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Hugerth lab

@h-mel.bsky.social
274 followers 492 following 121 posts

Human molecular ecology lab at Uppsala University. Microbiota as a modifiable risk factor in women's health. Bloops by @luhugerth.bsky.social

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Vagina Museum @vaginamuseum.bsky.social · 26/05/2026
At we swelter under another heatwave, let's dust off our guide to keeping your vulva as happy as possible, dearest moist goblins
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Claudio Cantù @claudiocantu81.bsky.social · 26/05/2026
FINAL CALL! Register by the end of May to this year's edition 23-26 June 2026 Focus will OMICS data integration, with hands-on computation🧬 💻 Check out the program and your stellar teachers: www.trippus.net/summerschool... @scilifelab.se @kawresearch.bsky.social @remeseiro-lab.bsky.social
trippus.net
Summer School 2026
Come to this beautiful Swedish inland scenario to learn the most advanced technologies to study transcriptional regulation.
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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
npr.org
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
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CEMUS Uppsala University @cemusuppsala.bsky.social · 26/05/2026
Join us for the Gender and Environment Symposium at 13:00 tomorrow! 📍 27 May 2026 🕐 13:00–16:15 📍 Loftet banquet hall, Swedish University of Agricultural Sciences (SLU) Duhrevägen 8, 756 51 Uppsala (maps.app.goo.gl/kdhS2apDskMJ...) We look forward to seeing you there 🌱
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Hugerth lab @h-mel.bsky.social · 26/05/2026
Great day at the #womher symposium, and first poster presentation for our PhD student Delaram Bameri!
Smiling PhD student next to her poster entitled "Beyond the bump: oral health as an overlooked dimension of perinatal care"
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Rauf Salamzade @raufs.bsky.social · 23/05/2026
New versions of skDER (github.com/raufs/skDER) and zol (github.com/Kalan-Lab/zol) are now on Bioconda. Both have automated downloading of genomes based on species / genus name according to classifications in GTDB R232. The latest zol also incorporates FAMSA2 which provides considerable speed boosts!
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naturepoker @binomicalabs.org · 21/05/2026
12 fold increase in papers citing non-existent references in two years. People who do this genuinely don't care. Also they likely have institutional affiliations and advanced degrees, 0 independent researchers. retractionwatch.com/2026/05/07/o... 🧪
retractionwatch.com
One in 277 PubMed-indexed papers in 2026 shows fabricated references, says analysis
Figure from correspondence to The Lancet by Maxim Topaz and colleagues. Fabricated citations in the biomedical literature have increased 12-fold in two years, according to an audit of nearly 2.5 mi…
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Nicola Low @nicolamlow.bsky.social · 21/05/2026
🧪 #PandemicPreparedness 💯 „Preparedness is not built during a crisis press conference or after a pathogen has already crossed borders.“ Hope that coincidence of World Health Assembly @who.int with 2 deadly outbreaks and slashed funding makes people #JoinTheDots and invest now archive.ph/EoSxW
archive.ph
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Ele Willoughby @minouette.bsky.social · 21/05/2026
For International Tea Day, my Green Tea Chemistry print. 🧪🐡 This linocut illustrates green tea and its chemistry. There’s a tea pot, 2 cups of tea & a tea plant (Camellia sinensis) on a tray, & in the steam, you can see some of the organic chemicals found in green tea. Up to 27% of the composition 🧵
This linocut illustrates green tea and its chemistry. There's a tea pot, two cups of tea and a tea plant (Camellia sinensis) on a tray, and in the steam, you can see some of the organic chemicals found in green tea. At the base of the tray is a chromatogram to illustate the L-Theanine (largest peak) and other amino acids in the green tea.⁠
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Camila Gazolla Volpiano, PhD @gazollavolpiano.bsky.social · 21/05/2026
New preprint! The first first-author work of my postdoc at the Baker! So, babies' airways are colonised from birth, and our group has shown that early colonisers shape respiratory health. 1/7 www.biorxiv.org/content/10.6...
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Piotr Rozwalak @prozwalak.bsky.social · 11/05/2026
Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...
