Laura Markey

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.

See thread for more information and reach out!

Intraspecies warfare restricts strain coexistence in human skin microbiomes - Nature Microbiology About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.

🚨Out now!

About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota @contaminatedsci.bsky.social @mancusosci.bsky.social #MicrobiomeSky

www.nature.com/articles/s41...

read here: rdcu.be/et7VP

Thank you!!

Thanks to labmate and co-author @quevan.bsky.social , additional co-authors and my PI @contaminatedsci.bsky.social ! 4/4

barplot of individual leg skin microbiome profiles demonstrates diverse composition across subjects including multiple species of Cutibacterium, Corynebacterium and Staphylococcus. 4/8 female subjects have multiple vaginal microbiome species including Gardnerella and Prevotella but not Lactobacillus present at >10% abundance.

Metagenomics enabled the surprising observation that common vaginal microbiome member Gardnerella (but not Lactobacillus) made up at >10% of the low biomass lower leg skin microbiome of 4/8 female subjects. 3/4

Left barplot shows that as mock community microbiome sample is diluted, qPCR and metagenomics continue to detect all taxa but 16S detects only Cutibacterium. Right barplot shows that for qPCR and metagenomics detect a diverse average microbiome from lower leg skin but 16S composition is dominated by Cutibacterium.

In high biomass samples, sequencing methods are comparable – however, as biomass decreases, minor taxa are rapidly lost with 16S as the limited amplicon library becomes biased towards the most abundant taxon. 2/4

Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass ...

Excited to share my new preprint: we show that for lab control and skin samples with low microbial biomass, metagenomics significantly outperforms 16S while DNA extraction method has minimal impact. 🧵 1/4
www.biorxiv.org/content/10.1...

Left side of image shows a barplot of mock microbiome sample dilution series analyzed by qPCR, metagenomics and 16S sequencing- as the sample is diluted, qPCR and metagenomics continue to recall all taxa while 16S is increasingly dominated by Cutibacterium. Right side of image shows that similarly qPCR and metagenomics detect a diverse average leg skin microbiome while 16S is dominated by Cutibacterium.

In high biomass samples, sequencing methods are comparable – however, as biomass decreases, minor taxa are rapidly lost with 16S as the limited amplicon library becomes biased towards the most abundant taxon. 2/4

The microbiome of the human facial skin is unique compared to that of other hominids | mSystems Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

Our work on the facial skin microbiome of non-human primates is out in mSystems!

We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer.

journals.asm.org/doi/10.1128/...

New pre-print from my grad thesis lab! So excited to see this interesting paper for itself and to see that the gut-Candida-brain arm of the Kumamoto lab continues on

Staph is so sticky!! Once thought I had suddenly forgotten how to make dilutions when CFU plating (for an OD/CFU curve) reps were terrible - nope just so sticky I had to use washed culture to get CFUs that were actually single cells dropping onto a plate

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https://go.nature.com/4aYn9Me

Intraspecies associations from strain-rich metagenome samples Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metage...

Excited to share my preprint describing a new microbiome analysis method, PHLAME, for detecting strain-level associations in difficult sample types. 🧵

www.biorxiv.org/content/10.1...

This work was done with my great coauthors and my amazing advisor @contaminatedsci.bsky.social

👋 yeah I've been trying to "just move to industry" for a year so uh good luck with that

Candida albicans enhance Staphylococcus aureus virulence by progressive generation of new phenotypes https://www.biorxiv.org/content/10.1101/2024.06.26.600854v1 Candida albicans and Staphylococcus aureus have been co-isolated from several biofilm-associated dis

Candida albicans enhance Staphylococcus aureus virulence by progressive generation of new phenotypes https://www.biorxiv.org/content/10.1101/2024.06.26.600854v1

Siderophore piracy enables the nasal commensal Staphylococcus lugdunensis to antagonize the pathogen Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2024.02.29.582731v1 Bacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human popula

Siderophore piracy enables the nasal commensal Staphylococcus lugdunensis to antagonize the pathogen Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2024.02.29.582731v1

Binning Singletons logo. A circle with 4 microbes. From left to right: a large pink vibrio on the left, smiling and pointing to the right; 4 yellow cocci looking around; a purple E. coli looking off to the right; and a green acetinobacter looking to the left. They represent the mentor and singletons at a large meeting and the mentor is helping them through all the facets of the meeting.

We're gearing up for #ASMicrobe in Atlanta! We help 1st-time and solo attendees have better experiences through networking and mentoring Here's a writeup on how it works

blog.addgene.org/binning-sing...

Ever wondered about the origin of the bacteria that call our faces home? 🤔 Our new preprint dives into the fascinating dynamics of the human facial skin microbiome (FSM) and explores the natural history of important microbiome species on people at high resolution. 🧫🧵

Highly-resolved within-species dynamics in the human facial skin microbiome https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1 Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibact

Highly-resolved within-species dynamics in the human facial skin microbiome https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1

Thanks! I'll have to check out what it's doing on cheese.
I don't know about most labs - but in our facility we can routinely recover S. xylosus both from the hairy, healthy skin of mice housed in the facility and from surfaces (lab benches, housing racks).

Thanks! I would add to what Tami said that we applied the bacteria (including E coli and L reuteri) every day - so even if they were at a disadvantage for survival on mouse skin, they were grown up in lab and reapplied daily and still did not delay healing

 Bonus: Neither E. coli nor L. reuteri delayed healing, indicating this phenotype is limited to skin commensals!

Thanks to co-first Veda Khadka, and co-author Magalie Boucher, PI @contaminatedsci.bsky.social and Lieberman Lab for feedback! [3/3]

The answer: not when the skin is damaged! We tested multiple bacterial species, including mouse commensal S. xylosus, C. accolens, and 3 different isolates of S. epidermidis.All delayed healing when applied to abraded mouse flank skin. [2/3]

Excited to announce a new preprint from the Lieberman Lab @contaminatedsci.bsky.social . We use a mouse model to ask: can we use commensal skin bacteria as topical probiotics? www.biorxiv.org/content/10.1...  [1/3]