Samay Pande

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

Bottleneck size drives the evolution of cooperative traits in an aggregative multicellular myxobacterium Population bottlenecks shape the evolution of cooperative traits in Myxococcus xanthus through life cycle trade-offs. This study shows that stringent bottlenecks favor growth and sporulation, while re...

Happy to share our new paper in PLOS Biology journals.plos.org/plosbiology/...

Showed that population bottlenecks don't uniformly drive “cooperation” but rather selectively shape which cooperative traits evolve #evolution #ecology #microbiology

@vishuguttal.bsky.social @iamsamayp.bsky.social

Bottleneck size drives the evolution of cooperative traits in an aggregative multicellular myxobacterium Population bottlenecks shape the evolution of cooperative traits in Myxococcus xanthus through life cycle trade-offs. This study shows that stringent bottlenecks favor growth and sporulation, while re...

Very cool paper by Jyotsna Kalathera et al. from @iamsamayp.bsky.social 's-lab on

Bottleneck size drives the evolution of
cooperative traits in an aggregative multicellular
myxobacterium

just out @plosbiology.org

Congratulations to all coauthors.

journals.plos.org/plosbiology/...

Thank you so much Christian!

n/n Because bottlenecks occur in many complex life cycles (from microbes to multicellular development) these results can have broad implications for understanding evolution beyond bacteria.

11/n When multiple cooperative traits are under selection, bottleneck size determines which traits persist, which fade, and how life histories evolve, not just whether cooperation survives.

10/n Thus, being efficient at only one trait (for example) sporulation alone isn’t enough. Fitness depends on how selection acts across multiple cooperative traits, and bottlenecks reshape that selection.

9/n Whole-genome sequencing linked trait evolution to mutations in key regulators, including a σ54-interacting protein and a DNA-binding response regulator. Different bottleneck sizes led to distinct molecular paths.

8/n To understand these patterns, Prakhar developed a population. It shows how bottleneck size, random fluctuations, and clonal interference shape the evolution of cooperative traits.

7/n Mechanistically, stringent bottlenecks remove cells that fail to sporulate before transfer. Sporulation becomes essential, while other traits experience weaker selection, limiting improvements in overall fitness.

6/n Looking at lifecycle-level fitness, only populations evolved under relaxed bottlenecks became fitter than the ancestor. Stringent bottlenecks improved some traits, but not enough to increase overall fitness.

5/n Relaxed bottlenecks produced the opposite pattern: predation and germination improved, while sporulation and growth declined. These results reveal strong trade-offs between cooperative traits.

4/n Under stringent bottlenecks, only sporulation and growth got better. Surprisingly, predation and germination declined, showing that bottlenecks don’t universally maintain cooperation

3/n We evolved M. xanthus through full life cycles under repeated stringent or relaxed bottlenecks while tracking four cooperative traits at once. This lets us see how cooperation evolves when multiple traits are under selection together.

2/n Led by Jyotsna, with help from Vishwa, Neha, and Prakhar, we show how population bottleneck size shapes the evolution of multiple cooperative traits in Myxococcus xanthus. Big thanks to Vishu Guttal and Sandeep Krishna for helping make this study possible.

1/n New paper alert!
Bottlenecks are common in life cycles, but how do they shape the evolution of multiple cooperative traits at once? We tested this in M. xanthus under stringent vs relaxed bottlenecks.

Outline of the life cycle experimental evolution of M. xanthus with either 1% (stringent) or 15% (relaxed) population bottlenecks. Four different colonies of M. xanthus (GV1) were used to establish four parallel evolving lines. One generation of the complex life cycle with multiple social traits involved the growth of M. xanthus populations in nutrient-rich CTT liquid (with gentamycin) medium till O.D. 600 nm reached 0.3–0.4. These cultures were then spotted on starvation TPM hard agar (1.5% agar) plate for sporulation and fruiting body development. Next, only the spores (and not vegetative cells that failed to sporulate) were harvested by first incubating the M. xanthus populations at 50°C, after which they were transferred onto TPM hard agar (supplemented with 0.025% glucose) beds overlaid with Escherichia coli lawns in flasks for germination and predation. After incubation for 4 days on E. coli lawns, populations were harvested by adding 4 mL TPM buffer, shaking at 200 rpm, and either (0.04 mL) 1%, or (0.6 mL) 15% of harvested populations were transferred to fresh CTT liquid media with gentamycin (M. xanthus is naturally resistant to gentamycin whereas E. coli is sensitive to it). This selection regimen was repeated for 10 cycles.

