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  1. Article: Draft Genome Analysis of

    Coil, David A / Jospin, Guillaume / Eisen, Jonathan A

    Journal of genomics

    2020  Volume 8, Page(s) 25–29

    Abstract: Christensenella ... ...

    Abstract Christensenella minuta
    Language English
    Publishing date 2020-02-21
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2692697-0
    ISSN 1839-9940
    ISSN 1839-9940
    DOI 10.7150/jgen.43162
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics.

    Rojas, Connie A / Marks, Stanley L / Borras, Eva / Lesea, Hira / McCartney, Mitchell M / Coil, David A / Davis, Cristina E / Eisen, Jonathan A

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 19382

    Abstract: Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic ... ...

    Abstract Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.
    MeSH term(s) Cats ; Animals ; Anal Canal ; Metabolomics ; Microbiota/genetics ; Metagenome ; Metabolome ; Mammals
    Language English
    Publishing date 2023-11-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-45997-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado.

    Coil, David A / Eisen, Jonathan A

    Genome announcements

    2015  Volume 3, Issue 6

    Abstract: Here, we present the draft genome of Porphyrobacter mercurialis strain Coronado, the proposed type strain for this species. The assembly contains 3,482,341 bp in 10 contigs. ...

    Abstract Here, we present the draft genome of Porphyrobacter mercurialis strain Coronado, the proposed type strain for this species. The assembly contains 3,482,341 bp in 10 contigs.
    Language English
    Publishing date 2015-11-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2704277-7
    ISSN 2169-8287
    ISSN 2169-8287
    DOI 10.1128/genomeA.00856-15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

    Zuniga-Montanez, Rogelio / Coil, David A / Eisen, Jonathan A / Pechacek, Randi / Guerrero, Roque G / Kim, Minji / Shapiro, Karen / Bischel, Heather N

    PloS one

    2022  Volume 17, Issue 4, Page(s) e0267212

    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 ... ...

    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 (n = 2,341 swabs). 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 through Healthy Davis Together (HDT). HDT also offered on-site clinical testing 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 contain relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. High-Ct positive results from environmental swabs detected in the absence of known active infections supports this conclusion. 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.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/prevention & control ; Dust ; Environmental Monitoring ; Humans ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Schools
    Chemical Substances Dust ; RNA, Viral
    Language English
    Publishing date 2022-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0267212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: SARS-CoV-2 RNA Is Readily Detectable at Least 8 Months after Shedding in an Isolation Facility.

    Coil, David A / Pechacek, Randi / Kaze, Mo / Zuniga-Montanez, Rogelio / Guerrero, Roque G / Eisen, Jonathan A / Shapiro, Karen / Bischel, Heather N

    mSphere

    2022  Volume 7, Issue 6, Page(s) e0017722

    Abstract: Environmental monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for research and public health purposes has grown exponentially throughout the coronavirus disease 2019 (COVID-19) pandemic. Monitoring wastewater for SARS-CoV-2 ... ...

    Abstract Environmental monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for research and public health purposes has grown exponentially throughout the coronavirus disease 2019 (COVID-19) pandemic. Monitoring wastewater for SARS-CoV-2 provides early warning signals of virus spread and information on trends in infections at a community scale. Indoor environmental monitoring (e.g., swabbing of surfaces and air filters) to identify potential outbreaks is less common, and the evidence for its utility is mixed. A significant challenge with surface and air filter monitoring in this context is the concern of "relic RNA," noninfectious RNA found in the environment that is not from recently deposited virus. Here, we report detection of SARS-CoV-2 RNA on surfaces in an isolation unit (a university dorm room) for up to 8 months after a COVID-19-positive individual vacated the space. Comparison of sequencing results from the same location over two time points indicated the presence of the entire viral genome, and sequence similarity confirmed a single source of the virus. Our findings highlight the need to develop approaches that account for relic RNA in environmental monitoring.
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2/genetics ; RNA, Viral/genetics ; Wastewater ; Pandemics
    Chemical Substances RNA, Viral ; Wastewater
    Language English
    Publishing date 2022-10-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/msphere.00177-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Network analysis to evaluate the impact of research funding on research community consolidation.

    Hicks, Daniel J / Coil, David A / Stahmer, Carl G / Eisen, Jonathan A

    PloS one

    2019  Volume 14, Issue 6, Page(s) e0218273

    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 ... ...

    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.
    MeSH term(s) Foundations ; Humans ; Peer Review, Research ; Research ; Research Personnel
    Language English
    Publishing date 2019-06-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0218273
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Draft Genome Sequence of

    Kincheloe, Gregory N / Eisen, Jonathan A / Coil, David A

    Genome announcements

    2017  Volume 5, Issue 6

    Abstract: Here we present the draft genome ... ...

    Abstract Here we present the draft genome of
    Language English
    Publishing date 2017-02-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2704277-7
    ISSN 2169-8287
    ISSN 2169-8287
    DOI 10.1128/genomeA.01599-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Draft Genome Sequences of

    Lujan, Karley M / Eisen, Jonathan A / Coil, David A

    Genome announcements

    2017  Volume 5, Issue 13

    Abstract: Here, we present the draft genome sequences for five bacterial strains. These strains were all isolated from seagrass ( ...

    Abstract Here, we present the draft genome sequences for five bacterial strains. These strains were all isolated from seagrass (
    Language English
    Publishing date 2017-03-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2704277-7
    ISSN 2169-8287
    ISSN 2169-8287
    DOI 10.1128/genomeA.00023-17
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Gut Check: The evolution of an educational board game.

    Coil, David A / Ettinger, Cassandra L / Eisen, Jonathan A

    PLoS biology

    2017  Volume 15, Issue 4, Page(s) e2001984

    Abstract: The "gamification" of science has gained a lot of traction in recent years, and games that convey scientific concepts or themes are increasingly popular. While a number of existing games touch on microbiology, very few consider the beneficial (as opposed ...

    Abstract The "gamification" of science has gained a lot of traction in recent years, and games that convey scientific concepts or themes are increasingly popular. While a number of existing games touch on microbiology, very few consider the beneficial (as opposed to the detrimental) aspects of microbes. We designed a board game called "Gut Check: The Microbiome Game" to fill this gap. The game is meant to be both educational as well as challenging and fun. Here we discuss the development of the game, some of the logistics of game development in this context, and offer suggestions for others thinking of similar projects.
    MeSH term(s) Educational Technology/trends ; Game Theory ; Games, Recreational ; Gastroenterology/education ; Gastroenterology/manpower ; Gastroenterology/trends ; Gastrointestinal Microbiome ; Humans ; Microbiology/education ; Microbiology/manpower ; Microbiology/trends ; Microbiota ; Teaching
    Language English
    Publishing date 2017-04-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.2001984
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Isolation and sequence-based characterization of a koala symbiont:

    Dahlhausen, Katherine E / Jospin, Guillaume / Coil, David A / Eisen, Jonathan A / Wilkins, Laetitia G E

    PeerJ

    2020  Volume 8, Page(s) e10177

    Abstract: Koalas ( ...

    Abstract Koalas (
    Language English
    Publishing date 2020-10-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.10177
    Database MEDical Literature Analysis and Retrieval System OnLINE

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