anti-tumour immunit...

OUT NOW: Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses

@pedicordlab.bsky.social #microsky

www.nature.com/articles/s41...

Phenotypic divergence between individuals with self-reported autistic traits and clinically ascertained autism - Nature Mental Health Comparing clinically diagnosed adults with autism spectrum disorder (ASD) with online participants with self-reported high autistic traits, this study detected higher rates of social anxiety and avoid...

New research. A team tries to work out if self-identity as autistic is valid.
www.nature.com/articles/s44... is the paper.
I'll do a thread on some of their peculiar statements in it, and on the Broad Autism Phenotype Questionnaire (BAPQ) that they use to try to make a point. Here we go../

Under fascism, no one is safe.

Universities stayed quiet as the admin targeted DEI & foreign aid, censored research, etc.

Now, they face devastating cuts to indirect cost rates, threatening research & operations.

Silence won’t protect institutions. It won’t protect people; it never does.