Author: 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 paper from Eisen lab and others … on challenges with relic RNA in SARS-CoV-2 environmental surveys

New paper out from my lab and other labs.

Zuniga-Montanez R, Coil DA, Eisen JA, Pechacek R, Guerrero RG, Kim M, Shapiro K, Bischel HN. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA? PLoS One. 2022 Apr 22;17(4):e0267212. doi: 10.1371/journal.pone.0267212. PMID: 35452479; PMCID: PMC9032406.

This was a collaboration between my lab and labs of Heather Bischel and Karen Shapiro.

Funding was provided by Healthy Yolo Together/Healthy Davis Together.

New preprint out from my lab and others about environmental monitoring for SARS-CoV-2 in schools and in part about how difficult this is

New preprint out on from the Eisen Lab and others. This is from a collaboration between David Coil, Heather Bischel, Karen Shapiro,  Randi Pechacek, Roque G. Guerrero, Minji Kim, and Rogelio Zuniga-Montanez (first author) at University of California, Davis.  

It is about environmental monitoring for SARS-CoV-2 in schools and, well, in part about how difficult this is.

See https://www.medrxiv.org/content/10.1101/2021.11.12.21266178v1

The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Abstract: 

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units. Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07–38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing. On-site clinical testing was offered in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to reflect relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. The high-Ct positive results from environmental swabs further suggest the absence of active infections. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions

Article about Dr. Connie Rojas getting UC Davis Chancellor’s Postdoctoral Fellow Award

See Researcher Studying the Microbiome and Chemical Communication of Cats Named a Chancellor’s Postdoctoral Fellow for an article by Greg Watry about Dr. Connie Rojas who is a post-doc in my lab. Dr. Rojas got a UC Davis Chancellor’s Postdoctoral Fellow Award to come to UC Davis to work on cats and the role of their microbiome in chemical signaling and scent production.

For more about Dr. Rojas see

Twitter: @ConnieLaBiologa

Web Site: conniearojas.weebly.com

The tale of the blue soy products – from contaminated soy milk to a new publication

A new paper is out from my lab. This one is a remarkable story of work by PhD Student Marina E. De León (https://phylogenomics.me/people/marina-de-leon/).

It started with her pouring out some soy milk from her fridge that was blue.

See her Tweet about this here: https://twitter.com/MicrobialFuture/status/1220399781165461504?s=20https://twitter.com/MicrobialFuture/status/1220399781165461504?s=20

https://platform.twitter.com/widgets.js

And then she isolated bacteria from the soy milk and from some blue tofu in her fridge, identified them, did experiments to see if these isolated bacteria could cause soy milk to turn blue, found some that did, sequenced their genomes, and analyzed them to show that these ones had similar properties to other bacteria known to cause blue discoloration of food products. A truly remarkable piece of work.

See the paper here: “Draft Genome Sequences and Genomic Analysis for Pigment Production in Bacteria Isolated from Blue Discolored Soymilk and Tofu“

And thanks to Guillaume Jospin and Harriet Wilson who helped with the work and all the people in my lab and via social media that encouraged and supported Marina along the way.

And see also:

https://platform.twitter.com/widgets.js

Post-Doc Position available in Ecology of Emerging Infectious Disease

Post-Doc Position available in Ecology of Emerging Infectious Disease

The Epicenter for Disease Dynamics at the One Health Institute in the School of Veterinary Medicine at UC Davis is seeking a post-doctoral researcher interested in the impacts of environmental change on the epidemiology, ecology and evolution of zoonotic diseases. Activities will focus on a new National Science Foundation Ecology and Evolution of Infectious Diseases project “Impacts of Rapid Landscape Change and Biodiversity on Virus Host Specificity”.

Primary responsibilities relate to both theoretical and data-informed modeling of virus evolution and transmission across landscape changes in Southeast Asia. This is a 3-year post-doctoral position, expected to begin January 2022 based at UC Davis with opportunities for collaboration and co-mentorship across the PIs on this project including Christine Kreuder Johnson (UCD), Tierra Smiley Evans (UCD), Lark Coffey (UCD), Michael Boots (UC Berkeley), and Rebekah Kading (CSU).

