Francesco Beghini
@fbeghini.bsky.social
Associate Research Scientist at Yale | Metagenomics and Human microbiome | Microbial transmission & social microbiome
Pinned
Francesco Beghini
@fbeghini.bsky.social
· Nov 21
Gut microbiome strain-sharing within isolated village social networks - Nature
An investigation into the relationship between network structure and gut microbiome composition among people living in 18 isolated Honduras villages reveals that strain-sharing can be mediated by...
www.nature.com
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Reposted by Francesco Beghini
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...
rdcu.be
October 28, 2025 at 7:51 AM
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Reposted by Francesco Beghini
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
doi.org
October 6, 2025 at 10:42 AM
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Reposted by Francesco Beghini
My colleagues are using ChatGPT to source data and plot analyses for them. I'm literally reviewing papers written this way.
Meanwhile....
Meanwhile....
![Query: Plot the number of plots of the number of published genomes on the vertical axis against the number of published genomes on the horizontal axis
ChatGPT answer: Number of Plots vs. Number of Published Genomes
Here is the plot showing the "number of plots" against the "number of published genomes."
[Image: plot of sqrt[x].
If you'd like a different approach or specific adjustments, feel free to ask!
Query: Where did you get the data from?
ChatGPT answer: The data used in the plot was artificially generated as an example. Specifically:
Number of Published Genomes: I created a simple range of values (from 1 to 100) to represent this axis.
Number of Plots: I applied a mathematical transformation (the square root function) to the "Number of Published Genomes" to create a plausible-looking relationship.
This approach was chosen to provide a visual illustration since no real-world dataset was provided. If you have actual data or a specific dataset you'd like to use, feel free to share it, and I can recreate the plot with real numbers!](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:tbqqvyv6pjjww44glrmycaxl/bafkreifn4u42wawsnt2bheyf5ehbqtbnu4dnfbiv2zx7d5s2cyo5wny3aa@jpeg)
December 31, 2024 at 7:38 AM
My colleagues are using ChatGPT to source data and plot analyses for them. I'm literally reviewing papers written this way.
Meanwhile....
Meanwhile....
Reposted by Francesco Beghini
A new study found that we share parts of our microbiome with people in our social networks, beyond family members.
Dr. @nachristakis.bsky.social joins us to discuss the research and how scientists can identify your friends—just by looking at your poop.
Dr. @nachristakis.bsky.social joins us to discuss the research and how scientists can identify your friends—just by looking at your poop.
You Share Your Gut Microbiome With Your Friends
New research suggests that we share parts of our microbiome with people in our social networks beyond family members.
buff.ly
December 6, 2024 at 7:41 PM
A new study found that we share parts of our microbiome with people in our social networks, beyond family members.
Dr. @nachristakis.bsky.social joins us to discuss the research and how scientists can identify your friends—just by looking at your poop.
Dr. @nachristakis.bsky.social joins us to discuss the research and how scientists can identify your friends—just by looking at your poop.
Reposted by Francesco Beghini
<taps the sign>
This chart is a decade old, and that gap between the United States and the rest of the developed world, which has better health outcomes by the way, has gotten larger.
We should morally, ethically, and fiscally move to a single payer system.
It’s also a national security issue.
This chart is a decade old, and that gap between the United States and the rest of the developed world, which has better health outcomes by the way, has gotten larger.
We should morally, ethically, and fiscally move to a single payer system.
It’s also a national security issue.
December 5, 2024 at 4:11 PM
<taps the sign>
This chart is a decade old, and that gap between the United States and the rest of the developed world, which has better health outcomes by the way, has gotten larger.
We should morally, ethically, and fiscally move to a single payer system.
It’s also a national security issue.
This chart is a decade old, and that gap between the United States and the rest of the developed world, which has better health outcomes by the way, has gotten larger.
We should morally, ethically, and fiscally move to a single payer system.
It’s also a national security issue.
Reposted by Francesco Beghini
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
December 3, 2024 at 2:00 PM
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
Reposted by Francesco Beghini
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
December 3, 2024 at 10:01 AM
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
Reposted by Francesco Beghini
Interesting look at gut strain-level dynamics: The human gut has low strain variation compared to other environments and has a limited capacity for strain richness. #microbiome
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gut microbiota strain richness is species specific and affects engraftment - Nature
Strain richness of gut microbiota ecosystems is a key characteristic underpinning engraftment in faecal microbiota transplantation, and could improve the design of defined live biotherapeuti...
www.nature.com
November 28, 2024 at 3:00 PM
Interesting look at gut strain-level dynamics: The human gut has low strain variation compared to other environments and has a limited capacity for strain richness. #microbiome
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Francesco Beghini
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Gut microbiome strain-sharing within isolated village social networks - Nature
An investigation into the relationship between network structure and gut microbiome composition among people living in 18 isolated Honduras villages reveals that strain-sharing can be mediated by...
www.nature.com
November 21, 2024 at 4:45 PM
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Reposted by Francesco Beghini
📣 Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in Nature 📣
Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
a couple of cartoon characters standing next to each other with one wearing a purple earring
Alt: a couple of cartoon characters standing next to each other with one wearing a purple earring
media.tenor.com
November 20, 2024 at 4:03 PM
📣 Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in Nature 📣
Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
Reposted by Francesco Beghini
The bacteria in your gut depend on where you are in the social network around you.
