Antti Karkman
@anttikarkman.bsky.social
University lecturer in microbial bionformatics at University of Helsinki (@helsinki.fi) Co-founder of Aluke (www.aluke.fi) (he/him)
At EDAR8 I will be co-hosting a workshop on Tuesday about novel, quantitative methods in AMR research and surveillance, and presenting our recent work on methylation based binning on Thursday morning in the session S4.1A. #EDAR8
New paper! 🧬 Melina Markkanen’s final PhD chapter is out in Genome Biology: using long-read PacBio metagenomics & methylation-based binning to trace antibiotic resistance genes back to their hidden bacterial hosts in wastewater. Congrats Dr. Markkanen! 🎉 doi.org/10.1186/s13059-026-04200-0
Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene–host associations in complex communities - Genome Biology
Background Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better understanding of the carriers of ARGs beyond the clinically most relevant species is urgently needed for longer-term resistance monitoring and intervention measures. While the risks of emerging ARGs from environmental sources have been recognized, the identification bottlenecks stem from the limitations of shotgun metagenomic sequencing and bioinformatic methods. Results We use long-read metagenomic sequencing and bacteria-specific methylation profiles to re-establish the links between established (well-described) or latent (absent in databases) ARGs and their bacterial and genetic contexts in wastewater. We analyze base modification data produced by PacBio SMRT sequencing using an in-house pipeline utilizing position weight matrices and UMAP visualizations, which we validate by a synthetic community with known bacterial composition. Our analysis reveals several previously unreported ARGs and ARG-host linkages in wastewater. For instance, we find that Arcobacter, a key wastewater associated taxon and emerging pathogen, carries a latent beta-lactamase gene with high predicted mobility potential. Of the other understudied beta-lactamases, we describe blaMCA within pdif-modules across highly varying contexts suggesting its recent acquisition events. Additionally, we uncover the wastewater resident taxa mediated carriage of clinically important ARGs. Conclusions By linking ARGs to their wider genetic contexts and hosts, our findings shed light on the previously unrecognized carriers of resistance genes in wastewater. The presented approach provides a valuable methodology for early identification of newly arising ARGs and their hosts.
doi.org
Found a better version of the Eddy Merchx quote ⬇️ "They always say cakes are bad for cyclists...but it's not the cakes its the climbs that are bad for you" 🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲🍰🚲
David N. Thomas@dnthomas01.bsky.social · 4w agoToday is the first time I have heard this quote from Eddy Merchx "It's not the cakes, it's the climbs that are bad for you" #cycling
Very happy that this piece of research finally sees the daylight! Super nice collaboration between Nanjing, York and Helsinki. Fun fact: we started this work over 10 years ago when I was working as a fellow at Imperial College. Sometimes good things come to those who wait.
Nature Microbiology@natmicrobiol.nature.com · 2mo agoOut Now! Bacteria–phage coevolution drives variation in bacterial wilt disease incidence via resistance–virulence trade-offs #MicroSky
”Tämä on suoraa jatkoa viime vuoden Rusta-sekoilulle. Valta pitäisi saada takaisin akateemiselle puolelle, eikä tehdä ratkaisuja hallinnon prioriteetit edellä”, Leino-Sandberg puuskahtaa. www.hs.fi/helsinki/art...
Helsingin yliopisto | ”Suoraa jatkoa Rusta-sekoilulle”, sanoo oikeustieteen professori kaavailluista tilaleikkauksista
Oikeustieteellisen tiedekunnan tilat supistuisivat yhteen kerrokseen, mikäli suunnitelmat toteutuvat. Ennen kerroksia oli neljä.
hs.fi
I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇
Thank you to the Research Council of Finland for funding my project: “Risks and Mitigation of Antimicrobial Resistance Across One Health Sectors – AMaRONE”. A big thanks also to the external reviewers for their constructive feedback — it will be invaluable throughout the project.
This is absolutely nuts, as HMMER is an integral part of NCBI (NLM/NIH) informatics pipelines. 🧪
Zamin Iqbal@zaminiqbal.bsky.social · 2mo agoThis 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...
HMMER, Pfam, and Rfam are critical to so many Bioinformatics pipelines. This is absolutely crazy
Zamin Iqbal@zaminiqbal.bsky.social · 2mo agoThis 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...
Our new advanced wastewater treatment paper in npj Clean Water: Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment www.nature.com/articles/s41...
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment - npj Clean Water
npj Clean Water - Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
nature.com
Seems wise: www.nature.com/articles/s44...
Stop messing with rumen microbes and focus on reducing ruminant populations for environmental and human health - npj Sustainable Agriculture
npj Sustainable Agriculture - Stop messing with rumen microbes and focus on reducing ruminant populations for environmental and human health
nature.com
Jätevesien ja maatalouden valumavesien tiedetään saastuttavan pintavesiä, mutta saastumisen lähde on usein jäänyt epäselväksi. Tuoreessa väitöstutkimuksessa kehitettiin menetelmä, jolla lähde voidaan jäljittää geenimarkkereiden avulla. Lue lisää: www.helsinki.fi/fi/uutiset/y...
Vesivälitteiset taudit kuriin – uusi menetelmä tunnistaa vesistöjen saastumisen lähteen | Helsingin yliopisto
Jätevesien ja maatalouden valumavesien tiedetään saastuttavan pintavesiä, mutta saastumisen lähde on usein jäänyt epäselväksi. Tuoreessa väitöstutkimuksessa kehitettiin menetelmä, jolla lähde voidaan jäljittää geenimarkkereiden avulla.
helsinki.fi
Sci-Hub is an evil website that pirated 85M+ research papers and made them freely available Now they've added AI to their database to make Sci-Bot. It answers your questions using latest, full-text articles. But DO NOT use it. We should all try to make billion-dollar academic publishers richer.
