Gang Fang
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gangfang.bsky.social
Gang Fang
@gangfang.bsky.social
Long read (DNA, RNA) | Epigenetics (bacteria, human) | Professor of Genomics @IcahnMountSinai | Humid Lab🧫💻🧪 http://fanglab.bio
Pinned
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!

Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/

📄 rdcu.be/eL8mR
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
Reposted by Gang Fang
New discovery in ulcerative colitis: a bacterial toxin that kills macrophages and increases inflammation, which could be the foundation for a new treatment
science.org/doi/10.1126/...
science.org/doi/10.1126/...
@science.org
A bacterial toxin disarms gut defenses against inflammation
Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice
science.org
November 20, 2025 at 7:25 PM
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!

Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/

📄 rdcu.be/eL8mR
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:39 PM
Reposted by Gang Fang
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
October 14, 2025 at 4:08 PM
Reposted by Gang Fang
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
April 9, 2025 at 5:15 PM
Reposted by Gang Fang
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
October 1, 2025 at 4:44 PM
Reposted by Gang Fang
⚠️ 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
July 3, 2025 at 3:29 PM
Reposted by Gang Fang
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
May 14, 2025 at 7:40 AM
Reposted by Gang Fang
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!
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
April 14, 2025 at 6:13 PM
Reposted by Gang Fang
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
April 9, 2025 at 4:51 PM
Reposted by Gang Fang
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
April 3, 2025 at 4:01 PM
Reposted by Gang Fang
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
January 13, 2025 at 9:35 AM
Reposted by Gang Fang
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
April 2, 2025 at 12:30 AM
Reposted by Gang Fang
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.
March 31, 2025 at 1:16 PM
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👏
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!
New online! Computational analysis of DNA methylation from long-read sequencing
March 30, 2025 at 8:56 PM
Reposted by Gang Fang
"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
February 6, 2025 at 1:46 AM
Reposted by Gang Fang
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.
March 27, 2025 at 6:45 PM
Reposted by Gang Fang
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
March 27, 2025 at 12:38 AM
Reposted by Gang Fang
- 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
March 24, 2025 at 8:47 AM
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
March 27, 2025 at 12:38 AM
Reposted by Gang Fang
Important note about this breakthrough:

Literally would not exist without the kind of Federal support the current administration is slashing.

Took 15+ years of research at a federal lab (Lawrence Berkeley) to get this to a point at which private enterprise could take over and make these at scale.
Thanks to Steve Jobs and Gorilla Glass, factories in America are now ramping up to make affordable windows, made from panes thinner than a credit card, that can:

* save Americans $25 billion / year

* withstand a 2x4 shot out of a cannon

(gift link)

www.wsj.com/business/cor...
A Piece of Glass Thinner Than a Credit Card Could Solve America’s $25 Billion Energy Problem
New windows can insulate better than most walls, and some can even survive being hit with a two-by-four shot from a cannon.
www.wsj.com
March 22, 2025 at 7:22 PM
"Proteasome-cleaved peptides may have previously overlooked functions downstream of degradation. From a translational standpoint, identifying proteasome-derived defence peptides could provide an untapped source of natural antibiotics for biotechnological applications and therapeutic interventions"
March 6, 2025 at 8:43 PM
Reposted by Gang Fang
Just one single gut bacteria is astonishingly sufficient to repress the antibiotic-resistant C. difficile infection. A real game changer from colleagues at the Center. AI and synthetic communities boiled it all down. Big vision by the trainees and faculty

www.psu.edu/news/researc...
Synthetic microbiome therapy suppresses bacterial infection without antibiotics | Penn State University
A synthetic microbiome therapy, tested in mice, holds promise as a new treatment for C. difficile, a notoriously difficult-to-treat bacterial infection, according to a team of researchers at Penn Stat...
www.psu.edu
March 6, 2025 at 11:01 AM
Reposted by Gang Fang
Ecstatic to see our paper "Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing" now published in @naturegenet.bsky.social with @trajnp.bsky.social and @panosroussos.bsky.social @sinaibrain.bsky.social www.nature.com/articles/s41...
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing - Nature Genetics
This isoform-centric microglia genomic atlas includes 35,879 novel human microglia isoforms identified by long-read RNA sequencing. A multi-ancestry quantitative trait locus meta-analysis of known and...
www.nature.com
March 4, 2025 at 5:47 PM
Very interesting study "hyperglycemia plays a dominant role facilitating the expansion and takeover of resistant mutants in diabetic infections" | Science Advances www.science.org/doi/10.1126/...
Diabetes potentiates the emergence and expansion of antibiotic resistance
Diabetic infections are a reservoir for the emergence and proliferation of antibiotic resistance in Staphylococcus aureus.
www.science.org
February 13, 2025 at 3:43 PM