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Taoran Fu

@taoranfu.bsky.social

Eco-evo | Postdoc in Brockhurst group at University of Manchester Microbiology | Pseudomonas | Quorum-sensing and defense system

32 Posts452 Follower624 Folgt
c0nc0rdance@c0nc0rdance.bsky.social · 4w ago

So the coua chicks have a species-specific "oral markers" which just happens to be shaped like a target, just in the throat. Parent couas use this as a test for imposters: No target, no food, no exceptions. As the babies grow, the oral markers fade away. (📷: Julie Larsen Maher)

A grey bird in a towel with weird targets inside the mouth on the throat and tongue.
Taoran Fu@taoranfu.bsky.social · 4mo ago

Fantastic two days at #Microbio26, with inspiring talks, posters and discussions on phage therapy, phage biology, defence systems, and a really enjoyable lecture on quorum sensing. Great to reconnect with friends and heading back with lots of food for thought.

Eduardo Rocha@epcrocha.bsky.social · 5mo ago

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

Jorge Moura de Sousa@jmouradesousa.bsky.social · 5mo ago

➡️ 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? 🤔 🧵👇

Jesse Shapiro@bjesseshapiro.bsky.social · 5mo ago

In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut? TLDR: Not much overall, in specific bacterial species. 🧵 www.biorxiv.org/content/10.6...

Species-specific prophage induction by ciprofloxacin in human gut metagenomes

Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut. Importance Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations. ### Competing Interest Statement The authors have declared no competing interest. NIH Common Fund, https://ror.org/001d55x84 Natural Sciences and Engineering Research Council

biorxiv.org

Michael Brockhurst@brockhurstlab.bsky.social · 6mo ago

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

Matthew J Shepherd@matthewjshepherd.bsky.social · 6mo ago

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Joe Bondy-Denomy@jbdsf.bsky.social · 8mo ago

Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh

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Simon Roux@simrouxvirus.bsky.social · 8mo ago

100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations

Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

academic.oup.com

Alexander Robertson@alexrob.bsky.social · 8mo ago

My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)

Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution

A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...

nature.com

Ákos T Kovács@evolvedbiofilm.bsky.social · 10mo ago

Metabolic interplay drives population cycles in a cross-feeding microbial community @natcomms.nature.com from @oventurelli2.bsky.social www.nature.com/articles/s41...

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications

Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

nature.com

Craig MacLean@craigmaclean.bsky.social · 10mo ago

New pre-print www.biorxiv.org/content/10.1... Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social! #phagesky#microsky

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage

Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

biorxiv.org

Ellinor Alseth@ellinoralseth.bsky.social · 9mo ago

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

Bacterial immune systems as causes and consequences of microbiome structure

Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

journals.plos.org

Michael Brockhurst@brockhurstlab.bsky.social · 10mo ago

New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

biorxiv.org

Sorek Lab@soreklab.bsky.social · 8mo ago

The mechanism of Lamassu, an abundant bacterial immune system, is now solved Lamassu evolved from a DNA repair complex Beautiful study from the Patel, Bernheim and Sternberg labs

Aude Bernheim@audeber.bsky.social · 8mo ago

🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org. 👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors! doi.org/10.1073/pnas...