PHLAME is available to try out on GitHub:
github.com/quevan/phlame

Il Dunce

Finally, a HUGE THANK YOU to Evan Qu, Chris Mancuso (@mancusosci.bsky.social), Delphine Tripp, Arolyn Conwill, and Tami Lieberman (@contaminatedsci.bsky.social) for their continuous feedback & critical contributions, including new algorithms to measure lineage-level abundances from metagenomics‼️

TLDR Our study reveals previously undetectable dynamics in human facial skin microbiomes and advances our comprehension of microbiome acquisition/development. These results also inform the design of therapeutics like durable, engrafting probiotics. Dive into our preprint for a detailed exploration!

🔁⬇️ In S. epidermidis, we don’t observe an adolescent-specific increase in colonizations, but rather than lineage turnover is faster than C. acnes overall and decelerates by adulthood.

🧐 So when does microbiome engraftment happen?

📈🦠 We find that C. acnes colonization surges in adolescence during population expansion, apparently alleviating barriers to colonization before leveling off in adulthood. This period seems crucial for shaping the skin microbiome long-term.

🧐 So when does microbiome engraftment happen?

👨‍👩‍👧‍👦 A fascinating aspect of within-family sharing: while family members commonly share lineages, individuals’ composition remains unique, indicating ecological barriers which prevent unmitigated sharing. Overcoming these barriers is key to the engraftment of bacteria in the microbiome.

🧑↔️🧔 Interestingly, in person-to-person spread, we see multiple transmitted genotypes of the same lineage coexist. This is a stark contrast to transmission in gut microbiomes where lineages originate from single founder cells, but supports previous work showing that skin pores allow coexistence.

☮️😌 We actually don’t find evidence of within-species metabolic niche partitioning (or adaptive selection) for either species, emphasizing the presence of neutrality and priority effects in the assembly of complex within-species communities.

Carrying multiple co-existing lineages of C. acnes and S. epi. lineages is the norm, so you would expect lineage-to-lineage competition to lead to selection or niche partitioning, right?

👶1️⃣👦2️⃣🧓2️⃣ We found that there are essentially two types of face skin microbiomes or “Facial Cutotypes”: the younger, more diverse type (FC1) and the less diverse, C. acnes dominated adult-type (FC2).

🧬 📊We also used metagenomics to quantitatively measure abundance of lineages on individuals, which enabled us to trace changes over time and measure the amount of sharing between people. With an expanded set (57 people in 23 families) we also investigated phylotype and species-level communities.

👨‍👩‍👧‍👦 A fascinating aspect of within-family sharing: while family members commonly share lineages, individuals’ composition remains unique, indicating ecological barriers which prevent unmitigated sharing. Overcoming these barriers is key to the engraftment of bacteria in the microbiome.

👨‍👩‍👧‍👦 A fascinating aspect of within-family sharing: while family members commonly share lineages, individuals’ composition remains unique, indicating ecological barriers which prevent unmitigated sharing. Overcoming these barriers is key to the engraftment of bacteria in the microbiome.

Carrying multiple co-existing lineages of C. acnes and S. epi. lineages is the norm, so you would expect lineage-to-lineage competition to lead to selection or niche partitioning, right⁉️

🧫🌳 Using 4,055 isolate genomes from 8 families, we identified extremely closely related lineages of C. acnes & S. epidermidis. Since lineages arose from recent ancestors on people (<100 SNPs/genome in the entire lineage) we could use them to directly trace transmissions with high precision.