Project Overview:

This study investigates the impacts of deforestation, landscape change, and biodiversity on virus characteristics that determine zoonotic potential, including virus “host plasticity”, which is the diversity of host species a virus can infect in nature. Findings from this research will contribute to ecological theory on the impact of environmental changes on microbial adaptation, with practical implications for management of ecosystems at high risk for pathogen spillover. Investigations will evaluate host range of bat-borne coronaviruses and mosquito- borne arboviruses (flaviviruses, alphaviruses and bunyaviruses) in the biodiverse tropical forests of Southeast Asia. Activities will include theoretical and computational modeling, underpinned by field investigations and in vitro experiments, to develop data and model driven insights into the role that mosquito vectors play in constraining or expanding virus host plasticity and genetic diversity. Characterization of bat-borne coronaviruses and host affinities in an ecosystem with SARS-CoV-related viruses will further inform on coronavirus evolution and emergence of zoonotic potential. This position will conduct research in a team science setting that is especially relevant to development of an evidence-base on the relationship between environmental change, biodiversity, disease outbreaks, and pandemics to underpin public policy.

65% SCIENTIFIC RESEARCH

  • Contribute to designing field studies to investigate virus host plasticity, evolution and transmission across forest gradients in Southeast Asia;
  • Develop methods and analyses to evaluate surveillance strategies to detect zoonotic pathogens at high-risk interfaces for disease emergence;
  • Analyze metadata on emerging zoonotic diseases, high-risk human-animal contact, and ecological risk and conduct data analyses needed to train models for emerging disease prediction;
  • Develop advanced analytical techniques and associated programming capabilities for infectious disease modeling, predictive frameworks, and social network analyses;
  • Conduct independent research and produce high quality scientific manuscripts related to biosurveillance and the ecology of emerging infectious disease.

35% PROJECT IMPLEMENTATION

  • Provide disease expertise, technical support, data analyses, and data-sharing tools for zoonotic disease prediction and biosurveillance projects;
  • Provide epidemiologic expertise to field staff in other countries on study design, data collection, data management, data analysis and interpretation, and publication preparation;
  • Contribute to regular summaries of surveillance data, assist in development of data collection and data management tools; and ensure open communication and coordination with international partners in project implementation;
  • Travel to international field sites to work with field staff, participate in field activities, and attend scientific meetings as needed.

Skills needed:

Background in infectious disease epidemiology or disease ecology and strong quantitative skills in biostatistics, epidemiology, and mathematical modeling with knowledge of animal health and wildlife disease. Experience with statistical software including R and STATA, as well as ability to write code for programming, including Python. Experience conducting independent, applied scientific research on infectious diseases with a promising publication track record.

Education:

PhD in biology, ecology, epidemiology, or related life-science (required)

Application:

Please email cover letter and CV by September 30th to:

Tierra Smiley Evans, DVM, PhD and Christine Kreuder Johnson, VMD, PhD EpiCenter for Disease Dynamics | One Health Institute
School of Veterinary Medicine
University of California
Davis, CA 95616
530-752-1238

tsmevans@ucdavis.edu, ckjohnson@ucdavis.edu

NSF EEID_Post_Doc_Position.pdf

The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies (talk video and slides)

Posted video of a recording I made of a talk for BIATA2021 meeting. Phylogenomic Case Studies: The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies

Slides here

New paper from the Eisen lab (with many others) on Global biogeography of chemosynthetic symbionts

Paper: Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups | PNAS

PR from MPG here: Symbionts without borders – Bacterial partners travel the world

Authors:

  • Co-First Authors: Jay T. Osvatic and Laetitia G. E. Wilkins
  • Co-Last Authors: Jillian M. Petersen and Benedict Yuen
  • Other authors: Lukas Leibrecht, Matthieu Leray, Sarah Zauner, Julia Polzin, Yolanda Camacho, Olivier Gros, Jan A. van Gils, Jonathan A. Eisen

Significance (from the paper)

Knowledge of host–symbiont biogeography is critical to understanding fundamental aspects of symbiosis such as host–symbiont specificity. Marine animals typically acquire their symbionts from the environment, a strategy that enables the host to associate with symbionts that are well-suited to local conditions. In contrast, we discovered that in the chemosymbiotic bivalve family Lucinidae several host species distributed across the globe are all associated with a single cosmopolitan bacterial symbiont. The genetic cohesiveness of this global symbiont species is maintained through homologous recombination across its extensive geographical range. The remarkable flexibility in the lucinid association is advantageous to both host and symbiont as it increases the likelihood of locating a compatible partner across diverse habitats spanning the globe.

