Martin Fenk

Martin Fenk

@mfenk.bsky.social

PhD student @MPIIB Berlin | Exploring the captivating realm of microbial evolution within microbiomes #Microbiology #Evolution

223 followers62 following14 posts

Martin Fenk reposted

Dina Grohmann
@curiousdina.bsky.social

๐ŸŒ™ Bringing Archaea to moon! Our latest study with the Orsi lab shows that M. okinawensis can survive, perform methanogenesis, and grow under simulated Enceladus conditions. Yet another reminder of how astonishingly adaptable Archaea are. www.science.org/doi/10.1126/...

science.orgEnceladus-like geochemistry fuels methanogenesis under extreme CO2 limitationSaturnโ€™s icy moon Enceladus features chemical signatures consistent with an alkaline soda ocean with H2 production via hydrothermal water-rock reactions. Chemolithoautotrophic methanogenesis is thermo...

Martin Fenk reposted

Dina Grohmann
@curiousdina.bsky.social

Ignicoccus is one of the most fascinating archaeal organisms due to its double membrane (and because of its tight interaction with Nanoarchaeum). But how does a cell like this divide? As so often, archaea invented their own way ... check out our new preprint and I promise you will be stunned!

Florian Mayer@florianmayer.bsky.social

Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6... Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social @tbharat-lab.bsky.social

biorxiv.orgThe life cycle of an archaeon with multiple membranesMany prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, onl...

Martin Fenk reposted

Nandita Garud
@nanditagarud.bsky.social

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

nature.comGene-specific selective sweeps are pervasive across human gut microbiomes - NatureDevelopment and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Martin Fenk reposted

Michael Baym
@baym.lol

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

science.orgIntracellular competition shapes plasmid population dynamicsFrom populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Martin Fenk reposted

Felix M Key
@keyfm.bsky.social

Our new preprint, led by Martin (@mfenk.bsky.social), is online. We address the microbiomeโ€™s role as a source and incubator of acute infections by combining prospective collection of native samples with population-wide, culture-based sequencing. Please check out Martinโ€™s wonderful thread. โฌ‡๏ธ๐Ÿงต๐ŸŽ‰

Martin Fenk@mfenk.bsky.social

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

doi.orgColonization, translocation, and evolution of opportunistic pathogens during hospital-associated infectionsMany commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...
Martin Fenk
@mfenk.bsky.social

But why was the ๐˜ง๐˜ช๐˜ฎ๐˜ก [F126L] mutant lost shortly after the HAI was cleared? Measuring the antibiotic resistance of isolates over time shows that the replacement was driven by multiple resistance-conferring mutations sweeping across the patientโ€™s body, which were present until the end of the study.

Martin Fenk
@mfenk.bsky.social

Our results highlight the power of prospective longitudinal investigations of the human microbiome during acute infection leading to yet unknown variants associated with the complex etiology of HAI.

Martin Fenk
@mfenk.bsky.social

Further, utilizing ๐˜ช๐˜ฏ ๐˜ท๐˜ช๐˜ท๐˜ฐ survival assays with immunocompromised Relish ๐˜‹๐˜ณ๐˜ฐ๐˜ด๐˜ฐ๐˜ฑ๐˜ฉ๐˜ช๐˜ญ๐˜ข ๐˜ฎ๐˜ฆ๐˜ญ๐˜ข๐˜ฏ๐˜ฐ๐˜จ๐˜ข๐˜ด๐˜ต๐˜ฆ๐˜ณ, we observed an increase in its virulence leading to a more rapid decline in survival rates. This suggests that the ๐˜ง๐˜ช๐˜ฎ๐˜ก [F126L] mutantsโ€™ fitness was elevated, potentially beneficial during pneumonia.

