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  1. Article ; Online: Erratum: Universal drivers of cheese microbiomes.

    Reuben, Rine Christopher / Langer, Désirée / Eisenhauer, Nico / Jurburg, Stephanie D

    iScience

    2024  Volume 27, Issue 5, Page(s) 109726

    Abstract: This corrects the article DOI: 10.1016/j.isci.2022.105744.]. ...

    Abstract [This corrects the article DOI: 10.1016/j.isci.2022.105744.].
    Language English
    Publishing date 2024-04-13
    Publishing country United States
    Document type Published Erratum
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109726
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  2. Article ; Online: COVID-19 alters human microbiomes: a meta-analysis.

    Reuben, Rine Christopher / Beugnon, Rémy / Jurburg, Stephanie D

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1211348

    Abstract: Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an ...

    Abstract Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential.
    Methods: We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries.
    Results: Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including
    Discussion: Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Gastrointestinal Microbiome
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-08-02
    Publishing country Switzerland
    Document type Meta-Analysis ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1211348
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  3. Article ; Online: Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere.

    Jurburg, Stephanie D / Hom, Erik F Y / Chatzinotas, Antonis

    PLoS biology

    2023  Volume 21, Issue 5, Page(s) e3002109

    Abstract: The public perception of viruses has historically been negative. We are now at a stage where the development of tools to study viruses is at an all-time high, but society's perception of viruses is at an all-time low. The literature regarding viral ... ...

    Abstract The public perception of viruses has historically been negative. We are now at a stage where the development of tools to study viruses is at an all-time high, but society's perception of viruses is at an all-time low. The literature regarding viral interactions has been skewed towards negative (i.e., pathogenic) symbioses, whereas viral mutualisms remain relatively underexplored. Viral interactions with their hosts are complex and some non-pathogenic viruses could have potential benefits to society. However, viral research is seldom designed to identify viral mutualists, a gap that merits considering new experimental designs. Determining whether antagonisms, mutualisms, and commensalisms are equally common ecological strategies requires more balanced research efforts that characterize the full spectrum of viral interactions.
    MeSH term(s) Viruses ; Symbiosis
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; 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.3002109
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  4. Article: Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life.

    Jurburg, Stephanie D / Bossers, Alex

    Frontiers in microbiology

    2021  Volume 12, Page(s) 564408

    Abstract: Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host's early life, when management ...

    Abstract Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host's early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community's taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.
    Language English
    Publishing date 2021-03-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.564408
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  5. Article ; Online: Synthesis of recovery patterns in microbial communities across environments.

    Jurburg, Stephanie D / Blowes, Shane A / Shade, Ashley / Eisenhauer, Nico / Chase, Jonathan M

    Microbiome

    2024  Volume 12, Issue 1, Page(s) 79

    Abstract: Background: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome ... ...

    Abstract Background: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.
    Results: To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.
    Conclusions: This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.
    MeSH term(s) Microbiota ; Soil Microbiology ; Bayes Theorem ; Animals ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Mammals/microbiology ; Biodiversity ; Water Microbiology
    Language English
    Publishing date 2024-05-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Video-Audio Media
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-024-01802-3
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  6. Article ; Online: Age Matters

    Jurburg, Stephanie D. / Bossers, Alex

    Frontiers in Microbiology

    Community Assembly in the Pig Fecal Microbiome in the First Month of Life

    2021  Volume 12

    Abstract: Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management ...

    Abstract Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.
    Keywords 16S rRNA gene ; community assembly ; fecal microbiome ; pig ; primary succession
    Subject code 630
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Universal drivers of cheese microbiomes.

    Reuben, Rine Christopher / Langer, Désirée / Eisenhauer, Nico / Jurburg, Stephanie D

    iScience

    2022  Volume 26, Issue 1, Page(s) 105744

    Abstract: The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a ... ...

    Abstract The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.
    Language English
    Publishing date 2022-12-09
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.105744
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  8. Article ; Online: Soil microbial composition varies in response to coffee agroecosystem management.

    Jurburg, Stephanie D / Shek, Katherine L / McGuire, Krista

    FEMS microbiology ecology

    2020  Volume 96, Issue 9

    Abstract: Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, ... ...

    Abstract Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).
    MeSH term(s) Agriculture ; Coffee ; Fungi/genetics ; Mycobiome ; Soil ; Soil Microbiology
    Chemical Substances Coffee ; Soil
    Language English
    Publishing date 2020-08-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 283722-5
    ISSN 1574-6941 ; 0168-6496
    ISSN (online) 1574-6941
    ISSN 0168-6496
    DOI 10.1093/femsec/fiaa164
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  9. Article ; Online: All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences.

    Jurburg, Stephanie D / Keil, Petr / Singh, Brajesh K / Chase, Jonathan M

    Molecular ecology resources

    2021  Volume 21, Issue 6, Page(s) 1759–1771

    Abstract: The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach ... ...

    Abstract The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data.
    MeSH term(s) Archaea/classification ; Bacteria/classification ; Biodiversity ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology
    Language English
    Publishing date 2021-05-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13401
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  10. Article: All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences

    Jurburg, Stephanie D. / Keil, Petr / Singh, Brajesh K. / Chase, Jonathan M.

    Molecular ecology resources. 2021 Aug., v. 21, no. 6

    2021  

    Abstract: The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach ... ...

    Abstract The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data.
    Keywords biodiversity ; edaphic factors ; eukaryotic cells ; phylogeny ; soil ; taxonomy
    Language English
    Dates of publication 2021-08
    Size p. 1759-1771.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2406816-0
    ISSN 1471-8286 ; 1755-098X
    ISSN (online) 1471-8286
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13401
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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