Ishan Bhatt

From genes to collective modes: biological constraints shape metabolic evolution https://www.biorxiv.org/content/10.64898/2026.03.11.711104v1

ICYMI: in our new paper, we contend there is "no current consensus on a definition of sex that is free of assumptions and limitations... and most importantly,...no biological definition of sex should be used to dictate human rights" #evolsky #LGBTQSTEM #ecology #evolution #biologicalsex

I adored working with students. I’m not a great teacher, and certainly not a great researcher. I am a good talent scout based on outcomes. I wish there was a way to keep doing it post retirement. PS: they are the ones with talent. But it is talent I am good at perceiving.

Art meets algae: Illustrator Daniela Gallego (Lulo Febril) is our Artist-in-Residence, creating illustrations of the brown algal life cycle - turning complex biology into clear visual stories and new ways to communicate science. Exhibition planned for May 26 - stay tuned: tinyurl.com/5n7ahect

Check out my new paper on the explanatory strenght of network models used in evolutionary sciences.
Here is the link: rdcu.be/e7ZWj

Schlafen sie nicht darauf

Prokaryotic defense systems: Diversity and evolutionary adaptation
#microbiology #virology #prokaryotes #archaea #bacteria #virus #phage
@mlifejournal.bsky.social
doi.org/10.1002/mlf2...

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).

A brief 🧵 (carried over from the old place)

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨

Let me hit you with some highlights on why spatial structure matters. (and why you should care!)

Sharing is appreciated 🙏 🧵👇

doi.org/10.1093/fems...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

𝐌𝐨𝐛𝐢𝐥𝐞 𝐠𝐞𝐧𝐞𝐭𝐢𝐜 𝐞𝐥𝐞𝐦𝐞𝐧𝐭𝐬 𝐝𝐨𝐧’𝐭 𝐣𝐮𝐬𝐭 𝐬𝐩𝐫𝐞𝐚𝐝 𝐫𝐞𝐬𝐢𝐬𝐭𝐚𝐧𝐜𝐞: 𝐭𝐡𝐞𝐲 𝐞𝐧𝐜𝐨𝐝𝐞 𝐚𝐧𝐭𝐢𝐛𝐢𝐨𝐭𝐢𝐜 𝐩𝐞𝐫𝐬𝐢𝐬𝐭𝐞𝐧𝐜𝐞, 𝐧𝐞𝐰 𝐬𝐭𝐮𝐝𝐲 𝐫𝐞𝐯𝐞𝐚𝐥𝐬.
In 𝐿. 𝑝𝑛𝑒𝑢𝑚𝑜𝑝ℎ𝑖𝑙𝑎, ICE pP36 generates growth heterogeneity, fuels persister formation, and transfers tolerance to clinical isolates.

✍️ @personniclab.bsky.social & coll.
📖 shorturl.at/jNqHS

Is “complexity” always in the eye of the beholder?

Is complexity in the system, or in the fit between the system and our description of it?

New #ComplexityThoughts:

open.substack.com/pub/manlius/...

Don’t deprioritize curiosity-driven research Around the world, governments are demanding that research funding follow broader political priorities. They should be careful what they wish for.

Don’t deprioritize curiosity-driven research www.nature.com/articles/d41...

Now nicely formatted!

See our newest manuscript dissecting emergent functions in a multispecies biofilm (metabolite cross-feeding, siderophore induction and cross-species utilization) that translates to plant growth promotion
Great work by @jiyuxie.bsky.social and Xinli Sun
www.biorxiv.org/content/10.6...

Should biology put complexity first? The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing dama…

Terrific essay on unavoidable complexity by @philipcball.bsky.social
"It is not yet clear what a curriculum—not to mention both a public and a professional narrative—that begins [w/pleiotropy + polygenicity] would look like. But it would surely look more like real biology.
doi.org/10.1016/j.ce...

When roots talk, bacteria respond: Comparative transcriptomics of three plant growth-promoting rhizobacteria growing on root exudates reveals plant-specific responses In the rhizosphere, plant roots release rhizodeposits, including a complex mixture of molecules known as root exudates. These compounds mediate the re…

When roots talk, bacteria respond: Comparative transcriptomics of three plant growth-promoting rhizobacteria growing on root exudates reveals plant-specific responses

-in Rhizospere

www.sciencedirect.com/science/arti...

PopGeneJS is a free web platform for teaching population genetics with 32 interactive modules on various topics. It offers real-time visualizations and requires no installation. Explore at https://popgenejs.bioinformat.org.

Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.

www.science.org/doi/10.1126/... wuuuuuut

Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis
www.biorxiv.org/content/10.6...

Spatial structure: shaping the ecology and evolution of microbial communities Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇

Happy birthday to a relatable fellow complainer.

An Explicit Test of Kill the Winner: Protistan Grazing and Phage Lysis Differentially Impact Fast‐Growing Bacterial Taxa in the Coastal Antarctic We evaluated whether predators ‘kill the winner’ wherein protists and phages preferentially impact the most abundant members of bacterial assemblages over an austral summer with weekly dilution exper...

An Explicit Test of Kill the Winner: Protistan Grazing and Phage Lysis Differentially Impact Fast‐Growing Bacterial Taxa in the Coastal Antarctic enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Ecological determinants of altruism in prokaryote antivirus defense - Biology Direct Prokaryote evolution is driven in large part by the incessant arms race with viruses. Genomic investments in antivirus defense can be coarsely classified into two categories, immune systems that abrog...

link.springer.com/article/10.1...

Regulation of chloroplast biogenesis and differentiation This review focuses on recent advances in chloroplast biogenesis and chromoplast differentiation, with emphasis on transcriptional regulation, and identifi

Regulation of #chloroplast biogenesis and differentiation

academic.oup.com/jxb/advance-...

@tamara-hverdeja.bsky.social @jxbotany.bsky.social @sebplants.bsky.social @sebiology.bsky.social @chloroplastics.bsky.social @cellwalldynamics.com @charlotte-dlslle.bsky.social @biogenesis.bsky.social

Describing endosymbiont–host interactions within the parasitism–mutualism continuum Bacteria that live inside the cells of arthropod hosts (“endosymbionts”) are gaining increasing interest as targets for pest control and for reducing the ability of arthropod vectors to transmit anim....

Reading and really liking this #openaccess paper by Ary Hoffman and @brandonscooper.bsky.social

onlinelibrary.wiley.com/doi/full/10....

Describing endosymbiont–host interactions within the parasitism–mutualism continuum