Abstract (from the paper)
 

In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host–symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that “promiscuously” form associations with multiple divergent cooccurring host species. This flexibility of host–microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.

Acknowledgements (from the paper)

We thank Gustav Paulay (FLMNH, Gainesville, FL), Amanda Bemis, and John Taylor (NHM, London) for providing preserved samples. John Taylor also provided high-resolution images of lucinid clams for Fig. 2. We thank Liz Hambleton (University of Vienna), Miriam Weber, Christian Lott, Boris Unger, Dorothée Makarow, Natalie Elisabeth (University of California, Berkeley), Diana Chin, Tim Oortwijn, and Arthur Curry for providing fresh samples. We also thank Thalassa for 300 million y of sheltering lucinids. We are grateful to Stephanie Markert for providing access to the proteomics data, Ipek Yamin Meric and Nora Grossschmidt for helping with DNA extractions, Marina DeLeón for help with fieldwork and travels in Costa Rica, Cassandra Ettinger for early discussions of the study, and Guillaume Jospin for support with the bioinformatic analyses. We thank Xavier Didelot for discussions on the recombination analysis. L.G.E.W. was supported by Grant GMBF5603 from the Gordon and Betty Moore Foundation (J.A.E. was Principal Investigator on the same grant). The work was also supported by the European Research Council Starting Grant EvoLucin and a Vienna Research Grant for Young Investigators from the Vienna Science and Technology Fund (WWTF, VRG14–021) and the Austrian Academy of Sciences. Sequencing was carried out at the DNA Technologies and Expression Analysis Cores at the University of California, Davis Genome Center (supported by NIH Shared Instrumentation Grant 1S10OD010786-01), the Biomedical Sequencing Facility at CeMM (https://www.biomedical-sequencing.org/) in Vienna, Austria, and at the Joint Microbiome Facility (JMF) of the Medical University of Vienna and the University of Vienna (project ID 1911-1). Thanks to Petra Pjevac and Gudrun Kohl for sample processing at JMF. The gill embedding was performed by the Histopathology Facility at Vienna BioCenter Core Facilities, a member of the Vienna BioCenter, Austria.

Funding: Gordon and Betty Moore Foundation (for the part from my lab at least). Part of a collaboration with STRI.

News Stories about air filter testing for SARS-CoV-2 in Davis, CA schools

David Coil has been coordinating a project to do air filter testing for Sars-CoV-2 in Davis, CA schools in collaboration with Heather Bischel, Karen Shapiro, Roque G Guerrero, Randi Pechacek, and others. This has been supported by the Healthy Davis Together project.

Recently there have been a few news stories about this work and I thought I would post some links here.

KCRA: Here’s the new way COVID-19 testing is happening at 2 Davis schools

Woodland Daily Democrat: Davis Joint Unified School District prepares against COVID-19 with air filters

Also see UC Davis Live on this topic: https://www.ucdavis.edu/news/media-advisory-uc-davis-live-back-to-school-safely

And see the Healthy Davis Together page on this: https://healthydavistogether.org/airfiltertesting/

New collaborative paper out: Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics 

A new paper is out from the lab from a large collaboration between UC Davis and Colorado State University.

See: Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics | mSystems

This was supported by a grant from the UC Davis Innovation Institute for Food and Health.

 

New preprint from the lab (in a collaboration with many others at UC Davis): SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

My lab has been involved in a collaboration with many others at UC Davis on studying SARS-CoV2 in surface samples from the UC Davis hospital. A preprint of a paper on this topic has been posted to medRxiv with David Coil as the first author.  See: SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis | medRxiv