Margot Bacino
@mbacino.bsky.social
PhD candidate//BCMM trainee ambassador
Lynch lab UCSF
studying the human oral microbiome in the context of periodontal disease and health
🪥🦠🫡🏳️🌈
Lynch lab UCSF
studying the human oral microbiome in the context of periodontal disease and health
🪥🦠🫡🏳️🌈
Reposted by Margot Bacino
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Reposted by Margot Bacino
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Reposted by Margot Bacino
GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/....
Thank you to @ebi.embl.org for support with setting up these links!
Thank you to @ebi.embl.org for support with setting up these links!
ENA Browser
ENA Browser
www.ebi.ac.uk
December 11, 2025 at 3:04 PM
GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/....
Thank you to @ebi.embl.org for support with setting up these links!
Thank you to @ebi.embl.org for support with setting up these links!
Reposted by Margot Bacino
I'm very happy to share our latest manuscript published today in @nature.com !!
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
December 10, 2025 at 5:26 PM
I'm very happy to share our latest manuscript published today in @nature.com !!
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
Reposted by Margot Bacino
My minimum goal is 100,000 signatures for my petition. I will be spamming, yapping, doing everything I can to get to that goal. We need to make it clear where we stand. c.org/xqYKGJhbs2 bsky.app/profile/rave...
November 10, 2025 at 1:24 PM
My minimum goal is 100,000 signatures for my petition. I will be spamming, yapping, doing everything I can to get to that goal. We need to make it clear where we stand. c.org/xqYKGJhbs2 bsky.app/profile/rave...
📢
Catalog of human oral microbiome:
Human reference oral microbiome (HROM) comprises 72,641 genomes from 3,426 species, including 2,019 novel species. HROM reveals disease-assoc. species & ectopic oral species in the gut predictive of systemic diseases
www.cell.com/cell-host-mi...
Human reference oral microbiome (HROM) comprises 72,641 genomes from 3,426 species, including 2,019 novel species. HROM reveals disease-assoc. species & ectopic oral species in the gut predictive of systemic diseases
www.cell.com/cell-host-mi...
A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights
Oral microbiome shows rising importance in human health. Cha et al. present the human
reference oral microbiome (HROM), comprising 72,641 high-quality genomes from 3,426
species, including 2,019 previ...
www.cell.com
October 30, 2025 at 4:08 AM
📢
Reposted by Margot Bacino
This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important
⚠️ Chinese researchers have invented bone glue that mimics how oysters stick to surfaces underwater.
The adhesive can reportedly repair orthopedic fractures in 2-3 minutes, even in blood-rich environments, and is bioabsorbable.
interestingengineering.com/science/chin...
The adhesive can reportedly repair orthopedic fractures in 2-3 minutes, even in blood-rich environments, and is bioabsorbable.
interestingengineering.com/science/chin...
China's oyster-inspired 'bone glue' bonds fractures in minutes
A new oyster-inspired Bone-02 adhesive can revolutionize bone repair without metal fasteners.
interestingengineering.com
September 30, 2025 at 10:35 PM
This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important
Reposted by Margot Bacino
Thanks, @ellecordova.bsky.social. We’re trying. 🧪
For our scientists
YouTube video by Elle Cordova
m.youtube.com
September 6, 2025 at 7:04 PM
Thanks, @ellecordova.bsky.social. We’re trying. 🧪
Reposted by Margot Bacino
Exciting new research from @salkinstitute.bsky.social: immune cells migrate from gut to breast during pregnancy and lactation - and microbes play a key role!
🤱🏽🤰🏻🦠🧪
www.salk.edu/news-release...
🤱🏽🤰🏻🦠🧪
www.salk.edu/news-release...
How does the immune system prepare for breastfeeding? - Salk Institute for Biological Studies
LA JOLLA—Of the 3.6 million babies born in the United States each year, around 80 percent begin breastfeeding in their first month of life. Breastfeeding has known benefits for both mother and child, ...
www.salk.edu
August 8, 2025 at 2:46 AM
Exciting new research from @salkinstitute.bsky.social: immune cells migrate from gut to breast during pregnancy and lactation - and microbes play a key role!
🤱🏽🤰🏻🦠🧪
www.salk.edu/news-release...
🤱🏽🤰🏻🦠🧪
www.salk.edu/news-release...
I am looking for a company with a quick turnaround for peptide synthesis. Any recommendations would be wonderful!
July 21, 2025 at 5:01 PM
I am looking for a company with a quick turnaround for peptide synthesis. Any recommendations would be wonderful!
I have have a great time at @iadr.bsky.social chatting about oral microbes
June 28, 2025 at 12:00 PM
I have have a great time at @iadr.bsky.social chatting about oral microbes
Reposted by Margot Bacino
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
forum.biobakery.org
June 11, 2025 at 6:15 AM
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
I will be at IADR this week sharing a poster on the 27th in the microbiome section from 3:45-5. I’m curious about the oral microbiome, periodontitis, third generation sequencing approaches, CPR bacteria to name a few!
June 24, 2025 at 3:08 PM
I will be at IADR this week sharing a poster on the 27th in the microbiome section from 3:45-5. I’m curious about the oral microbiome, periodontitis, third generation sequencing approaches, CPR bacteria to name a few!