Population bottlenecks shape the evolution of #cooperative traits in #Myxococcus via #LifeCycle trade-offs. @iamsamayp.bsky.social &co show that stringent bottlenecks favor growth & sporulation, while relaxed bottlenecks favor predation & germination @plosbiology.org 🧪 plos.io/3N1nia7

Outline of the life cycle experimental evolution of M. xanthus with either 1% (stringent) or 15% (relaxed) population bottlenecks. Four different colonies of M. xanthus (GV1) were used to establish four parallel evolving lines. One generation of the complex life cycle with multiple social traits involved the growth of M. xanthus populations in nutrient-rich CTT liquid (with gentamycin) medium till O.D. 600 nm reached 0.3–0.4. These cultures were then spotted on starvation TPM hard agar (1.5% agar) plate for sporulation and fruiting body development. Next, only the spores (and not vegetative cells that failed to sporulate) were harvested by first incubating the M. xanthus populations at 50°C, after which they were transferred onto TPM hard agar (supplemented with 0.025% glucose) beds overlaid with Escherichia coli lawns in flasks for germination and predation. After incubation for 4 days on E. coli lawns, populations were harvested by adding 4 mL TPM buffer, shaking at 200 rpm, and either (0.04 mL) 1%, or (0.6 mL) 15% of harvested populations were transferred to fresh CTT liquid media with gentamycin (M. xanthus is naturally resistant to gentamycin whereas E. coli is sensitive to it). This selection regimen was repeated for 10 cycles.

Population bottlenecks shape the evolution of #cooperative traits in #Myxococcus via #LifeCycle trade-offs. @iamsamayp.bsky.social &co show that stringent bottlenecks favor growth & sporulation, while relaxed bottlenecks favor predation & germination @plosbiology.org 🧪 plos.io/3N1nia7

📢 Postdoc position: Cell Biology of Cyanobacteria

in my group, as part of the Excellence Cluster "Microbes for Climate" (M4C) in Marburg, Germany.

More information at shorturl.at/wNnDT (see Project 2)

🔗Apply at shorturl.at/VsEDl
📅Deadline: Nov 16, 2025

Please repost. #Postdoc

Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome

Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky

www.biorxiv.org/content/10.1...

Learn how Bacillus siderophore benefit various plant species and the role of the biofilm matrix: our collaboration with Zhihui Xu's group published in @cp-cellreports.bsky.social

Siderophore-mediated iron enrichment in the biofilm matrix enhances plant iron nutrition

www.cell.com/cell-reports...

Who would have thought: nitrogen-fixing vibrios 😱 that interact with Pokkali rice roots and promote plant growth in brackish water. Amazing! Wonderful to see this detailed and careful investigation out for all to oogle. Many congratulations Ramesh 🎉

journals.asm.org/doi/10.1128/...

Genome-wide screen to identify Escherichia coli gene knockouts hypersensitive to trimethoprim and chloramphenicol. Top left: Schematic showing the screening strategy for identifying hypersensitive gene knockouts from the Keio mutant library. All mutants were cultured in LB and LB supplemented with trimethoprim (TMP) and chloramphenicol (CMP) at their respective IC50s. Top right: Distribution of drug-susceptibilities of Keio mutants grown in indicated growth media obtained after normalizing the growth of each mutant to wild type (set to 1). Mean ± S.D. derived after fitting each distribution to a Gaussian function are shown. Bottom left: Analysis of gene functional categories for hypersensitive mutants compared with the frequency of genes in each category encoded by E. coli K-12 MG1655. Percentage of the total in each case is provided above each bar. Bottom right: Comparison of hypersensitive mutants identified in the trimethoprim and chloramphenicol screens shown as a Venn diagram. Representative genes from each set are named and gene names are colored by functional categories.

Intrinsic resistance pathways & #ResistanceBreaking. Study shows that inhibiting efflux pumps & cell envelope biogenesis sensitizes #bacteria to #antibiotics, but rapid evolutionary recovery may limit long-term effectiveness of resistance-breaking strategies #AMR @plosbiology.org 🧪 plos.io/4huAtvo

Multiple small, curved, predatory bacteria (Bdellovibrio bacteriovorus) lyse the bacterial prey remnants below. How are they doing this & which predator proteins are involved in this process?

See our newly released research article 📑
=> rdcu.be/eL6gu

🦠 #microsky #bacteria #PredatoryBacteria

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...

Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community - Microbial Ecology The species that make up a microbial community determine its potential function. A major goal of microbial ecology is to make assemblages of microbes — synthetic communities — with targeted applicatio...

Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community

Microbial Ecology

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

Strong promoters are mutationally robust Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...

A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...

www.biorxiv.org/content/10.1...

#microsky #mevosky @spp2389.bsky.social

A PhD position is available in my lab to work on:

Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.

Please RT

Deadline: 12.11.25

More infos 👇
shorturl.at/rAKAT

Big thanks to Rekha (lead), an absolute rockstar who drove the project, and Jyotsna for pushing this work forward!
Also grateful to our collaborator Prof. Siva Umapathy for the Raman spectroscopy expertise.

This is one of the first demonstrations linking biochemical markers of spores to their germination efficiency, using a non-invasive, label-free approach.