Lightnews — Scholar-powered news

Reposted by Samir Giri

Oded Rechavi @odedrechavi.bsky.social · 5h

Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social

q.e.d Science

Critical Thinking AI for constructive criticism and science evaluation

qedscience.com

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Reposted by Samir Giri

Cameron Thrash @jcamthrash.bsky.social · 3h

Predicting functions of uncharacterized gene products from microbial communities www.nature.com/articles/s41... #jcampubs

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology

FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

www.nature.com

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Reposted by Samir Giri

Typas Lab @typaslab.bsky.social · 2d

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

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Samir Giri @isamirgiri.bsky.social · 4d

New Preprint from Voogdt et al 👇

Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics

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Reposted by Samir Giri

C. Brandon Ogbunu @cbo.bsky.social · 7d

www.pnas.org/doi/10.1073/...

In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS

Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...

www.pnas.org

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Cell - a Cell Press journal @cp-cell.bsky.social · Apr 2

Now online! A chemical radar allows bacteria to detect and kill predators

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.

dlvr.it

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Reposted by Samir Giri

Nature Microbiology @natmicrobiol.nature.com · 14d

#Perspective

Estrela and Huang discuss nutrient starvation in the context of the gut microbiome, outlining what is known and highlighting key questions for future research to address knowledge gaps.

#MicroSky #MicrobiomeSky 🦠

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

How nutrient starvation impacts the gut microbiome - Nature Microbiology

In this Perspective, Estrela and Huang discuss nutrient starvation in the context of the gut microbiome, outlining what is known and highlighting key questions for future research to address knowledge gaps.

www.nature.com

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Reposted by Samir Giri

Julius Brennecke @juliusbrennecke.bsky.social · 10d

The Vienna BioCenter PhD Program application deadline is approaching: October 10!

Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!

training.vbc.ac.at/phd-program/

#PhD #LifeSciences

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Craig MacLean @craigmaclean.bsky.social · 16d

New pre-print: Eco-evolutionary responses of phage to different thermal regimes.

Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2

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

Evolutionary rescue accelerates competitive exclusion in a parasite community

Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

www.biorxiv.org

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Paul Rainey @paulbrainey.bsky.social · 21d

A ghost in the machine? It appears when parts merge, a new logic takes hold, and a higher-level individual emerges. Life showed it in eukaryogenesis. Humans and AI could unwittingly stumble into something similar.

Proceedings of the National Academy of Sciences @pnas.org · 21d

Opinion: As human–AI interdependence deepens, could they form an integrated evolutionary individual, subject to collective selection? Explore this perspective in PNAS Front Matter: www.pnas.org/doi/10.1073/...

#AI #evolution #singularity #ChatGPT #LLM #MajorEvolutionaryTransition

An illustration of a human and a robot watering a tree together.
Image credit: Dave Cutler (artist).

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Reposted by Samir Giri

Ákos T Kovács @evolvedbiofilm.bsky.social · 19d

Cool PNAS paper by @jordivangestel.bsky.social and colleagues
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]

Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation

www.pnas.org/doi/10.1073/...

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Zamin Iqbal @zaminiqbal.bsky.social · 19d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Hall Lab @halllab.bsky.social · Sep 11

Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦

Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential

Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · Sep 11

Bifido adaptations across hosts

@halllab.bsky.social survey insects, reptiles, birds & mammals to uncover how Bifidobacterium adapts to hosts. Bifidobacterium & host exhibit strong co-phylogenetic associations, driven by vertical transmission & dietary selection
www.cell.com/cell-host-mi...

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals, particularly primates, a...

www.cell.com

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Samir Giri @isamirgiri.bsky.social · Sep 9

Unusual reproductive strategy in Iberian harvester ants challenges the conventional biological boundaries that define "species" as one queen effectively produces two genetically distinct species (into males of their own species and males of another species) within a single colony 😲👇

Nature @nature.com · Sep 5

Nature research paper: One mother for two species via obligate cross-species cloning in ants

go.nature.com/45PYV6d

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same mother having distinct genomes and morphologies.

go.nature.com

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Reposted by Samir Giri

Nature @nature.com · Sep 5

Nature research paper: Commensal yeast promotes Salmonella Typhimurium virulence

go.nature.com/4mTnRzG

Commensal yeast promotes Salmonella Typhimurium virulence - Nature

Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

go.nature.com

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Reposted by Samir Giri

Germán Orizaola @gorizaola.bsky.social · Sep 9

Nice interview to Katie Peichel @currentbiology.bsky.social

I completely agree with her claims for more funding for curiosity-driven research, basic Science... Science.

www.cell.com/current-biol...