I had a great time at the annual BCMM retreat learning about my colleagues projects,sharing some of my thesis work, and building community among my fellow microbiome researchers! 🦠🧫🧢 microbiome.ucsf.edu Home | The Benioff Center for Microbiome Medicine
Home
microbiome.ucsf.edu
June 22, 2025 at 5:53 PM
I had a great time at the annual BCMM retreat learning about my colleagues projects,sharing some of my thesis work, and building community among my fellow microbiome researchers! 🦠🧫🧢 microbiome.ucsf.edu Home | The Benioff Center for Microbiome Medicine
Reposted by Margot Bacino
Graduate Students Push Back Against Science Funding Cuts www.nytimes.com/2025/06/16/s...
Graduate Students Push Back Against Science Funding Cuts
Hundreds of graduate students are writing to their hometown newspapers to defend their research, as the Trump administration drastically reduces science funding.
www.nytimes.com
June 16, 2025 at 10:53 PM
Graduate Students Push Back Against Science Funding Cuts www.nytimes.com/2025/06/16/s...
Reposted by Margot Bacino
Exciting progress! In our new preprint, we show that episymbiont Saccharibacteria can directly modulate epithelial immunity—a big step in understanding how these elusive microbes interact with the human host. Kudos to Deepak Chouhan and our amazing collaborators! www.biorxiv.org/content/10.1...
June 3, 2025 at 12:30 PM
Exciting progress! In our new preprint, we show that episymbiont Saccharibacteria can directly modulate epithelial immunity—a big step in understanding how these elusive microbes interact with the human host. Kudos to Deepak Chouhan and our amazing collaborators! www.biorxiv.org/content/10.1...
I had a great time at @nanoporetech.com WYMM Tour: Bay Area yesterday. It was lovely connecting with other researchers and sharing a little bit of my thesis work. 🪥🧬👩🏼🔬
June 6, 2025 at 4:28 PM
I had a great time at @nanoporetech.com WYMM Tour: Bay Area yesterday. It was lovely connecting with other researchers and sharing a little bit of my thesis work. 🪥🧬👩🏼🔬
🧪 I will be presenting some of my research on the oral microbiome at @nanoporetech.com WYMM tour: Bay Area This coming Thursday June 5th. I hope to see you there! 🦷🧫🫡
nanoporetech.com/about/events...
nanoporetech.com/about/events...
WYMM: Bay Area
What you're missing matters. Stay on top of what's next. Hear about the latest technical updates for Oxford Nanopore Technologies as well as talks from local scientists about their latest work using ...
nanoporetech.com
May 29, 2025 at 3:24 PM
🧪 I will be presenting some of my research on the oral microbiome at @nanoporetech.com WYMM tour: Bay Area This coming Thursday June 5th. I hope to see you there! 🦷🧫🫡
nanoporetech.com/about/events...
nanoporetech.com/about/events...
Reposted by Margot Bacino
A special issue on #WomensHealth in #ScienceAdvances highlights a growing wave of research focusing on women’s unique biological and psychological experiences.
Learn more: scim.ag/3R59fPe (THREAD 🧵)
Learn more: scim.ag/3R59fPe (THREAD 🧵)
March 11, 2025 at 7:46 PM
A special issue on #WomensHealth in #ScienceAdvances highlights a growing wave of research focusing on women’s unique biological and psychological experiences.
Learn more: scim.ag/3R59fPe (THREAD 🧵)
Learn more: scim.ag/3R59fPe (THREAD 🧵)
Reposted by Margot Bacino
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
February 12, 2025 at 5:04 PM
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Reposted by Margot Bacino
"How do you strategize around an unpredictable funding landscape?" #ScienceWorkingLife https://scim.ag/4gPIkBz
February 24, 2025 at 5:35 PM
"How do you strategize around an unpredictable funding landscape?" #ScienceWorkingLife https://scim.ag/4gPIkBz
🧪 Great conversation with Let’s Get Oral podcast! open.spotify.com/episode/7qDa...
Tooth Mineralization , Periodontal Health & the Oral Microbiome with Margôt Bacino!
Let's Get Oral · Episode
open.spotify.com
January 16, 2025 at 7:50 PM
🧪 Great conversation with Let’s Get Oral podcast! open.spotify.com/episode/7qDa...
🧪 What I’ve been working on the past 4 years. More exciting research to come! www.ucsf.edu/news/2024/10...
How the Oral Microbiome is Connected to Overall Human Health
Oral health has long been siloed from the rest of a person's health. But increasingly, researchers and clinicians, including those at UCSF, are finding ties between a person's oral health and their ov...
www.ucsf.edu
November 28, 2024 at 3:25 PM
🧪 What I’ve been working on the past 4 years. More exciting research to come! www.ucsf.edu/news/2024/10...
Reposted by Margot Bacino
About 40% of dementia cases could be prevented or delayed by healthy lifestyle choices and preventive medicine. Here's a tool to gauge your brain care and track your progress.
You can reduce your risk of dementia. Here's how to get started
About 40% of dementia cases could be prevented or delayed by healthy lifestyle choices and preventive medicine. Here's a tool to gauge your brain care and track your progress.
www.npr.org
November 25, 2024 at 4:14 PM
About 40% of dementia cases could be prevented or delayed by healthy lifestyle choices and preventive medicine. Here's a tool to gauge your brain care and track your progress.