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Reposted by Gang Fang

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

I'm thrilled to share that our study is now published in Cell:
Extensive N4 cytosine methylation is essential for Marchantia sperm function.
www.cell.com/cell/fulltex...
This paper confirms our 4mC discovery in Marchantia sperm and takes it much further.
A thread: 0/13

Extensive N4 cytosine methylation is essential for Marchantia sperm function

Global N4 cytosine methylation in Marchantia polymorpha sperm regulates gene expression and promotes sperm fertility.

www.cell.com

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Reposted by Gang Fang

Dan Portik @dportik.bsky.social · 7d

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

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Reposted by Gang Fang

Madeleine Kline @mckline98.bsky.social · Jul 3

⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10]
www.medrxiv.org/content/10.1...

Comparing Strategies to Introduce Two New Antibiotics for Gonorrhea: A Modeling Study

Introduction Drug resistance in Neisseria gonorrhoeae is an urgent public health threat. The anticipated approval of two new antimicrobials for gonorrhea prompts the need for evidence-based rollout st...

www.medrxiv.org

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Reposted by Gang Fang

Wiep Klaas Smits (ExpBac/CMAT) @smitslab.bsky.social · May 14

Important: if a bug does not make the WHO's priority list, this does not mean it is not relevant. We present arguments why investment in R&D for surveillance, control and treatment of C. difficile (CDI) is of critical importance: www.sciencedirect.com/science/arti...

Clostridioides difficile is a bacterial priority pathogen

www.sciencedirect.com

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Reposted by Gang Fang

Kristen Brennand @kristenbrennand.bsky.social · Apr 14

I am beyond thrilled to highlight @mbfneuro.bsky.social's thesis work! I've learned so much through his studies and am excited to take this project in new directions!

Michael Fernando, PhD @mbfneuro.bsky.social · Apr 9

I’m so proud and beyond thrilled to share the final product of my thesis work from @sinaibrain.bsky.social , now published in @nature.com! Here, we explored the complex functional impact of rare neurexin-1 deletions across human glutamatergic and GABAergic neurons!

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

Phenotypic complexities of rare heterozygous neurexin-1 deletions - Nature

How NRXN1 variants affect multiple neuropsychiatric disorders is explored.

www.nature.com

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Reposted by Gang Fang

Michael Fernando, PhD @mbfneuro.bsky.social · Apr 9

I’m so proud and beyond thrilled to share the final product of my thesis work from @sinaibrain.bsky.social , now published in @nature.com! Here, we explored the complex functional impact of rare neurexin-1 deletions across human glutamatergic and GABAergic neurons!

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

Phenotypic complexities of rare heterozygous neurexin-1 deletions - Nature

How NRXN1 variants affect multiple neuropsychiatric disorders is explored.

www.nature.com

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Reposted by Gang Fang

Fritz Sedlazeck @sedlazeck.bsky.social · Apr 3

Long reads such as @nanoporetech.com or @pacbio.bsky.social can provide insights into epigenetic. We
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu

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Reposted by Gang Fang

James Marsh @jmarsh.bsky.social · Jan 13

I've been waiting for someone to do this: Phase variation via DNA methylation enables gut bacteria to adapt to environmental changes by regulating gene expression and enhancing phenotypic diversity. #microbiome

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

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase va...

www.biorxiv.org

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Reposted by Gang Fang

Alex Arzamasov @arzamasovalex.bsky.social · Apr 2

ELGG paper has the following the statement about Bifidobacterium bifidum MAGs: "For instance, the MAGs from B. bifidum contain 27 CAZy families, 10 of which were not found in reference isolate genomes ... GH3, GH5, GH9, GH43, GH127, GH38, CE10, GH8, CBM6, and GH94"
www.nature.com/articles/s41...

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome - Nature Communications

Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 s...

www.nature.com

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Reposted by Gang Fang

Alex Crits-Christoph @acritschristoph.bsky.social · Mar 31

Does anyone have examples of a (high profile?) paper that likely made an incorrect biological claim due to a contaminated genome from a metagenome?

Don't worry, not a loaded question, because I think the answer should be.... yes! Just wondering what cases are out there.

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Gang Fang @gangfang.bsky.social · Mar 30

Great new review @natrevgenet.bsky.social by @sedlazeck.bsky.social @timp0.bsky.social and @yileifu.bsky.social! 👇highlighting both the promise of long read DNA methylation analysis and remaining challenges such as the difficulty to benchmark 5hmC and non-CG 5mC given their low abundance👏

Yilei Fu @yileifu.bsky.social · Mar 29

We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!

