Research focus

I study why bacteria live where they do, what they are doing there, how they interact with each other, and how they change over time. Bacteria live everywhere we can imagine, and they often exhibit biogeography (patterns of certain bacteria appearing in certain places) across many different scales - some bacteria live only next to certain other bacteria (the micron scale), others live in certain regions of the human body but not others (centimeter scales), others might live at hydrothermal vents separated by hundreds of kilmeters.

For those who think about human health, why microbes live where they do is especially important. Many microbe-associated medical problems (like opportunistic infections) are essentially the right microbe in the wrong place. Figuring out what keeps the right microbes in the right places in healthy people is critical for medical professionals to be able to keep microbes where they’re supposed to be to keep us healthy. And understanding how microbes change over time in healthy populations is essential for us to be able to distinguish between change for the better or for the worse.

Outside of humans, it’s much the same - microbes might be doing the same big-picture job (like consuming methane), but the rates at which they do their task can vary substantially depending on their localized environment.

Some recent projects I’ve worked on:

Some thesis projects:

  • How different are strains of a given bacterial species? - [paper] [methods]
    • Bacteria in the human oral microbiome exhibit striking biogeography despite salivary mixing
    • We compared the genomes of many cultured strains to compare their differences, and detect patterns about where they lived, and found some exciting clues about what genes underpin their biogeography
  • How do oral bacterial populations change over time? - [biorxiv] [methods]
    • The oral microbiome is a dynamic place, and so are bacterial populations
    • We wanted to study how bacterial populations change over short timescales, so reconstructed microbial genomes and tracked them over intervals of days to weeks
    • We found genomes of some strains of a species differing by ~100s of genes fluctuated over a matter of days, substantially changing the genetic (and implied functional) composition of a population
  • Genomics of individual-specific populations [in preparation]

Some collaborations:

  • TM7x host range - [paper] [methods]
    • TM7x is an obligate bacterial symbiont that grows attached to other bacteria. Usually, TM7x is considered a parasite becuase it impedes host growth in the lab
    • Working with Bat Bor, who found that not all hosts were affected as strongly, we compared host genomes to identify putative genes and sequence variants associated with symbiotic phenotypes
  • Santa Barbara Basin foraminifera - [article] [methods]
    • Most foraminifera are dependent on oxygen, and can only briefly survive without oxygen. But in the hypoxic to anoxic mud of the Santa Barbara Basin, certain forams thrive - how do they do it?
    • Led by Fatma Gomaa, we used transcriptomes to identify multiple metabolic strategies that worked together to allow their growth in such a eukaryote-harsh environment
    • And, we found transcriptionally-active kleptoplasts in these forams, despite them living in the sediments >300m below the surface?!
  • Toxin evolution in Proteus mirabilis - [biorxiv] [methods]
    • The Gibbs lab works on bacterial toxins used for self/non-self recognition in Proteus mirabilis (among other things).
    • After the Gibbs’ group terrific molecular work characterized the enzyme down to the domain level, we worked to characterize the toxin’s representation in the global human metagenome and discovered how inter- and intra-species variability within metagenomes tracked domain function