We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇

Spatial Gut-Microbiome MegaTranscriptomics

Use in situ polyadenylation on #Visium #StereoSeq to enhance host & bacterial RNA recovery (⏫99-fold)

Fresh-frozen🐭GI

Non-coding RNAs enriched to gut wall

Microorganisms enriched at CRC tumor boundary

#NatMicrobiol 2026
www.nature.com/articles/s41...

What do I do in my free time, you ask? Well, sometimes I write papers with my husband
www.sciencedirect.com/science/arti...

bsky.app/profile/h-me...

We also had a rare opportunity to assess the possible role of the microbiome in second trimester miscarriages, led by @unnurgudna.bsky.social

bsky.app/profile/unnu...

We could confirm that obesity-associated differences in the gut microbiome persist in pregnancy (but whether this contributes to pregnancy complications is ongoing work)
link.springer.com/article/10.1...

The gut microbiome in early pregnancy is associated with the severity of nausea and vomiting: a nested case‒control study Approximately 70% of all pregnancies are affected by nausea and vomiting (NVP), yet the mechanisms controlling this phenomenon are not well known. Pregnancy hormones explain a large part of this ef...

Back to pregnancy, we could identify gut-brain pathways associated with thr severity of nausea symptoms in early pregnancy
www.tandfonline.com/doi/full/10....

Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring - Nature Communications SARS-COV-2 wastewater surveillance may enable early identification of emerging variants. Here, authors compare variants detected in wastewater from Stockholm city, its airport, aircraft, the wider air...

A little bit of a detour, but a fun one while the lab was getting started! Here we genotyped SARS-CoV2 from wastewater from the aircraft to the city levels. Each one really shows a different picture, and very early warning signs would require very fine data granularity
www.nature.com/articles/s41...

Predicting allergy and postpartum depression from an incomplete compositional microbiome - BMC Genomics Time series of compositional data are a common format for many high-throughput studies of biological molecules, e.g., analyzing the response to a treatment or with the aim of predicting an outcome. Ho...

This improved the predictive value from a coin toss to 0.72 balanced accuracy - not clinical grade, but cool!
link.springer.com/article/10.1...

But because this data is so finicky, and with small numbers of cases and high missingness in the time-series, we joined forces with Prashant Singh at IT/UU to develop more powerful statistical approaches.

PCA plot of gut-brain modules with 21% of variance explained in the first axis and 13.5% in the second PC. Four clusters are clearly visible, corresponding to high/low PC1 and high/low PC2. A very small fraction of the data is between two clusters and nothing is in the empty space between all four.

Although what really stayed with me are these clear clusters of gut-brain modules, much clearer than gut microbiome patterns tend to be. We've since observed similar patterns in other data, and I'd love to work with a neuroscientist to figure this out.

Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relatio…

And then also among pregnant and postpartum volunteers in Sweden and the US. Very little in common between the two countries species-wise, but much better agreement in terms of gut-brain axis function
www.sciencedirect.com/science/arti...

Frontiers | Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women BackgroundDespite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niche...

Also from 2024, we had a couple publications on the interaction between the gut-brain axis and sex hormones, first in non-pregnant volunteers
www.frontiersin.org/journals/cel...

bsky.app/profile/h-me...

We identified low abundance bacteria, bacteriocins and the relative abundance of phages as factors that covaried strongly with these patterns. Still, would need bigger data to pinpoint the mechanisms!

Some women were high Lactobacillus, low diversity all the time; some had high diversity all the time; some had high diversity only in the menstrual period; and some shifted rapidly with no clear pattern.

Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes - Microbiome Background The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these...

Another postdoc paper in collaboration between @ki.se and Copenhagen U. The source of most of my vaginomic hypotheses. Here we followed healthy women with daily vaginal swabs for a full menstrual cycle and identified four temporal patterns.
link.springer.com/article/10.1...

Starting with the last bits of my postdoc at @ki.se, on which H-MEL is built. Here we describe the SweMaMi cohort, sampling fecal, oral and vaginal microbiome at three time-points from 3000+ pregnancies in Sweden
bmjopen.bmj.com/content/bmjo...

I haven't been good at posting the lab's achievements, but here I'll start a thread of paper threads.

Some papers may be single bloops; some may not have had most of the work done by us; but I'll do my best to keep it interesting!

And on the odd chance that they're actually brilliant and I don't get it, it gives them a chance to explain, heh

There's something very satisfying about asking authors that are engaging in wild speculation in their discussion section to please go on. "That's a very bold hypothesis. For the benefit of the readership, please be as specific as possible about this proposed mechanism."

🎉🎉🎉 New preprint to start the new year 🎉🎉🎉

Patients recovering from bowel surgery may have stomas formed to divert the flow of faeces to the opening on the skin, away from healing intestinal tissue. The visible sign of this process is an ileostomy or colostomy bag. /1

#surgerysky #medsky

We found:
- High-dose VOWST enabled rapid, durable engraftment and rescued efficacy in phase 3 vs phase 2
- VOWST shifted the gut toward a healthy-like community, reducing Proteobacteria and C. diff
- Engrafted Firmicutes restored key metabolites (secondary bile acids, SCFAs) that inhibit C. diff

In the foreground, a print of a grant application with an Eppendorf pen on top. In the background, an enormous mug of hot chocolate covered in mini marshmallows with a mountain of whipped cream on the side

Revising a large grant for the last time before submission, and all means are fair

Driven by the pain of endometriosis, this scientist is uncovering clues to its causes Katie Burns is helping reveal the immune system’s role in the long-neglected disease

Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment

www.science.org/content/arti...

We concluded that plasmids evolve through a birth-death process, involving fusion (birth of a new "species"),
but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive
16/n

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

3/
Bioinformatics is not just about the data.
It’s about the biology behind the data.
Without that, your code is just noise in a terminal.

Glad to have been a tiny part in this consortium!

An entirely empty lecture hall at a renowned university

I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.

In Which The Rube Goldberg Machine Behind Retractions Delivers A Limp Payload A Year Late No, I'm not thinking of a better title.

About fifteen months ago, someone handed me a bad study. Today it was retracted. So far, so normal.

But do I just want to yell at journals and publishers again? Hell no. What could they actually DO to be better at handling this sort of nonsense?

open.substack.com/pub/jamescla...