Eisen Lab Blog

Congrats to newly minted “Dr” – Katie Dahlhausen

Congratulations to Katie Dahlhausen (actually, I should write this as “Dr. Katie Dahlhausen”) for finishing her PhD in the Biophysics Graduate Group here at UC Davis.  Her thesis was  entitled “Koala Poop Smells Good: How I Know This and Ways to Increase the Impact of Research Through Education & Outreach”.

Here are some pics / Tweets from her exit seminar and PhD bell ringing ceremony.












Exit Seminar: Katherine Dahlhausen 8/27/19

Exit Seminar: Katherine Dahlhausen

PI: Dr. Jonathan Eisen


Koala Poop Smells Good

How I know this and ways to increase the impact of research through education & outreach


Tuesday, 27th of August

11:00 am – 12:00 pm

Genome and Biomedical Sciences Facility Auditorium (Room 1005)

Open to all ages

New preprint from the Eisen Lab: Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids

A new preprint is out from the lab (also been submitted for publication).  Paper led by PhD Student Cassie Ettinger.  We would love comments and feedback.

Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids https://www.biorxiv.org/content/10.1101/735050v2 

Cassandra L. Ettinger and Jonathan A. Eisen.


Seagrasses are globally distributed marine flowering plants that are foundation species in coastal ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling and in protecting the coastline from erosion. Although many studies have focused on seagrass ecology, only a limited number have investigated their associated fungi. In terrestrial systems, fungi can have beneficial and detrimental effects on plant fitness. However, not much is known about marine fungi and even less is known about seagrass associated fungi. Here we used culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to characterize the taxonomic diversity of fungi associated with the seagrass, Zostera marina. We sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal diversity within and between plants. Our results indicate that there are many fungal taxa for which a taxonomic assignment cannot be made living on and inside Z. marina leaves, roots and rhizomes and that these plant tissues harbor distinct fungal communities. The most prevalent ITS amplicon sequence variant (ASV) associated with Z. marina leaves was classified as fungal, but could not initially be assigned to a fungal phylum. We then used PCR with a primer targeting unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA gene to amplify part of the 28S rRNA gene region and link it to this ASV. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is possible this chytrid is directly infecting Z. marina leaf tissues. This work highlights a need for further studies focusing on marine fungi and the potential importance of these understudied communities to the larger seagrass ecosystem.

Figures from the paper are below:



At @UCDavis 8/6 – Richard Jefferson Hormones and the Holobiont: Origins and some implications of hologenome theory.

Special Seminar at UC Davis:

Richard Jefferson

Queensland University of Technology

Hormones and the Holobiont:

Origins and some implications of hologenome theory.

August 6, 2019

GBSF 4202

11:30 am – 1:00 pm

Below are some materials provided by Dr. Jefferson in relation to his talk


Multicellularity requires coordination of spatially distal cells and temporally diverse actions. In vertebrates, much of this is mediated by hormones, frequently steroids, most of which are excreted through apocrine, exocrine and endocrine secretions as inactive conjugates of glucuronic acid or sulfate. Myriad, diverse microbiota populate the epithelia and through cleavage by diverse glucuronidases (GUS) and arylsulfatases (ARS), release the active form of the hormone which can then be resorbed or presented with altered kinetics, bioactivity and concentrations to diverse sites of action. The microbial populations thus modulate hormone action.

From 1980-1990, we developed and distributed GUS from E. coli as a reporter gene for plant, fungal and animal transgenesis and for microbial ecology studies. In our efforts to improve its efficacy, we explored glucuronide operon function in enteric microbes, and sought natural GUS variants in populations of soil, water, epithelial or fecal microbes that might have improved properties. We made field trips to Africa to isolate fecal and environmental microbes that were unlikely to be present due to human action and contamination. In parallel we revisited neglected literature on the function of the enzymes in vertebrate biology. In combination with stunning advances in microbial discovery and identification (e.g. David Ward’s & Steve Giovannoni’s discoveries of the ubiquity of uncultured microbes), and some neglected industrial R&D we were led to a major rethink on much of our framework around biology and evolution, science and society. This led to articulation of the hologenome theory of evolution at Cold Spring Harbor in 1994 and the extended proposal that hormone activity in metazoa and metaphyta was modulated by the dynamic population structures of associated microbes. The pleiotropic and powerful effect that hormone modulation could have to reorient and impact virtually all fitness-related traits, and indeed all reproductive activity of plants and animals, stimulated new insights into living systems. In this presentation, I’ll review the coincidences and congruences that led to the theory and some of the possible implications for science and society, in the form of some conjectures.