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Hugerth lab @h-mel.bsky.social · 11/05/2026
Starting now! @scilifelab.se Uppsala mini-symposium. Getting ready to be wowed.
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Pioneer Labs @pioneerlabs.bsky.social · 05/05/2026
This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded. 🧪Growth + barcode sequencing = data on millions of mutations. 📄 Report: www.biorxiv.org/content/10.6... Retweet if you want more data, and read on if you want to use the library! 🧵
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 07/05/2026
🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇
biorxiv.org
Multireplicon plasmids emerge under predictable rules and drive the spread of antimicrobial resistance across bacterial hosts
Plasmids are DNA molecules that replicate independently of the bacterial chromosome and are typically associated with the spread of antimicrobial resistance (AMR) and virulence determinants, among other relevant traits. Fusion events between plasmids generate larger, complex backbones that carry two or more replication systems, known as multireplicon plasmids. Despite decades of study, we are still far from understanding how multireplicon plasmids arise, persist, and shape the evolution of AMR. Here, we analyzed 24,000 non-redundant plasmids across bacterial genera and found that more than 30% of them encoded multiple replicons. Compared to single-replicon plasmids, multireplicon plasmids were larger, were enriched in genes encoding antimicrobial, metal, and biocide resistance as well as virulence factors, and showed higher mobility and a broader host range. We also found that multireplicon assembly is not random. Some replicon pairs repeatedly merge into stable multireplicon plasmids, while other pairs rarely fuse even when they commonly coexist intracellularly. We also show that replicon pairs tend to be localized either in close proximity to one another or on opposite poles of the plasmid. We further highlight that multireplicon plasmids can be broadly classified into two groups: long-term coevolving replicon pairs and transient associations that lack a shared evolutionary history. Finally, we reveal the molecular mechanisms underlying multireplicon formation and highlight the role of insertion sequences in their formation and maintenance. Together, our work sheds light on the abundance, gene content, evolutionary patterns, and formation dynamics of multireplicon plasmids and pinpoints their relevance to bacterial evolution and human health. ### Competing Interest Statement The authors have declared no competing interest. Instituto de Salud Carlos III, https://ror.org/00ca2c886, PI23/01945, PFIS - FI22/00265, Miguel Servet - CP22/00164 European Research Council, https://ror.org/0472cxd90, HorizonGT, 101077809 Fundación Ramón Areces, "Ayudas Fundación Ramón Areces para la realización de Tesis Doctorales en Ciencias de la Vida y de la Materia 2025" Coordenação de Aperfeicoamento de Pessoal de Nível Superior, https://ror.org/00x0ma614, 88881.128025/2025-01
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Andreas Gustavsson @andreasgustavsson.bsky.social · 04/05/2026
Isabelle Letellier nekades svenskt medborgarskap med hänvisning till hennes klimataktivism. Nu frias hon från misstankar om brott i samband med en protestaktion på Bromma flygplats.
etc.se
Forskaren Isabelle frias efter klimataktion: ”En seger för demokratin”
Hon är en av 15 som frias efter aktion riktad mot superrikas privatjet på Bromma flygplats 2023.
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Hugerth lab @h-mel.bsky.social · 04/05/2026
That blissful second between "Oh, yay, I got the grant!" and "Oh, crap, I gotta deliver what I promised"
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Teresa M. Coque @tmcoque.bsky.social · 26/03/2026
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👇
rdcu.be
The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...
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Hao Yin @haoyin.bsky.social · 26/03/2026
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...
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Hugerth lab @h-mel.bsky.social · 21/03/2026
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...
link.springer.com
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...
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Hugerth lab @h-mel.bsky.social · 21/03/2026
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!
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Hugerth lab @h-mel.bsky.social · 06/02/2026
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."
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Professor Lesley Hoyles @bugsinyourguts.bsky.social · 07/01/2026
🎉🎉🎉 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
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Tim Straub @timothystraub.com · 06/01/2026
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
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Hugerth lab @h-mel.bsky.social · 13/10/2025
Revising a large grant for the last time before submission, and all means are fair
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
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Hugerth lab @h-mel.bsky.social · 28/09/2025
Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment www.science.org/content/arti...
science.org
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
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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
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
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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
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
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Ming Tommy Tang @tommytang.bsky.social · 26/09/2025
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.