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
November 21, 2024 at 3:45 PM
The bacteria in your gut depend on where you are in the social network around you.
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Gut microbiome strain-sharing within isolated village social networks - Nature
An investigation into the relationship between network structure and gut microbiome composition among people living in 18 isolated Honduras villages reveals that strain-sharing can be mediated by...
www.nature.com
November 21, 2024 at 4:45 PM
Excited to share our last work on microbiome transmission and social interactions published on Nature!
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
The more people you interact with, the more similar your microbiome is.
www.nature.com/articles/s41...
Reposted by Francesco Beghini
🥁 New Publication Alert:
Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:
www.nature.com/articles/s41...
1/12
Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:
www.nature.com/articles/s41...
1/12
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts - Nature Microbiology
Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome.
www.nature.com
November 18, 2024 at 11:24 AM
🥁 New Publication Alert:
Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:
www.nature.com/articles/s41...
1/12
Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:
www.nature.com/articles/s41...
1/12
Reposted by Francesco Beghini
Reposted by Francesco Beghini
The march of the mRNA vaccines goes on. Clostridiodes difficile (C diff) next...
#IDSky #MicroSky #MedSky 🧪
www.science.org/doi/10.1126/...
#IDSky #MicroSky #MedSky 🧪
www.science.org/doi/10.1126/...
A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection
Clostridioides difficile infection (CDI) is an urgent public health threat with limited preventative options. In this work, we developed a messenger RNA (mRNA)–lipid nanoparticle (LNP) vaccine targeti...
www.science.org
October 4, 2024 at 9:19 PM
The march of the mRNA vaccines goes on. Clostridiodes difficile (C diff) next...
#IDSky #MicroSky #MedSky 🧪
www.science.org/doi/10.1126/...
#IDSky #MicroSky #MedSky 🧪
www.science.org/doi/10.1126/...
Reposted by Francesco Beghini
Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...
www.biorxiv.org
November 15, 2024 at 7:06 PM
Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Francesco Beghini
New GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵
📄 www.biorxiv.org/content/10.1...
💾 mmseqs.com
🗞️ developer.nvidia.com/blog/boost-a...
📄 www.biorxiv.org/content/10.1...
💾 mmseqs.com
🗞️ developer.nvidia.com/blog/boost-a...
November 15, 2024 at 11:02 PM
New GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵
📄 www.biorxiv.org/content/10.1...
💾 mmseqs.com
🗞️ developer.nvidia.com/blog/boost-a...
📄 www.biorxiv.org/content/10.1...
💾 mmseqs.com
🗞️ developer.nvidia.com/blog/boost-a...
Reposted by Francesco Beghini
Geometriphylogenetics xkcd.com/3010
November 13, 2024 at 1:03 PM
Geometriphylogenetics xkcd.com/3010
Reposted by Francesco Beghini
Dear International Taxonomy Committee.
I am yet again proposing a series of changes to the common names of animals for the Internet Era. Your prompt response is appreciated.
1. Texas Turtle-Rat.
Alternative: Tactical Assault Possum
I am yet again proposing a series of changes to the common names of animals for the Internet Era. Your prompt response is appreciated.
1. Texas Turtle-Rat.
Alternative: Tactical Assault Possum
November 11, 2023 at 5:13 PM
Dear International Taxonomy Committee.
I am yet again proposing a series of changes to the common names of animals for the Internet Era. Your prompt response is appreciated.
1. Texas Turtle-Rat.
Alternative: Tactical Assault Possum
I am yet again proposing a series of changes to the common names of animals for the Internet Era. Your prompt response is appreciated.
1. Texas Turtle-Rat.
Alternative: Tactical Assault Possum
Reposted by Francesco Beghini
Fantastic investigation by Rina Raphael on Viome, which sells you a problem and then sells you a solution.
It's microbiome diagnostic scienceploitation + a supplement bonanza.
She spoke to a dozen former employees.
www.bloomberg.com/news/feature...
(Readable through Apple News, BTW)
It's microbiome diagnostic scienceploitation + a supplement bonanza.
She spoke to a dozen former employees.
www.bloomberg.com/news/feature...
(Readable through Apple News, BTW)
Is This Poop-Test Startup Just Wellness Theater?
Viome—Naveen Jain’s latest company—says its microbiome tests and customized supplements hold the secret to better health. Scientists and former employees aren’t so sure.
www.bloomberg.com
October 31, 2023 at 6:24 PM
Fantastic investigation by Rina Raphael on Viome, which sells you a problem and then sells you a solution.
It's microbiome diagnostic scienceploitation + a supplement bonanza.
She spoke to a dozen former employees.
www.bloomberg.com/news/feature...
(Readable through Apple News, BTW)
It's microbiome diagnostic scienceploitation + a supplement bonanza.
She spoke to a dozen former employees.
www.bloomberg.com/news/feature...
(Readable through Apple News, BTW)
Reposted by Francesco Beghini
Now this is REALLY scary!
October 31, 2023 at 4:37 PM
Now this is REALLY scary!