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Jacob Baker @microjacob.bsky.social · 04/04/2025

Taxa is hiring! We're looking for a Computational Biologist to spearhead the analysis of massive genomic datasets for our flagship probiotics. Exciting science, great team, and transparent compensation. Apply here 👇

linkedin.com

Taxa hiring Computational Biologist in San Francisco, CA | LinkedIn

Posted 4:13:15 PM. The OpportunityWe are looking for a talented Computational Biologist to spearhead the analysis of…See this and similar jobs on LinkedIn.

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Reposted by Jacob Baker

Evan Qu @quevan.bsky.social · 11/02/2025

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

biorxiv.org

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...

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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‼️

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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!

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🔁⬇️ 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🧐 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🧐 So when does microbiome engraftment happen?

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Jacob Baker @microjacob.bsky.social · 11/01/2024

👨‍👩‍👧‍👦 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🧑↔️🧔 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

☮️😌 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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?

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Jacob Baker @microjacob.bsky.social · 11/01/2024

👶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).

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🧬 📊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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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⁉️

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Jacob Baker @microjacob.bsky.social · 11/01/2024

🧫🌳 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.

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Jacob Baker @microjacob.bsky.social · 11/01/2024

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. 🧫🧵

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