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Hugerth lab @h-mel.bsky.social · 27/09/2025
Glad to have been a tiny part in this consortium!
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Hugerth lab @h-mel.bsky.social · 24/09/2025
I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.
An entirely empty lecture hall at a renowned university
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Luisa Hugerth @luhugerth.bsky.social · 23/09/2025
The Nordic medical and drug registries are amazing because you not only can tell RFK to fuck off and start making some sense, you have the numbers to back it up www.dn.se/sverige/sven...
dn.se
Svensk forskning: Ingen koppling mellan paracetamol och autism
Trots att det finns evidens för att paracetamol under graviditeten inte orsakar autism, pekar Trumpadministrationen ut medlet som en orsak.
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...
biorxiv.org
Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort
Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...
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IJOS_Editorial Office @ijosjournal.bsky.social · 22/08/2025
Fusobacterium nucleatum, a common mouth bacterium, may worsen oral cancer by using waste and changing cell behavior. This study offers clues for better oral cancer prevention!👇 #oral #cancer @ijosjournal.bsky.social www.nature.com/articles/s41...
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 22/08/2025
This is a major issue is that the incentives are to output false positives in your tools If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it! open.substack.com/pub/luispedr...
open.substack.com
Why are bioinformatics results so full of false positives?
It's what the incentives
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Vagina Museum @vaginamuseum.bsky.social · 22/08/2025
The legs-up-in-stirrups position sometimes used in birth or gynaecological procedures is called the lithotomy position. Etymology fans among you might note that this derives from the Greek for "stone cut". Let's explain why...
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Rosa Fernández @rosafernandez.bsky.social · 15/08/2025
FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...
nature.com
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 31/07/2025
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵
journals.asm.org
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...
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Hugerth lab @h-mel.bsky.social · 21/08/2025
Anyone know what happened to hmpdacc.org? More importantly, does anyone know how to apply for HMP participant data nowadays?
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Mel Andrews @bayesianboy.bsky.social · 19/08/2025
Practice-engaged and practice-critical philosophy of science is needed now more than ever in light of widespread AI-integration into science and its oversight mechanisms.
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Larry R. Nittler 🚀🎹🌖☄️ @larrynittler.bsky.social · 15/08/2025
I do miss when things were called "neural networks" and "principal components analysis" etc instead of lumping everything as "ML" and then "AI"
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Torsten Günther @trstngnthr.bsky.social · 12/08/2025
The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment: www.uu.se/en/about-uu/...
uu.se
Bioinformatician - Uppsala University
Bioinformatician, Department of Organismal Biology, Uppsala University
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Angie Rasmussen @angierasmussen.bsky.social · 15/08/2025
Best comment on Jay Bhattacharya that I've read to date.
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John Lees @johnlees.bacpop.org · 15/08/2025
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples
ebi.ac.uk
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
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Luisa Hugerth @luhugerth.bsky.social · 15/08/2025
Niche bloop but: The endocrine system is the original object-oriented program.
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Richard Sever @richardsever.bsky.social · 11/07/2025
NIH Director say journals "bully scientists into paying large fees". No. Academia is a prestige economy in which scientific leadership chose to make journals the currency & Gold OA was deemed 'the way'. Publishers just cashed in; you don't have to pay $10K www.insidehighered.com/news/governm...
insidehighered.com
NIH Plans to Cap Publisher Fees, Dilute “Scientific Elite”
Director of the National Institutes of Health says that capping research journals’ open-access fees will help rein in the $19 billion academic publishing industry and bolster scientific debate.
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Hugerth lab @h-mel.bsky.social · 27/06/2025
Mixed feelings when a question I've been musing about for a long time gets answered in a paper. Yes, we have an answer! But also oh no, I wanted to study that!
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Hugerth lab @h-mel.bsky.social · 18/06/2025
Out now in @natcomms.nature.com: we show how wastewater surveillance identifies viral strains several weeks before the clinics, and study the trade-offs between the size of the catchment area for the sewer and the number of unique variants identified www.nature.com/articles/s41...
nature.com
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...
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