Martin Fenk
@mfenk.bsky.social

Intrigued by the infection-associated fitness effects, we wondered whether ๐˜ง๐˜ช๐˜ฎ๐˜ก [F126L] is a common marker of infection. Analyzing >400 global ๐˜Œ. ๐˜ฉ๐˜ฐ๐˜ณ๐˜ฎ๐˜ข๐˜ฆ๐˜ค๐˜ฉ๐˜ฆ๐˜ช genomes from clinical contexts revealed the ๐˜ง๐˜ช๐˜ฎ operon evolves under purifying selection and nonsynonyoums mutations in ๐˜ง๐˜ช๐˜ฎ๐˜ก are rare.

Martin Fenk
@mfenk.bsky.social

During an ๐˜Œ๐˜ฏ๐˜ต๐˜ฆ๐˜ณ๐˜ฐ๐˜ฃ๐˜ข๐˜ค๐˜ต๐˜ฆ๐˜ณ ๐˜ฉ๐˜ฐ๐˜ณ๐˜ฎ๐˜ข๐˜ฆ๐˜ค๐˜ฉ๐˜ฆ๐˜ช infection, we observe a short-lived, non-synonymous mutation in the fimbriae regulator gene ๐˜ง๐˜ช๐˜ฎ๐˜ก [F126L] that is first observed in the gut, before being associated with HAI but subsequently swiftly replaced by repeated body-wide sweeps of independent genotypes.

Martin Fenk
@mfenk.bsky.social

Does the ๐˜ง๐˜ช๐˜ฎ๐˜ก [F126L] mutant convey a fitness effect? To answer this, we performed ๐˜ช๐˜ฏ ๐˜ท๐˜ช๐˜ต๐˜ณ๐˜ฐ assays and found this genotype translates into a hyperpilated phenotype with increased biofilm formation and adherence to lung epithelia.

Martin Fenk
@mfenk.bsky.social

But were those pathogens acquired within the hospital or outside? Inferring the time to the most common recent ancestor reveals, that some lineages arose from a recent bottleneck during the hospital stay, while others have been colonizing the patient already before hospitalization.

Martin Fenk
@mfenk.bsky.social

The evolutionary trajectory of opportunistic pathogens from asymptomatic carriage to HAI - a critical period for possible pathoadaptation โ€“ is rarely studied due to the logistical challenges in prospective sampling. Our population-wide whole-genome sequencing data allowed us to investigate that.

Martin Fenk
@mfenk.bsky.social

Of those, 3 patients developed HAIs by 9 different species. We performed culture-based sequencing of each pathogen of โ‰ค10 isolates from the site of infection and โ‰ค20 isolates/microbiome site/timepoint. This uncovered a closely related strain of the pathogens within the microbiome in 73% of cases.

Martin Fenk
@mfenk.bsky.social

While we have not seen one common reservoir microbiome niche for those pathogens, we identified that most pathogen strains are observable within the patientโ€™s microbiome either before or within 6 h of HAI onset โ€“ pointing at the importance of the microbiome for HAI.

Martin Fenk
@mfenk.bsky.social

To gain insights into the hidden evolutionary processes before, during and after HAI, we enrolled 13 critically ill patients and prospectively collected every week native nasal, oral, rectal and skin microbiome samples during their hospital stay.

Martin Fenk reposted

i-light-maka.bsky.social
@i-light-maka.bsky.social

Finally getting some of my research for my PhD out there! Hopefully soon in a journal near you ;) Ancient Y. pestis infection from a sheep falls on the LNBA lineage, previously only known from humans! +molecular evolutionary analysis to leverage the ever increasing number of ancient genomes known!

Felix M Key@keyfm.bsky.social

Many zoonotic diseases are believed to have emerged during prehistory, but can we actually identify their past host range using ancient DNA? In the first publication of the Key Lab we present a 4000y old Yersinia pestis genome reconstructed from domesticated sheep. ๐Ÿงต www.biorxiv.org/content/10.1...

biorxiv.orgBronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineageMost human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direc...

You are up to date.