Antti Karkman

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

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...

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...

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 ...

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...

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.

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

Application deadline for this postdoc position in my group closing next week 🦠 thank you all who have shared so far!

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...

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

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.

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.

We would have some from Arcobacter butzleri and cryaerophilus. Already in ENA but not public yet.

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

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

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.

GitHub - sheinasim-USDA/HiFiAdapterFilt: Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). - sheinasim-USDA/HiFiAdapterFilt

This tool should do the work.

github.com/sheinasim-US...

Taiwanese ambassador to Finland performs with his metal band at Taiwan-Finland cultural event! 🤘✊️
That's what I call great ambassador

💥CONTAM CALENDAR GIVEAWAY💥

Here's your chance to win a ContamCalendar 2026! 🗓️🍄🦠

Just follow @contamclub.bsky.social and repost this post to enter the competition

Winner will be randomly selected from Bluesky or Twitter on Wednesday @ 6pm UTC

We are organising an AMR meeting next spring in Helsinki. Meeting includes evolution of AMR and environmental AMR sessions. Please submit your abstract now! Deadline Dec 1st.

Doctoral Researcher: Gut microbiome metabolism and molecular mechanisms mediating gut microbiome-host interactions? A 3-year Doctoral Researcher position is available at the Department of Biological and Environmental Sciences, University of Jyväskylä, Finland, in the group of Dr. Suvi Ruuskanen. The Doctoral Resear...

3-year #PhD student #position open in my group @uniofjyvaskyla.bsky.social Finland on #gut #microbe- host communication in #birds. DL 20.12, start date in April2026. #microbiome #metabolomics #vesicles, please RT

ats.talentadore.com/apply/doctor...

We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!

Please find more information on the venue, program, and the application form here, and spread the word 😇

anvio.org/workshops/20...

Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts | Microbiology Spectrum Antibiotic resistance is an ancient phenomenon and a common trait of many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacteria’s ability to exchange ...

Our latest article examines the sulfonamide resistance gene sul4. By using long-read metagenomics and methylation patterns, we show that sul4 appears in diverse genetic contexts and hosts, expanding our understanding of its environmental distribution.
doi.org/10.1128/spec...
#AntibioticResistance

New #EEA briefing published yesterday on European #Antibiotic awareness day:

👉 #AntimicrobialResistance in surface waters - developing #EnvironmentalMonitoring for better #RiskManagement

Feeling very honoured to have contributed with my group ...

#OneHealth #AMR #EAAD

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ECR connection: Meet Meren when you need to A means for ECRs to get advice from a senior scientist outside of their support network

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.

Here is a blog that explains my motivation for this and how to schedule a meeting:

merenlab.org/2025/11/16/E...

Metagenomic classification survey Background: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

Orchestrating Microbiome Analysis with Bioconductor The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous…

Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

Nordic AMR Conference 2026 flyer. Keynote speakers are Timothy Walsh, Dan Andersson, Claas Kirchhelle, Barth Smets and Anu Kantele. Abstract deadline 1st of December and registration opens on 8th of December..

The abstract deadline for Nordic AMR Conference 2026 has been extended. Also see the list of keynote speakers.
More information at www.helsinki.fi/en/conferenc...

Reformation of science publishing: the Stockholm Declaration | Royal Society Open Science Science relies on integrity and trustworthiness. But scientists under career pressure are lured to purchase fake publications from ‘paper mills’ that use AI-generated data, text and image fabrication....

Newly released Stockholm Declaration recommends the following reforms to publishing:

1. Academia resumes control of publishing

2. Incentive systems to merit quality, not quantity

3. Independent fraud detection and prevention

4. Legislation and policies to protect science quality and integrity

This year the sequencing was not perfect, but we got one circular (hopefully complete) genome.
On Wednesday we continue with more in depth annotations and will learn more.

Metalog: curated and harmonised contextual data for global metagenomics samples Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...

Hapanjuureen leivottua ruislimppua.

En voisi olla enempää samaa mieltä.

Kun pidät tieteellisen seminaarin jossa tarjolla ”pientä purtavaa”, pidä se ravitsemustieteilijöiden kanssa. Koska TOTTA KAI niiden väitöskirjatutkija on artesaanileipuri! Niissä piireissä tiedetään, että ruoalla on paitsi terveys-, myös mielenterveysvaikutuksia.