Nature Reviews Genetics @natrevgenet.nature.com · Mar 28

New online! Computational analysis of DNA methylation from long-read sequencing

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Reposted by Gang Fang

Jeremy Wilkinson @jewilki.bsky.social · Feb 6

"As #longread sequencing is more often used in #microbiome studies, we anticipate that our findings will open new dimensions to characterize how gut bacteria adapt to various stress conditions and host interactions using #epigenetic mechanisms." #PacBio 🧵 1/5

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

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase va...

www.biorxiv.org

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Reposted by Gang Fang

Eduardo Rocha @epcrocha.bsky.social · Mar 27

Phage satellites are now known to be very diverse, numerous and ancient. They pose many evolutionary, ecological and mechanistic questions. Lots of fun in perspective!
Great pleasure to write this review to show it, with @jrpenades.bsky.social @dbikard.bsky.social Kim Seed & John Chen.

Nature Reviews Microbiology @natrevmicro.nature.com · Mar 27

New online! Genetics, ecology and evolution of phage satellites

Genetics, ecology and evolution of phage satellites

Nature Reviews Microbiology, Published online: 27 March 2025; doi:10.1038/s41579-025-01156-zIn this Review, Penadés et al. explore the genetics, potential origins and life cycle of phage satellites, and they discuss the impact of these elements on the evolution of other mobile genetic elements and their host bacteria.

www.nature.com

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Reposted by Gang Fang

Gang Fang @gangfang.bsky.social · Mar 27

Preprint Alert 🧵Epigenetic phase variation in the gut microbiome enhances bacterial
adaptation 🔎a hidden layer shaping gut microbiome. 👏5+ Yr journey by @fannimi2001.bsky.social in collab w/ @drvaldivia.bsky.social MartinBlaser WenyanJiang, LaurenDavey #Microbiome #Epigenetics

bit.ly/43rX9at 👇 1/n

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Reposted by Gang Fang

Justine Collier @justinecollier.bsky.social · Mar 24

- What are the roles of m5C bases in bacterial genomes?
- If a DNA methyltransferase is not genetically linked with a restriction enzyme (“solitary”), what is its role?
- Are “solitary” Vsr-like proteins functional?
--> Insights in our latest Preprint: doi.org/10.1101/2025...

Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein

While methylated cytosines are known to play important roles in eukaryotes, their significance in bacteria remains poorly understood especially when they are added on genomes by DNA methyltransferases...

doi.org

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Gang Fang @gangfang.bsky.social · Mar 27

The big picture: Understanding bacterial epigenetics opens exciting doors: which may help improve probiotics, targeted microbiome therapies, etc.

BIG congrats to first author @fannimi2001.bsky.social👏 & collaborating labs of @drvaldivia.bsky.social, Martin Blaser, Wenyan Jiang, Lauren Davey! 13/n

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Gang Fang @gangfang.bsky.social · Mar 27

How to interpret ePV in the context of other genetic mechanisms? Our findings highlight ePV as a crucial additional layer to understanding microbiome adaptation and heterogeneity: for a single bacterial strain, different clones can take different adaptation pathways: MANY roads lead to Rome! 12/n

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Gang Fang @gangfang.bsky.social · Mar 27

**Interesting twist**: while amoxicillin selected the high-mucC ePV states, another antibiotic (ciprofloxacin) selected the opposite state (low mucC). This epigenetic **bet-hedging** underscores how an ePV can enhance the Akkermansia muciniphila strain’s adaptation to different antibiotics. 11/n

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Gang Fang @gangfang.bsky.social · Mar 27

Comprehensive experimental and multi-omics analyses identified an ePV-regulated gene, mucC, that boosts this Akkermansia strain’s tolerance to amoxicillin, a common antibiotics. 10/n

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Gang Fang @gangfang.bsky.social · Mar 27

Now, it's time to spotlight the functional characterization of a specific ePV in an Akkermansia muciniphila strain from an infant gut microbiome. A. muciniphila has been linked to several human diseases and treatment responses, and is considered a promising next-gen probiotic 9/n

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Gang Fang @gangfang.bsky.social · Mar 27

We also analyzed a large collection of short-read metagenomic shotgun data to detect **putative ePVs** suggesting its greater prevalence across diverse taxa in bacterial adaptation. 8/n

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Gang Fang @gangfang.bsky.social · Mar 27

We found that ePV is widespread across many gut bacterial species, responding dynamically to
antibiotics, probiotic engraftment and fecal microbiota transplantation (FMT). 7/n

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Gang Fang @gangfang.bsky.social · Mar 27

Using long-read metagenomic shotgun sequencing (we used both @pacbio.bsky.social and @nanoporetech.com ), which can detect bacterial DNA methylation, we dove deep into gut samples from infants and adults to uncover these hidden methylation shifts. 6/n

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Gang Fang @gangfang.bsky.social · Mar 27

ePV may occur in 2 flavors:

1. Genome-wide ePV: driven by methyltransferase switches affecting thousands of methylation sites simultaneously.

2. Site-specific ePV: local methylation switches mediated by competitive binding between a methyltransferase & another DNA binding protein (e.g. a TF). 5/n

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Gang Fang @gangfang.bsky.social · Mar 27

What benefit? ePV can enhance clonal heterogeneity within a single bacterial strain, more advantageous (in addition to genetic variations) at the **population level** to adapt to various stress conditions. 4/n

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