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 CoilHeather 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

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

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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:

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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.


Abstract

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:

 

 

New publication from Cassie Ettinger (aka @casettron) and others: Fungi in the Marine Environment: Open Questions and Unsolved Problems 

New paper from Cassie Ettinger in the Eisen Lab:

Full citation:
Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. 2019. Fungi in the marine environment: open questions and unsolved problems. mBio 10:e01189-18. https://doi.org/10.1128/mBio.01189-18.

Abstract:

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Definitely worth a look if you are interested in fungi and/or marine microbes.

 

New paper from the Eisen lab on MAGs from two thermal pools in Kamchatka (great work led by Laetitia Wilkins @M_helvetiae and Cassie Ettinger @casettron) 

A new paper just out from the lab:

Laetitia G. E. Wilkins & Cassandra L. Ettinger (co-1st authors), Guillaume Jospin & Jonathan A. Eisen. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Scientific Reports. volume 9, Article number: 3059

This was truly a remarkable piece of work led by Laetitia G. E. Wilkins & Cassandra L. Ettinger who are co-first authors on the paper.  Also contributing to the work was Guillaume Jospin, the lab bioinformatics guru. I will write a much longer “story behind the paper” about this in the next week or two but wanted to give a brief summary here.

This paper had its beginnings just after September 11, 2001.  Yes. that September 11.  We had a meeting planned in September in Yellowstone National Park that had to be delayed due to 9/11.  The meeting then happened in October.  The meeting was between a group of US researchers and a group of Russian researchers to plan an NSF proposal on comparing the microbes living in hot springs in Yellowstone with those living in hot springs in Kamchatka.  The meeting went well and eventually we got a grant from NSF’s Biocomplexity program for this work.

At the time I was at TIGR (The Institute for Genomic Research) and I had a minor role in the grant – I was supposed to do coordinate some metagenomic sequencing of samples from Kamchatka.  We got some samples from Juergen Wiegel from U. Georgia and did a small amount of Sanger sequencing of them but this was right around the time I moved to UC Davis and right around the time that TIGR kind of dissolved.  We did not end up writing a paper on that small amount of Sanger sequencing.  Years later, Russell Neches in my lab got interested in this project and went to Kamchatka with Frank Robb and others on a collecting trip. See some details about this trip and plans back then in this blog post.  Russell then coordinated some Illumina sequencing of the same DNA samples we had done Sanger sequencing for at TIGR.  And Russell did some preliminary analysis of the samples but did not end up writing up a paper on it.

Fast forward again to a few years ago and we decided in my lab to try and rescue orphan data and try to at least get the data into the public domain and, if it was of interest to someone, write a paper on the data.  We thus created some “Reboot” channels within the lab Slack site and Laetitia Wilkins and Cassie Ettinger decided to try and do something with the Kamchatka data.  And they did.  This is what led to this paper.

A few other notes I would like to make here.  This paper certainly is a testament to the remarkable work of Cassie Ettinger and Laetitia Wilkins as well as Guillaume Jospin who helped them with some of the informatics.  I am really proud to have them all in my lab.  In addition, this paper is a culmination of contributions of all sorts of people.  We tried to acknowledge many of them in the Acknowledgement section of the paper and I am posting that below for the record here.

We would like to thank Russell Neches (ORCID: 0000-0002-2055-8381) for the use of photographs taken on a trip to Kamchatka, Russia in 2012. We also would like to thank Elizabeth A. Burgess and Juergen Wiegel for providing JAE with the DNA used here. We are also grateful to Christopher Brown (ORCID: 0000-0002-7758-6447) and Laura Hug (ORCID: 0000-0001-5974-9428) for their help getting access to the genomes used in Figure 2. A special thank you goes to Alexandros Stamatakis (ORCID: 0000-0003-0353-0691), Wayne Pfeiffer and Mark Miller for offering their help with getting the CIPRES Science Gateway server to run RAxML-HPC2 v.8 on XSEDE. We also thank two anonymous reviewers for comments on earlier versions of this manuscript. A. Murat Eren (ORCID: 0000-0001-9013-4827) provided constructive feedback on the publicly available preprint version of this article. LGEW was supported by a fellowship of the Swiss National Science Foundation P2LAP3_164915. Funding for the sequencing at TIGR was provided by a a subcontract to JAE for a grant from the National Science Foundation (MCB-MO 0238407). Funding for some of the work on this project was also provided by grant from the Gordon and Betty Moore Foundation (GBMF5603) to JAE.

New preprint from the lab on “Network analysis to evaluate the impact of research funding on research community consolidation”

We (me and David Coil) have a new preprint out on analysis we did in collaboration with Daniel Hicks and Carl Stahmer also from UC Davis. The paper is an analysis of the Microbiology of the Built Environment program funded by the Alfred P. Sloan Foundation via analysis of publications from within and outside the program. We would love feedback …

Citation:

Network analysis to evaluate the impact of research funding on research community consolidation. Daniel J Hicks, David A Coil, Carl G Stahmer, Jonathan A. Eisen.

Abstract:

In 2004, the Alfred P. Sloan Foundation launched a new program focused on incubating a new field, “Microbiology of the Built Environment” (MoBE). By the end of 2017, the program had supported the publication of hundreds of scholarly works, but it was unclear to what extent it had stimulated the development of a new research community. We identified 307 works funded by the MoBE program, as well as a comparison set of 698 authors who published in the same journals during the same period of time but were not part of the Sloan Foundation-funded collaboration. Our analysis of collaboration networks for both groups of authors suggests that the Sloan Foundation’s program resulted in a more consolidated community of researchers, specifically in terms of number of components, diameter, density, and transitivity of the coauthor networks. In addition to highlighting the success of this particular program, our method could be applied to other fields to examine the impact of funding programs and other large-scale initiatives on the formation of research communities.

New preprint from the lab: Bacterial communities associated with cell phones and shoes 

We have a new preprint out in BioRXiv.  Would love comments and feedback

Bacterial communities associated with cell phones and shoes [PeerJ Preprints]

Full citation:

Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. 2019. Bacterial communities associated with cell phones and shoes. PeerJ Preprints 7:e27514v1 https://doi.org/10.7287/peerj.preprints.27514v1

 

New preprint from lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka

A new preprint has been posted from the lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia | bioRxiv

Paper was led by Laetitia Wilkins and Cassie Ettinger (Guillaume Jospin and I are co authors).  

Abstract:

Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. Using a shotgun metagenomics approach, we assembled population-level genomes of bacteria and archaea from two pools using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and placed them in the context of the current microbial tree of life. We highlight MAGs representing previously underrepresented archaeal phyla (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study can be considered complementary to foregoing studies in the same ecosystem as it adds more comprehensive information about phylogenetic diversity and functional potential within this highly selective habitat.

I will try to write more about it later – I am so impressed by what Laetitia and Cassie did here.  This is what we call a “reboot” project in the lab – this was data that was generated and then not turned into a paper and was just sitting there.  A while ago we started a “reboot” program to start to try to turn such data sets into papers and they adopted this data set.  The data is Solexa shotgun metagenomic data from samples from hot springs in Kamchatka (yes, Solexa, read the paper for details).  The DNA used was leftover from an old project which included a collaboration with Juergen Wiegel’s lab (and some others) that had started, at least in terms of discussions, in 2001.  Anyway – I will try to write out more on the story behind this work soon.  But please, check out the paper, and feel free to provide feedback.

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:e4827https://doi.org/10.7717/peerj.4827

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