Did the advent of agriculture and the concomitant rise in sedentary and concentrated populations cause massive inbreeding depression of the microbiome and become the origin of disease – plant, animal and human – as dysbiosis? Is the germ theory of disease opportunistically right but structurally wrong? Did commensalism and community tactility/touching – the hallmarks of social behavior – cause harmonization and reinforce convergent microbial populations and thus congruent hormone action and hence behavior? Has all of evolutionary thought been compromised by scale bias? Is it reasonable that the logic of evolution is embedded in macro-organisms (e.g. anything we can see) rather than the vast majority of all living systems that we can’t? Is the holobiont – in the case of all systems that have experienced the post agricultural microbial collapse – really a merobiont, with at best metastable populations that do not reflect an empirical steady state? Is Darwin’s natural selection an ‘edge-case’ in evolution, working well at medium physical and temporal scales, but not truly reflecting the primacy of information-state persistence that could describe microbial life? Could the hologenome theory and the microbiome provide the missing mechanism to the late 19th century’s other great evolutionist – now largely forgotten – Pyotr Kropotkin, who proposed ‘Mutual Aid: a factor in evolution” in 1902? Could the real driver of evolution not be replication and reproduction, but persistence and pooing? Can the role of macro-apobionts be largely as dynamic scaffolds to recruit, select, nurture, amplify and disseminate microbial populations?


Richard Jefferson is a Professor of Biological Innovation at the Queensland University of Technology (QUT) and founder and CEO of Cambia & The Lens. Richard received a PhD in Molecular, Cellular and Development Biology from University of Colorado at Boulder in 1985, where he developed the glucuronidase (GUS) system as a molecular heuristic tool for transgenesis, developmental and ecosystem studies.

During his NIH postdoc at the Plant Breeding Institute in Cambridge, UK, Richard adapted GUS for agricultural biotechnology and pioneered an open source paradigm by distributing the toolkits to hundreds of labs around the world before publication. This enabled the genetic engineering of virtually all commercial crops, and is now the most cited molecular technology in agriculture. In 1987, with colleagues at PBI, Richard led the world’s first field release of a biotech food crop. In 1989 Richard was appointed the first Molecular Biologist for the United Nations FAO/IAEA in Vienna, and in 1991 founded Cambia, an autonomous global social enterprise to democratize science- enabled problem solving. Besides Cambia’s role in inventing and distributing open source enabling technologies it runs Lens.org, now the longest operating, largest and most comprehensive free, open and secure platform for scholarly and patent discovery, analytics and metrics.

Based on work done on diverse microbial GUS and arylsulfatases since 1980, and their essential role in modulating hormone action in the holobiont, Richard proposed the landmark hologenome theory of evolution in 1994 at Cold Spring Harbor. He was the first to describe the role of the microbiome as the driver of biological evolution, and its role in understanding and optimizing performance of biological systems. In 1997, Richard proposed the concept of ecotherapeutics as a strategy for modulating agriculture and health systems performance by adjusting population structures of microbial constituents. The hologenome theory has profound implications for how we think about ourselves, living systems, the origin of disease, the origins of social behavior and even social institutions in innovation.

Richard is an ‘Outstanding Social Entrepreneur’ of the Schwab Foundation and a regular panelist at the World Economic Forum’s (WEF) Davos annual meetings and Summits. Richard served on the WEF Global Agenda Council on Intellectual Property and the Global Agenda Council on the Economics of Innovation. He was named to Scientific American’s list of the world’s 50 Most Influential Technologists. His work has featured in countless media, including The Economist, New York Times, Newsweek, Red Herring, Nature, Science, Nature Biotechnology.

UPDATE – posting my notes for his talk.  They are hand drawn notes on paper.  I will try to write up something later but really really busy right now so it will have to wait

At #UCDavis today: Dr. Denada Dibra on “Mutant p53 in triple negative breast cancers”

Sent on behalf of Dr. Satya Dandekar, Chair, Department of Medical Microbiology and Immunology

Dear UC Davis Health Community,

We are pleased to announce that Denada Dibra, Ph.D., from The University of Texas MD Anderson Cancer Center, will be visiting campus this Wednesday and Thursday, July 24-25, as one of the candidates for the Cancer Immunology faculty position the Medical Microbiology & Immunology department.