Catherine Peichel

Interview with Katie Peichel, who studies the evolutionary genetics of sticklebacks at the University of Bern, Switzerland.

www.cell.com

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Itai Yanai @itaiyanai.bsky.social · Sep 6

Microbiomes are interactive, multispecies communities, but bulk analysis obscures functional diversification from environmental and genetic heterogeneity. In our new review we describe how single-bacterium transcriptomics dissects microbiomes at cellular resolution.
www.science.org/doi/10.1126/...

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Reposted by Samir Giri

Nature @nature.com · Sep 5

Nature research paper: One mother for two species via obligate cross-species cloning in ants

go.nature.com/45PYV6d

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same mother having distinct genomes and morphologies.

go.nature.com

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Reposted by Samir Giri

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Aug 26

Engineering Synthetic Phase Variation for Control of Microbial consortium https://www.biorxiv.org/content/10.1101/2025.08.25.672192v1

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Seth Bordenstein @symbionticism.bsky.social · Aug 25

Seaweed aquaculture eyes holobiont optimization. More evidence that breeding programs are starting to get on top of it.

Host-Microbiome Ecology in a Seaweed Holobiont: Current Understanding, Technological Advancements, and Manipulation Approaches

papers.ssrn.com/sol3/papers....

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John M. Drake @jdrakephd.bsky.social · Aug 21

Given the tremendous diversity of microorganisms in the world, why do only a small fraction cause disease?

My essay in #PLOSBiology argues that the answer is lack of opportunity and that humans encounter only one new bacterial pathogen for every 1.4b years lived.

journals.plos.org/plosbiology/...

Why are there so few pathogens? Ecology and evolution in pathogen emergence

Why are there so few pathogens, and what determines their emergence? This Perspective argues that ecological and evolutionary forces (host availability, geographic exposure and microbial innovation) w...

journals.plos.org

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Aaron Straight @astraight.bsky.social · Aug 18

@currentbiology.bsky.social has always been one of my favorite journals but I think they have now outdone themselves www.cell.com/current-biol.... And picked up by the @nytimes.com as well! www.nytimes.com/2025/08/18/s...

Periodic excretion patterns of seabirds in flight

Uesaka and Sato report on the excretion patterns of seabirds in the open ocean determined using a rear-facing video logger.

www.cell.com

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Samir Giri @isamirgiri.bsky.social · Aug 18

Defined synthetic microbial starters reproduce the key attributes of fine flavour chocolate 🍫 fermentation in the lab; enable controlled, consistent production of complex chocolate flavours, providing an alternative to the variable traditional farm fermentation process. 👇

Emily White @emily-white.bsky.social · Aug 18

One of my favourite papers of 2025 so far and its on chocolate! 🍫

A defined microbial community reproduces attributes of fine flavour chocolate fermentation

🧪 Read the paper here: www.nature.com/articles/s41...
🔎 The associated news & views here: www.nature.com/articles/s41...

A defined microbial community reproduces attributes of fine flavour chocolate fermentation - Nature Microbiology

An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocol...

www.nature.com

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Reposted by Samir Giri

Emily White @emily-white.bsky.social · Aug 18

One of my favourite papers of 2025 so far and its on chocolate! 🍫

A defined microbial community reproduces attributes of fine flavour chocolate fermentation

🧪 Read the paper here: www.nature.com/articles/s41...
🔎 The associated news & views here: www.nature.com/articles/s41...

A defined microbial community reproduces attributes of fine flavour chocolate fermentation - Nature Microbiology

An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocol...

www.nature.com

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Reposted by Samir Giri

Sarah Ross @sarahhross.bsky.social · Aug 16

The human immune system evolved over millennia - and can adapt within a single lifetime. This review examines how the immune responses change over the life course. By Jessica Metcalf, Andrea Graham, Andrew Yates and Derek Cummings @science.org

buff.ly/GJpPUO7

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