All posts by Jonathan Eisen

About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

New lab paper: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

New paper out from the lab. This is from a collaboration with Stan Marks in the Vet School at UC Davis. The work was led by Katti Horng with assistance from Holly Ganz.

Citation: Horng KR, Ganz HH, Eisen JA, Marks SL. (2018) Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6:e4827

Abstract: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

Source: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

Tomorrow at @ucdavis: Raquel Peixoto on “Marine probiotics: increasing coral resilience to bleaching through m icrobiome manipulation”

week’s Ecology and Evolution Seminarwill be given by Raquel Peixoto on May 17th at 4:10pm in 176 Everson Hall. Come hear the exciting work she’s been doing manipulating microbiomes to increase coral health! Her talk is titled “MARINE PROBIOTICS: INCREASING CORAL RESILIENCE TO BLEACHING THROUGH MICROBIOME MANIPULATION”

Raquel is an Associate Professor in Molecular Microbial Ecology at the Federal University of Rio de Janeiro and has spent most of the last year on sabbatical at UC Davis working with Jonathan Eisen

5/18 at @ucdavis: Kristen Beck on “Large scale analysis of food ingredient metatranscriptomes reveals insights about hazards and food quality”


Large scale analysis of food ingredient metatranscriptomes reveals insights about hazards and food quality

Kristen Beck, Ph.D.

Research Staff Member, Industrial and Applied Genomics

IBM Almaden Research Center, San Jose

Friday, May 18, 2018
11:00am * 1022 Life Sciences

Abstract: As the challenges of protecting global food supply chains become more complex, the technical approaches being used to understand and guard against threats are becoming more sophisticated. Food safety testing is beginning to adopt new technologies such as next generation sequencing of DNA or RNA in their monitoring procedures and the cost of next generation sequencing is only decreasing with time. Together, this makes providing food safety solutions a very data-intensive problem. By surveilling the microbiome of food ingredients, we can develop methods and best practices that can be used to improve food testing standards and security of the food supply chain. As part of the Consortium for Sequencing the Food Supply Chain, we’ve utilized hundreds of terabytes of raw sequencing and derivative data to show that microbes will respond to perturbations in their environment and can be useful as an indicator of food safety hazards. By monitoring food microbiomes, we can better understand food safety hazards and quality issues that may arise in the supply chain.

Bio: Dr. Beck is a research staff member in the Industrial and Applied Genomics group in the Accelerated Discovery Lab of IBM Research. She has been involved in food-related research for over a decade. She has published contributions in mechanistic studies of omega-3 fatty acids in tumorigenesis as well as composition of primate breast milks among other topics. Since joining IBM Research in 2015, she has been an essential member of the Consortium for Sequencing the Food Supply Chain and now serves as the IBM Technical Lead. Her current research focuses on analyzing next generation sequencing data to gain insights about microbial ecology in food ingredients as well as confidently determining of the presence of various hazards such as pathogenic organisms, antimicrobial resistance genes, and food fraud. She received a Ph.D. in Biochemistry, Molecular, Cellular, and Developmental Biology with a Designated Emphasis in Biotechnology from the University of California, Davis and is a proud almuna and trainee of the Biotechnology Program.


Karley Lujan receives “Outstanding Senior Award” at UC Davis

Kudos to Karley Lujan, a UC Davis undergraduate who has been working in the lab for a few years. Last night she received one of the “Outstanding Senior Awards” at a ceremony at the UC Davis Convention Center.

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Today @ucdavis: Dr. Emilia Huerta Sanchez “Archaic introgression, D-statistics and the contributions of female programmers”

This week’s Evolution and Ecology seminar speaker is Dr. Emilia Huerta-Sanchez, an Assistant Professor at UC Merced. Dr. Huerta-Sanchez investigates the genomics of adaptation and introgression in modern and ancient human populations. Please join us for her seminar at 4:10pm May 10th in 176 Everson Hall.

Title: Archaic introgression, D-statistics and the contributions of female programmers

Microbial Interactions in Marine Systems – Invitation to MIMAS2 Symposium

Just got this by email:

We are pleased to inform you that the International Symposium

“MIMAS2 – Microbial Interactions in Marine Systems”

will be held

in Greifswald, Germany,

from August 20th to 22nd, 2018.

The conference will focus on:

  • Microbial-mediated ecosystem functions and adaptation strategies of marine bacteria
  • The physiology of uncultivable marine symbionts
  • Ecophysiological interdependencies of bacteria within marine microbial assemblages
  • Molecular mechanisms of bacterial degradation of marine polysaccharides

For further information on the conference, abstract submission and registration please visit:

Abstracts for the symposium may be submitted until June 30th, 2018. The deadline for early bird registration is June 1st, 2018.

We would be glad to welcome you in Greifswald and hope to spark your interest with the scientific focus of our meeting. Additionally,
we recommend combining your conference participation in Greifswald with a visit to the beautiful islands Rügen ( and
Usedom ( with their unique and marvellous beaches. 

We are looking forward to meeting you in Greifswald in August 2018.

Rudi Amman, Uwe Bornscheuer, Jan-Hendrik Hehemann, Katharina Riedel, Thomas Schweder (on behalf of the organizing committee)

Today @ucdavis: Prof. Janelle Burke from Howard University “An evolutionary exploration of plant sexual systems”

Janelle Burke from Howard University will be giving the Ecology and Evolution seminar today, 3 May. Her talk is titled,

An evolutionary exploration of plant sexual systems

176 Everson

Thursday 3 May, 4:10pm

Janelle writes,

The Burke Lab specializes in plant systematics and plant evolutionary biology, using two groups, the Polygonaceae (knotweeds) and Melastomataceae (princess flowers), as systems. We utilize phylogenetic methodology as a tool to investigate facets of plant evolution, such as breeding systems, pollination syndromes and morphology. In turn, these data are used to revise taxonomy, the plant classification scheme. Current projects also investigate drivers of speciation, plant/ insect interactions and plant distribution changes in line with climate change projections.