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Laurence Ettwiller @ettwiller.bsky.social · 2d

A wonderful collaboration with Dr. Jackson Buss, Dr. Kyle Brumfield and Dr. Rita R. Colwell

Laurence Ettwiller @ettwiller.bsky.social · 2d

This study demonstrates that it is possible to elicit and track functional responses directly within a microbiome, and to discover new enzymes in a hypothesis-free, reference-independent manner

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Laurence Ettwiller @ettwiller.bsky.social · 2d

By searching for protein domains that mirrored this behavior (rather than relying on homology), she found GH18 to be the most significantly associated family — the very domain found in known chitinases.

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Laurence Ettwiller @ettwiller.bsky.social · 2d

Chitinases were expected to increase during the bait phase and be rapidly downregulated after the switch — providing a measurable, dynamic phenotype within the native microbiome.

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Laurence Ettwiller @ettwiller.bsky.social · 2d

To make this possible, Colleen developed a “Bait-and-Switch” strategy:
first, she triggered a community succession toward chitin degraders (the bait), and then shifted the nutrient source to simple sugars (the switch).

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Laurence Ettwiller @ettwiller.bsky.social · 2d

So happy to share our new study
“A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.”
In this work, we discovered novel chitinases directly on microbiome; a study brilliantly led by Dr. Colleen Yancey
www.biorxiv.org/content/10.1...

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Reposted by Laurence Ettwiller

Oliver Strimpel @geologybites.bsky.social · 28d

🧪⚒️Just released an episode on the dynamics of subduction zones with Claudio Faccenna. Not only do trenches roll back and move laterally, they also advance and flip polarity. But when they penetrate the viscous lower mantle they get locked in place. Enjoy listening!

The figure shows sections of P-wave tomography anomalies along the yellow lines on the map (Fukao & Obayashi, 2013), seismicity (orange dots on profiles; Engdahl et al., 1998), plate velocities (orange vectors; Argus et al., 2011), and volcanoes (cyan inverted triangles; Siebert & Simkin, 2023). The Western Pacific and Japan subduction zones (the two most northerly zones) do not appear to penetrate the lower mantle, unlike those of Indonesia and Kermadec (north of New Zealand). Whether a slab penetrates the lower mantle depends on factors such as the duration of subduction and the angle at which the slab reaches the 660-km discontinuity, with steeper angles favoring descent.

Becker, T and Faccenna, C. (2025), Tectonic Geodynamics, Princeton University Press

Subduction zones along the west coast of the Americas. In the podcast, Faccenna described how the slab subducting below the Andes has entered the lower mantle where its lateral movement is restricted by the higher viscosity there. The subduction zones beneath northern South America and Central America show evidence of penetration into the lower mantle, reaching depths of 1,300 km or more. By contrast, the younger Caribbean subduction zone does not.

Becker, T and Faccenna, C. (2025), Tectonic Geodynamics, Princeton University Press

Left: map showing seafloor ages in the western Pacific. The back-arc basins shown appear mainly as the red and orange regions, i.e., having the youngest ages of 0 and 30 million years. Center: more detailed seafloor age map of the Izu-Bonin-Marianas region. Right: P-wave tomography sections along the green lines labeled A, B, and C, revealing the varying shape of the subduction zone going from north to south.

The western Pacific subduction zone is characterized by back-arc extension in the overriding plate that began within the last 30 million years (left panel). Tomography and seismicity data show that along the Izu–Bonin region (section B1–B2), a double subduction system is present, resulting from subduction of both the Pacific Plate (to the east) and the Philippine Plate (to the west).

Becker, T and Faccenna, C. (2025), Tectonic Geodynamics, Princeton University Press

The Izu–Mariana subduction system is unique in that the trench is advancing toward the overriding plate (right panel). Bottom left: tomographic section along the red line on the map at right shows the two subducting slabs. Top left: numerical model of single subduction and double subduction. The double subduction simulation replicates quite a few features appearing on the tomographic section, such as the apparent flattening out of the subducting slabs between the depths of 400 and 600 km. In a single-slab system, the trench migrates backward, whereas in a double-slab system, the rear slab drives trench advance. The simulation also reproduces the tomographic section (bottom left, section along the red line on the map at right), which clearly shows the presence of two subducting slabs.

Faccenna, C. et al. (2018), Tectonophysics, 746, 229

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Reposted by Laurence Ettwiller

bioRxiv Genomics @biorxiv-genomic.bsky.social · Aug 3

A novel NGS-compatible Enzymatic Strategy Enables Carryover Contamination Removal and Enhances Sequencing Performance. https://www.biorxiv.org/content/10.1101/2025.08.01.668201v1

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Read the full story & explore the data here:
www.biorxiv.org/content/10.1...