Wednesday, July 24th at 10:30 am in the Valley Hall Room 1043.

Dibra Announcement.pdf

Claudia Solis-Lemus at @ucdavis 5/23 “Statistical methods on phylogenetic networks”




Dr. Claudia Solis-Lemus

Postdoctoral Fellow

Emory University

“Statistical methods on phylogenetic networks”

Thursday, May 23, 2019

1:30pm 1022 Life Sciences Building

Faculty contact: Chair Jay Stachowicz, Department of Evolution and Ecology

Today at @ucdavis: Dennis Montoya ““Computational reconstruction of the tissue cellular microenvironment””

Recruitment Seminar

Dennis Montoya

UC Los Angeles

Department of Molecular, Cell & Developmental Biology

Computational reconstruction of the tissue cellular microenvironment"

Thursday, May 16, 2019

1:30 pm

1022 Life Sciences

Dennis Montoya flyer, May 16 2019.pdf

At @ucdavis May 16 – Dennis Montoya on “Computational reconstruction of the tissue cellular microenvironment”

Recruitment Seminar

Dennis Montoya

UC Los Angeles

Department of Molecular, Cell & Developmental Biology

Computational reconstruction of the tissue cellular microenvironment"

Thursday, May 16, 2019

1:30 pm

1022 Life Sciences

At @ucdavis today: Mike Gil “How collective behavior can shape ecosystems”

Job talk today of potential interest (focus is on coral reef fish behavior)

Dr. Mike Gil
Postdoctoral Scholar
Institute of Marine Sciences
University of California, Santa Cruz

“How collective behavior can shape ecosystems”

1:30 pm

Monday May 13
1022 Life Sciences.

Gil Seminar flyer.pdf

My observations for the City Nature Challenge 2019 – Sacramento #iNaturalist

So – last week I participated in the City Nature Challenge 2019 Sacramento Area effort.  See https://www.inaturalist.org/projects/city-nature-challenge-2019-sacramento-region for more details on the challenge.

My colleague Laci Gerhart-Barley was one of the co-organizers for our region and I saw some posts from her in the run up to the event and, as I have gotten more and more into iNaturalist I decided to participate.  Fortunately in a way, I got a nasty bug with fever and chills and such and this meant (1) I did not want to go to work and (2) I wanted to avoid people.  This gave me some extra time to go around.  The vent ran from Friday to Monday April 26-29.  And I tooled around UC Davis campus a few times and Sac State Campus once (on Saturday where my daughter had a concert) and around Yolo County and also my yard a bit.  And I took a lot of pictures and posted as many as seemed interesting to iNaturalist.  And the most amazing thing was the community of people that Laci and others had gathered together did an incredible job of helping ID many many many of my posts.

So here are some more details

Day 1. Link to observations.  Screen capture below.

Day 2. Link to observations

Day 3. Link to observations

Day 4. Link to observations.

Some of my favorite observations from these days are below;


And many many more.

Thanks to all the people who helped ID many of my pics and thanks to Laci and the other coorganizers for running the show.  It was a great experience.

Oh and below I have tried to copy the images and links to many of the actual entries using their calendar display option.  It only shows 200 per day so Day 1 I could not get all of them in this format..  I am not sure how well this will work.

Day 1 .


Day 1 extras:

Loggerhead ShrikeLanius ludovicianus


Northern MockingbirdMimus polyglottos


Cattle EgretBubulcus ibis


Cattle EgretBubulcus ibis


Rock PigeonColumba livia


Black-tailed JackrabbitLepus californicus


Western Honey BeeApis mellifera


Western Honey BeeApis mellifera


Western Honey BeeApis mellifera


BeesEpifamily Anthophila


West Coast LadyVanessa annabella


Greater Lady BeetlesGenus Harmonia


Rose AphidMacrosiphum rosae



Asian Lady BeetleHarmonia axyridis


Phaneropterine KatydidsSubfamily Phaneropterinae


Phaneropterine KatydidsSubfamily Phaneropterinae


FliesOrder Diptera


FliesOrder Diptera


Burrowing OwlAthene cunicularia
Great Horned OwlBubo virginianus


Wild TurkeyMeleagris gallopavo

Day 2