Ramya balasubramanian

Biomedical and life science articles by female researchers spend longer under review Women are underrepresented in academia, especially in STEMM fields, at top institutions, and in senior positions. This study analyzes millions of biomedical and life science articles, revealing that f...

Cost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky

journals.plos.org/plosbiology/...

Sending babies to nursery completely reshapes their microbiomes Socializing at a young age helps to develop greater diversity in their microbiota, according to an analysis of baby-to-baby transmission of gut bacteria.

. @nature.com NEWS: Sending babies to nursery completely reshapes their microbiomes

“Maybe in 20 years, we will find that people still need to thank their friends at day care for the microbes they got when they were there” Nicola Segata says.

www.nature.com/articles/d41...

Thank you so much Mireia! The discussion was truly an enriching experience.

So proud of @rabal97.bsky.social who successfully defended her PhD yesterday. Her work on fermented foods was an outstanding collaborative effort between @pauldcotter.bsky.social lab at Teagasc and my own.

Huge thanks to her excellent Examiners @mireiavallesc.bsky.social & Aonghus Lavelle

If you're interested in using the questionnaire for your own research, you can find it in the online supplemental materials

I'm pleased to share our newest publication where we developed and validated a questionnaire to assess fermented food intake, led by PhD student and dietitian Aimone Ferri!

lnkd.in/duU8Jfd2

@jfcryan.bsky.social @pauldcotter.bsky.social @rabal97.bsky.social

A great scientist for computational biology 😢

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

Two postdoc positions open now: let's work together to understand microbial regulation of the gut-brain axis in ageing:

buff.ly/UuJciHZ
buff.ly/vjp98fx

Metagenomics colleagues!

I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.

Please help and share!

Hey are you looking for a postdoc focusing on microbial
ecology/bioinformatics? Hit me up - it’s not my lab but trying to help someone else staff their lab. If you have a student about to defend, this could be a great chance to get a ton of papers.

Started off as a reading group and led to a nice mini-review of microbiome evolution in natural communities. Complete credit to Abby for leading this fun collab! #mevosky

Investigating bacterial evolution in nature with metagenomics
doi.org/10.1016/j.mi...

Just saw this cool preprint from @contaminatedsci.bsky.social's lab that used the bacterial-to-host (B:H) read ratio (doi.org/10.1128/msys...) to quantify absolute bacterial biomass in skin swab samples: www.biorxiv.org/content/10.1...

Worked well in high, but not so well in low biomass settings.

A blueprint for contemporary studies of microbiomes - Microbiome This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...

Today's highlight: "A blueprint for contemporary studies of microbiomes" as part of 'Microbiome 101: what you need to know' theme for #worldmicrobiomeday @jacquesravel.bsky.social @laurebindels.bsky.social @sharonhuws.bsky.social
microbiomejournal.biomedcentral.com/articles/10....

Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass ...

Excited to share my new preprint: we show that for lab control and skin samples with low microbial biomass, metagenomics significantly outperforms 16S while DNA extraction method has minimal impact. 🧵 1/4
www.biorxiv.org/content/10.1...

Left barplot shows that as mock community microbiome sample is diluted, qPCR and metagenomics continue to detect all taxa but 16S detects only Cutibacterium. Right barplot shows that for qPCR and metagenomics detect a diverse average microbiome from lower leg skin but 16S composition is dominated by Cutibacterium.

In high biomass samples, sequencing methods are comparable – however, as biomass decreases, minor taxa are rapidly lost with 16S as the limited amplicon library becomes biased towards the most abundant taxon. 2/4

Haunted by hopelessness: 12 Zambians share their stories as HIV drugs run out Mothers and children, husbands and wives, doctors, truck drivers and religious leaders are all grappling with the fallout from the sudden U.S. cuts in aid.

Haunted by hopelessness: 12 Zambians share their stories as HIV drugs run out : Goats and Soda

www.npr.org/sections/goa...

Thrilled to share our review (with @mireiavallesc.bsky.social and Nicola Segata) on "Human microbiome acquisition and transmission" just published @naturerevmicro.bsky.social

Happy March! While there’s so much to say about our friendly neighborhood Riboflavin, here we show some highlights. It’s amazing how we can engineer bacteria for commercial production!

Check out more at cmmc.gnps2.org

🚨Spring 2025 Updated Microbiome Informatics Webinar Series starts tomorrow Feb. 25!🚨 Free to attend, join us to learn with leaders in the field. More info and registration: coms.osu.edu/webinars/mic...

Introducing "Metagenomic Estimation of Dietary Intake", or "MEDI": a data-driven approach to estimating dietary and nutritional intake from stool DNA 💩 - 🍌🥦🐟🥩📈

See @cdiener.com's excellent thread below.

We are really proud of this work, and we hope it is useful to the scientific community.

Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...

Environmental factors shaping the gut microbiome in a Dutch population - Nature A study in which gut microbiomes of 8,208 individuals from 2,756 families were characterized and correlated to 241 host and environmental factors defines microbiome patterns shared across diverse dise...

www.nature.com/articles/s41... was the first thing i thought of, cool study

Join us May 19th for our annual Harvard Chan Microbiome in Public Health Center Symposium! This year we will be highlighting the microbiome's role in food systems. However, all microbiome related topics are welcome! Check on the flyer below for information on submitting abstracts.

We are looking for a postdoc in bioinformatics interested in broad questions about the ecology and evolution of host-associated microbiomes using social bees as model. Please share with potential candidates and if interested apply here: career5.successfactors.eu/career?caree...

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 biotherapeutic…

#reading "Gut microbiota strain richness is species specific and affects engraftment" by Chen-Liaw et al.

As usual, quoted text is from manuscript [slight edits], unquoted is mine

These are idiosyncratic personal notes, not a comprehensive review!

https://www.nature.com/articles/s41586…

Predictions in #NGS and #SingleCell #Multiomics for 2025.

Just as the year ends, I wanted to share some news! I will be starting at the University of Calgary as an Assistant Professor in Sept. 2025 🇨🇦
Very excited to continue to work on understanding and editing microbiomes using ecology with new colleagues and coworkers! Stay tuned for recruitment updates

Glad to share our preprint 🏃 **LongTrack**: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after 💩 fecal microbiota transplantation. A 4+ years journey and tour de force by ** @yufan01.bsky.social ** & team. A long 🧵 www.biorxiv.org/content/10.1...

Pulled together this starter pack for Microbiota-Gut-Brain Axis Research.
🧠🦠🥼

Hope it is helpful for the people joining in here and nucleating a community.

May have missed people, please leave a reply and I can then add to the pack.

Cheers.

go.bsky.app/PZhXP7R