Lightnews — Scholar-powered news

Alex Crits-Christoph @acritschristoph.bsky.social · 1h

Great paper, and also nice evidence that you can create large+diverse RB-TnSeq libraries in liquid selection, without the need to scrape tons of plates for your library.

Typas Lab @typaslab.bsky.social · 7h

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...

1 8

Reposted by Alex Crits-Christoph

Typas Lab @typaslab.bsky.social · 7h

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...

1 23 29

Reposted by Alex Crits-Christoph

Frédérique Le Roux @fredoleroux.bsky.social · 17h

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community

Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

www.biorxiv.org

35 54

Reposted by Alex Crits-Christoph

Nature Portfolio @natureportfolio.nature.com · 16h

Hopes of securing a UN treaty on plastic pollution are fading after the final round of negotiations ended without an agreement. Nature spoke to Samuel Winton, a researcher who is studying the treaty’s progress, about what went wrong, and what can be done to salvage the treaty. 🧪

The world’s first plastics treaty is in crisis: can it be salvaged?

Hopes of securing a United Nations treaty on plastic pollution are fading after the final round of negotiations ended without an agreement.

go.nature.com

15 28

Reposted by Alex Crits-Christoph

T&E @transportenvironment.org · 4d

NEW: Biofuels globally emit more than the fossil fuels they replace, our latest study shows.

The first-of-a-kind study looks at global biofuels production today and the potential impacts of government biofuel targets.
🧵⤵️

10 240 440

Reposted by Alex Crits-Christoph

Joel Selkrig @jselkrig.bsky.social · 1d

Important (and meticulous) genetic groundwork by the @typaslab.bsky.social and Carlos Voogt on gut microbiome Bacteroides species! Enormous value for the functional microbiome research community

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 2d

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://www.biorxiv.org/content/10.1101/2025.10.10.681549v1

4 10

Reposted by Alex Crits-Christoph

Samir Giri @isamirgiri.bsky.social · 1d

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

3 12

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

www.reddit.com/r/AskReddit/...

From the AskReddit community on Reddit

Explore this post and more from the AskReddit community

www.reddit.com

1 2

Reposted by Alex Crits-Christoph

Johannes Cairns @jcairns.bsky.social · 2d

Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.

Teppo Hiltunen @teppo-h.bsky.social · 2d

Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...

Evolution induced state shifts in a long-term microbial community experiment

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

www.biorxiv.org

7 16

Reposted by Alex Crits-Christoph

Sheryl Gay Stolberg @sherylnyt.bsky.social · 2d

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:

860 8.5K 15K

Reposted by Alex Crits-Christoph

Jeremy Faust, MD @jeremyfaust.bsky.social · 2d

We have breaking news in Inside Medicine.

We had heard rumors of RIFs to CDC.

But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.

Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...

9 170 300

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

Because when some audiences hear "Make the proof" they do not hear "Make up the proof" because they don't have the (correct) prior intuition that everything he does is a scam.

So when a comment *assumes* someone hears "make up", it misses the mark with the audience most important to reach

1 2

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

HOWEVER, we also know his process is going to be irrevocably flawed and politically motivated, and so in practice everything he does we should assume is in fact going to be "making up the proof".

Imo it can be good to push back on short viral gotchas like this bc they can hurt with some audiences.

1 1

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

Yeah "make the proof" vs "make up the proof" is key.

RFK isn't consciously saying he's going to make up evidence here, he pretty clearly genuinely believes he's searching for confirmatory truth and means as much. It's silly to think he meant "We're gonna make up data to fit our beliefs", he didn't!

1 1

Reposted by Alex Crits-Christoph

Kevin Zollman @kevinzollman.com · 2d

A reoccurring frustration for philosophers of science: Many scientists know how to do science like people know how to ride a bike. When they reflect on the practice of science, they repeat platitudes about how science works. Those platitudes are often wrong, sometimes even about their own field

D. J. Hicks @danhicks.bsky.social · 3d

*sighs in philosopher of science*

Looking for confirmatory evidence is an entirely normal part of science. The primary problem here is the eugenics and the fascism, not the lies to children about "the scientific method."

One Bluesky account is quoting another. Inner post has a video of RFK Jr., some person I don't recognize (Tylenol and autism guy, maybe?), Marco Rubio (I think), and Trump. Post text: "RFK Jr on Tylenol and autism: 'It is not proof. We're doing the studies to make the proof."

Outer post text: "We're doing studies to prove it (* not how studies work)"

2 10 52

Reposted by Alex Crits-Christoph

D. J. Hicks @danhicks.bsky.social · 2d

The "gold standard science" stuff plays on the same oversimplified picture of science, and that's part of the reason scientists have had such weak-ass responses to it

Kevin Zollman @kevinzollman.com · 2d

It's not that I think RFK is going to do good science on this topic. I think it's important to criticize it for the right reasons.

I think perpetuating the children's version of the scientific method leads to scientific skepticism.

2 2 11

Reposted by Alex Crits-Christoph

Emmanuele Severi @emmseveri.bsky.social · 3d

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

#microsky #microbiome

DGRs FTW

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...

www.science.org

7 16

Reposted by Alex Crits-Christoph

Rachel M. Wheatley @rachelmwheatley.bsky.social · 3d

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The Lancet Microbe @lancetmicrobe.bsky.social · 4d

New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA

2 26 64

Reposted by Alex Crits-Christoph

Noah Fierer @noahfierer.bsky.social · 2d

New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium)
academic.oup.com/ismej/advanc...

Validate User

academic.oup.com

2 4 6

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

well limited by 300 chars, but the full claim would be "Statistically significant increase in organisms A and B, which are more likely than the average member to encode for genes X and Y. Therefore these genes and the phenotype they can be inferred to likely confer may play a role in the difference"

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

(Well actually, the genes quite literally are changing in abundance along with the organisms, but this is a metaphorical argument that it's better to frame gene function in the context of the organisms that encode them instead of in isolation)

1

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

I dislike that much more typical framing of functional questions in metagenomes, because (with some rare exceptions), metabolic genes are not increasing or decreasing in abundance in a study

Organisms with these genes are, not the genes themselves.
But the genes may explain why the organisms are!

1

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

What I really like about your approach here and EnrichM is that the question is framed like: "We saw these differently abundant organisms, can we statistically identify which genes may explain that" instead of the very typical metagenomic "gene go up, gene go down".

It's also how we did it here:

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms - Nature Microbiology

Using metagenomics and proteomics on Mediterranean grassland soil samples resulted in the recovery of 793 metagenome-assembled genomes and provided insights into microbial activity in this environment, and how this changes with soil depth and exposure to extended rainfall.

www.nature.com

1 1

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

So that [and similar arguments] is why it's best to report this like "increases in organisms A and B, which encode genes X and Y" and not necessarily claim changes in metabolic fluxes or products

I do think it's then reasonable to suggest how this may impact phenotype, while making caveats clear

1

Reposted by Alex Crits-Christoph

Filip Husnik @filiphusnik.bsky.social · 3d

Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...

41 81