Open postdoc position at Tampere University, Finland. More details behind the link. tuni.rekrytointi.com/paikat/?o=A_...
Tutkijatohtori (Data-analyytikko psykologian ja ihmisen mikrobiomitutkimuksen alalla)/ Postdoctoral Researcher (Data analyst in psychology and human microbiome research)
tuni.rekrytointi.com
I have a research joke but before I publish it I need to pay Elsevier a couple thousand euros.
Deal Elsevier. Just a little FYI. No - I will not review for any of your journals. Oh, and another FYI - because your company is so bad for science, I will also not answer any of your requests to review.
New paper alert Bioplastic biodegradability shapes microbial communities in a coastal brackish environment A new term "bioplastisphere" describes the microbial communities associated with biodegradable plastics Well led @igorspp.bsky.social & @eevaer.bsky.social academic.oup.com/ismej/advanc...
Bioplastic biodegradability shapes microbial communities in a coastal brackish environment
Abstract. Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade differe
academic.oup.com
Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities https://www.medrxiv.org/content/10.64898/2026.02.18.26346558v1
Our latest work is available as a pre-print. We used methylation analysis to link #AMR genes to their hosts in sewage. Work by excellent PhD researcher Melina Markkanen. doi.org/10.64898/202...
Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities
Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better unde...
doi.org
Suomen akateemisten tutkijoiden yhdistys SATY pelkää Suomen ympäristökeskuksen henkilöstövähennysten vaikuttavan viranomaistehtävien laatuun, korkeatasoisen tutkimuksen tekemisen edellytyksiin ja henkilöstön jaksamiseen. Lue kannanotto! @syke.fi tieteentekijat.fi/syken-henkil...
Syken henkilöstöleikkaukset uhkaavat horjuttaa ympäristötiedon ja viranomaispalvelujen laatua
Kannanotto Syken yt-neuvotteluista 29.1.2026 Suomen akateemisten tutkijoiden yhdistys ry (SATY) kantaa huolta Syken irtisanomisista ja valtion tutkimuslaitosten ja virastojen tilanteesta. Merkittävät ...
tieteentekijat.fi
The University of Helsinki seeks a postdoctoral researcher for a 3-year role in statistical ecology and evolution, focusing on sex-specific differences in immunity and life history. Apply by Feb 28, 2026. More in… https://www.helsinki.fi/en/faculty-science/faculty/mathematics-and-statistics #postdoc
Mathematics and statistics | Faculty of Science | University of Helsinki
The Department of Mathematics and Statistics is Finland’s largest university department for mathematical sciences. Its multifaceted research has received the highest points in numerous assessments. The Department collaborates actively with other higher education institutions and with several government research institutes both in Finland and abroad.
helsinki.fi
Application deadline for this postdoc position in my group closing next week 🦠 thank you all who have shared so far!
Rachel M. Wheatley@rachelmwheatley.bsky.social · 7mo ago🔊 Job Opportunity: Postdoctoral Research Fellow in Bacterial Evolution. Looking to recruit a postdoc to join a UKRI FLF-funded project on antibiotic resistance evolution in the microbiome 🦠 3 years funding, deadline 26th Jan, please share! hrwebapp.qub.ac.uk/tlive_webrec...
The position for a postdoc is now officially open. I can answer any questions related to the position, but please apply only thru the university system. jobs.helsinki.fi/job/Helsinki...
Postdoctoral researcher in microbiology and/or bioinformatics
Postdoctoral researcher in microbiology and/or bioinformatics
jobs.helsinki.fi
Antti Karkman@anttikarkman.bsky.social · 8mo agoExcellent news for the end of the year! Our project on past and present bacteria with @jmuurine.bsky.social and great collaborators got funded. We will be looking for a postdoc for 2026-27 with expertise in bacterial genomics and/or molecular dating methods. If interested, DM me. Please share.
We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n
Researchers from the Quadram Institute have come together to develop a new open access book filled with cutting-edge methods and protocols to ensure best practice in microbiome research.
New book shares Quadram’s Best Practice in Microbiome Research - Quadram Institute
Researchers from the Quadram Institute have developed an open access book to help ensure best practice in microbiome research.
buff.ly
Our work on palsa permafrost, ultra-small microbes and carbon is out! "Carbon and microbes in a degrading palsa mire are distinct from a peatland and a wider connected sub-Arctic fluvial system" doi.org/10.1093/isme... @isme-microbes.bsky.social @dnthomas01.bsky.social @jennihultman.bsky.social
Carbon and microbes in a degrading palsa mire are distinct from a peatland and a wider connected sub-Arctic fluvial system
Abstract. Climate change is altering the biogeochemical cycling of carbon and nutrients in the northern peatland and permafrost regions, which provide one
track.smtpsendmail.com
Excellent news for the end of the year! Our project on past and present bacteria with @jmuurine.bsky.social and great collaborators got funded. We will be looking for a postdoc for 2026-27 with expertise in bacterial genomics and/or molecular dating methods. If interested, DM me. Please share.
Taiwanese ambassador to Finland performs with his metal band at Taiwan-Finland cultural event! 🤘✊️ That's what I call great ambassador