👏 This is an amazing work from Amanda DeLiberto at #NEB @nebiolabs.bsky.social

#NGS #genomics #molecularbiology #preprint #contamination #sequencing

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

This dual-function strategy is ideal for:
🔹 Clinical & diagnostic sequencing
🔹 Low-input or precious samples
🔹 Metagenomics
🔹 Any workflow where contamination is a problem

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Implementation is simple:
➕ Add Fpg & 7-deaza-dGTP directly to your PCR mix
⏱️ Brief pre-amplification incubation
No added steps, no workflow disruption

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Why is this different?
7-deaza-dGTP is accepted by high-fidelity polymerases (unlike dUTP)
Fpg cleaves 7-deaza-dG-containing contaminants
Bonus: 7-deaza-dGTP reduces GC bias and improves sequencing coverage!

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Our method changes that.
We introduce a new strategy using:
✅ 7-deaza-dGTP
✅ Fpg glycosylase
Together, they provide similar carryover contamination removal as dUTP/UDG and work seamlessly in standard NGS pipelines.

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Contamination between NGS runs can compromise sensitive applications—from clinical diagnostics to ancient DNA.
Until now, enzymatic solutions like dUTP/UDG had one major flaw: they're are not compatible with high-fidelity NGS workflows.

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Laurence Ettwiller @ettwiller.bsky.social · Aug 3

Dream of avoiding carryover contamination in your NGS experiment?
Check out our latest preprint:
🧬 “A Novel NGS-Compatible Enzymatic Strategy Enables Carryover Contamination Removal and Enhances Sequencing Performance” www.biorxiv.org/content/10.1...

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

(Sorry for the late reply - I was hiking the Alpine section of the GR5 trail over the past six days)

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

Phages containing dU can be sequenced using polymerases that tolerate dU, such as Taq or Q5U. But thermostable polymerases are not strictly required, as only the first round of amplification needs to successfully copy the dU-containing templates to allow their propagation in downstream PCR cycles.

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

dU containing phages have been described (for ex : PMID: 34033748, PMID: 35934259) while Mikael Skurnik's lab isolated YerA41, a Yersinia ruckeri Bacteriophage that cannot be sequenced due to bulky modifications (PMID: 32517038).

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

And yes- standard high-throughput sequencing misses bulky DNA modifications and those recognized as damage, like deoxyuridine (dU), because most standard protocols use high-fidelity polymerases that typically contain a dU pocket and stall at dU.

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

This estimate comes from metaGPA for which high-throughput sequencing of DNA resistant to cytosine deamination is compared to total viral metagenomic DNA. Of course, only DNA that can be amplified (e.g., with Q5 polymerase) is detectable.

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Laurence Ettwiller @ettwiller.bsky.social · Jul 27

We estimate that 2–3% of contigs from viral metagenomes originate from genomes in which all canonical cytosines (C) have been replaced by modified bases (elifesciences.org/articles/70021). And that’s just for cytosine. (data from sewage and coastal metagenomes)

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Reposted by Laurence Ettwiller

Eric Topol @erictopol.bsky.social · Jun 23

This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...

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Reposted by Laurence Ettwiller

Di Jiang @dijiang319.bsky.social · May 2

🧬🧫🦠 @science.org Bacterial reverse transcriptase synthesizes long poly-A–rich cDNA for antiphage defense | Science www.science.org/doi/10.1126/... #microbiology #bacteriophage #antiphage #immunity #DNA #RNAsky #RT #Cryo-EM #DRT9

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Reposted by Laurence Ettwiller

PLOS Biology @plosbiology.org · Apr 8

The BASEL collection of E. coli #phages is limited by its host strain. @humollidorentina.bsky.social @damienpiel.bsky.social @aharms485.bsky.social &co use a modified host to add 36 new phages, revealing roles of O-antigen in recognition & R-M systems in immunity @plosbiology.org 🧪 plos.io/4jirGvX

A fanciful depiction of BASEL phages on a roadmap. Credit: Fabienne Estermann

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Laurence Ettwiller @ettwiller.bsky.social · Mar 31

Here is the link : academic.oup.com/nar/article/...

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities

Abstract. Methylation patterns in bacteria can be used to study restriction–modification or other defense systems with novel properties. While m4C and m6A

academic.oup.com