Human and bacterial genetic variation shape oral microbiomes and health - Nature Human genetic loci that associate with composition of the oral microbiome are identified using saliva-derived DNA, where the same host genetics also shapes oral health and genetic varia...

Largest oral microbiome GWAS (n=12519; SPARK): 11 host loci (incl FUT2 and AMY1 CNV) shape oral community composition and even bacterial genomes. Signals colocalize with dentures/tooth-loss risk in UKB, suggesting specific host–microbe interactions in cariogenesis
www.nature.com/articles/s41...

High-resolution metagenome assembly for modern long reads with myloasm - Nature Biotechnology A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

Great to see this paper published pushing the field of microbial metagenomics forward!
www.nature.com/articles/s41... @jimshaw.bsky.social

Single-cell profiling of the subgingival bacteria reveals transcriptional heterogeneity and niche-specific programs Subgingival microbial communities drive periodontitis, yet their single-cell-specific functions remain poorly defined. Using an optimized mscRNA-seq workflow, Ding et al. map a single-cell transcripti...

Profiling subgingival bacteria

Single-cell transcriptional atlas of subgingival bacteria reveals hallmarks of health vs periodontitis. Periodontitis yields loss of health-assoc subpopulations & species-specific amino acid-related transcriptional programs
www.cell.com/cell-host-mi...

Love an update, especially with long read functionality 🥳

💾 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...

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

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!

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.

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...

📢

This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important

For our scientists YouTube video by Elle Cordova

Thanks, @ellecordova.bsky.social. We’re trying. 🧪

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, ...

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...

Each kit comes with enough reagents for I think 5 or 6 library preps so using 4 barcodes instead of 2 shouldn’t strain your resources too much. I have used the same V24 kit for many sequencing runs.

The reason for this I believe in part is pore occupancy. If it’s sample that you have a lot of DNA you could take each sample split it in two and use four barcodes. After the run you could then just pool the reads for the two barcodes. ONT calls for high input DNA but I’ve run it much lower.

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

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...

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-...

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!

Home

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

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.

Graduate Students Push Back Against Science Funding Cuts www.nytimes.com/2025/06/16/s...

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...

You/your team should fact check your podcasts before they’re released. There are so many people go to you as a source of scientific truth.

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. 🪥🧬👩🏼‍🔬

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 ...

🧪 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...

Science Advances’ special issue on women’s health highlights a growing wave of research focusing on women’s unique biological and psychological experiences. Articles cover a range of studies from the interplay between menopause and Alzheimer’s risk to the menstrual cycle’s influence on the brain-heart connection. It also describes the opportunities pregnancy provides to research aspects of both physical and mental health. By prioritizing women’s unique physiological and psychological experiences, research can expand the frontiers of knowledge in ways that benefit everyone.

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 🧵)

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

A conceptual illustration of worried scientists at computers. Hedline reads: I'm an NIH-funded researcher, drowning in uncertainty

"How do you strategize around an unpredictable funding landscape?" #ScienceWorkingLife https://scim.ag/4gPIkBz

Tooth Mineralization , Periodontal Health & the Oral Microbiome with Margôt Bacino! Let's Get Oral · Episode

🧪 Great conversation with Let’s Get Oral podcast! open.spotify.com/episode/7qDa...

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...

🧪 What I’ve been working on the past 4 years. More exciting research to come! www.ucsf.edu/news/2024/10...