Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1

Every two years a bunch of microbial ecology and microbial genomics folks descend upon the UCLA Lake Arrowhead center for a fabulous conference.  See this search result for numerous posts here at microBEnet about the meetings past.  This year (as in 2012) there is a session on the Microbiology of the Built Environment.  But that’s not until Wednesday.   Here’s the summary of Day #1.  Or not really so much a summary as things that particularly caught my interest.

The first talk of the morning was by Julia Oh, “The Human Skin Microbiome: Metagenomes to Therapeutics”.  Julia works at Jackson labs and they are doing some awesome research translating microbiome survey data into actual experiments with an eye towards actual treatments.   Really cools stuff.  I loved her example of the Brassica vegetables to illustrate how important strain variation is (they’re all the same species)… as a limitation of just surveying taxa.   The other concept I’d never heard before was the idea that perhaps sufficient strain variation within a species could result in a pan-genome that saturated space resulting in niche exclusion.  Cool.

Next talk was Huiying Li “The Skin Microbiome”.  She talked about some really detailed skin microbiome studies, focusing on acne.  The etiology of acne isn’t really well understood but she presented some compelling data of strain variation and interactions with host factors.  In particular vitamin B-12 has been known to play some role in acne but she presented a possible mechanism.   Loving seeing these kind of detailed experimental studies.

Elaine Hsaio gave a great talk “The Gut Microbiome and Human Brain Disease”.  She started by giving a good review of existing studies that related the microbiome to either the brain or behavior (far more than I though there were).   She mentioned that the correlations and understanding related to depression were the furthest along but that it’s all very complicated to disentangle.

Parag Vaishampayan went next… I’ve seen him talk once about Planetary Protection, once about live-dead staining, and this time about “Differences in the Breast Duct Microbiome in Healthy Women Compared to Women with a History of Breast Cancer”.  Busy man!  He showed some nice data about how while the skin surface microbiome was similar in both cohorts, there were very large differences between the communities inside the ducts.   What’s clearly needed now is some sort of perspective study since it’s hard to disentangle the effects of having had cancer from having been treated for cancer.

Tami Lieberman talked about “Microbial Diversification Within Individual People”.   She has some awesome bacterial genome data where they looked at hundreds of bacterial genomes from human isolates and looked for variation and evolution within individuals.  And found it.  I had also never realized that in addition to fecal transplants (my favorite conversation topic) that some UTI infections are treated with asymptomatic E. coli as well.

The last talk of the morning was Jessica Mark Welch “Spatial Organization of Human Microbiomes at the Micron Scale”.   She started off with an awesome analogy that when we swab a surface for metagenomics, on a spatial scale that’s the equivalent of taking an entire hectare of coral reef, bulldozing it, extracting the nucleic acids and attempting to understand community organization.   Awesome analogy!   She then proceeded to show the most amazing microscope images… using 9 different taxa-specific FISH probes to human dental plaque samples.   You could see an amazing and complex level of spatial organization that would be invisible by any other method.

After dinner the keynote speaker was Jefferey F. Miller “Accelerated Protein Evolution by Diversity-Generating Retroelements”.  Nice to see some phage work… viruses tend to get the short stick these days in microbiome work.  Talked about Bordetella phage… really cool RT-mediated phage accelerated evolution, but in a directed manner.  Turn out this is just one example of “diversity generating retroelements (DGRs)”… found many in metagenomic data.  Gave a lot of interesting detailed mechanism, as well as showing that the host can modulate this activity.

Next was Yonatan Grad “The Emergence and Spread of Antibiotic Resistant N. gonorrhoeae in the US”.  Gave a pretty scary intro about the speed of antibiotic resistance in this organism and the failure of front-line antibiotics.  Fewer and fewer labs test for N. gonorrhoeae by culture, but this is the only way to test for antibiotic resistance.  Trying to get at mechanisms of resistance, sequenced 1102 isolates.   Happy to see this increasing trend of sequencing genomes… so much valuable information there.  There is a major need for rapid diagnostic tests for antibiotic resistance.  One really interesting idea was that if you knew which resistances carried a higher fitness cost, you could use those drugs with higher preference (other things being equal) because resistance might be lost.

Last talk of the day was Tatum Mortimer “An Ancient Emerging Infection as a Cause of Maternal Sepsis in Late Byzantine Troy”.  Really interesting talk where they took calcified nodules from an 800-year old skeleton and extracted the DNA.  There were able to identify the casual pathogens, and even sequence their genomes.  One is a virtually complete genome… that is so cool!

Update 9/18/18

See Wakelets.