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  • 1
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    Predicted bacterial interactions affect in vivo microbial colonization dynamics in Nematostella (2018)
    Frontiers
    In:  Frontiers in Microbiology, 9 . Art.Nr. 728.
    Details
    Publication Date: 2021-02-08
    Description: The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition and diet. In contrast, the importance of bacteria-bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria-bacteria interactions through co-occurrence networks. The analysis indicates that bacteria-bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within three days of recolonization all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Already one week after recolonization almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within one week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. Hanna Domin1, Yazmín H. Zurita-Gutiérrez2, Marco Scotti3, Jann Buttlar1, Ute Hentschel Humeida2 and Sebastian Fraune1*
    Type: Article , PeerReviewed
    Format: text
    Format: archive
    DOI: 10.3389/fmicb.2018.00728
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? (2018)
    Elsevier
    In:  Zoology, 127 . pp. 1-19.
    Details
    Publication Date: 2021-02-08
    Description: From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.zool.2018.02.004
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat (2018)
    Frontiers
    In:  Frontiers in Microbiology, 9 . Art.Nr. 443.
    Details
    Publication Date: 2021-02-08
    Description: Most eukaryotic species are colonized by a microbial community – the microbiota – that is acquired during early life stages and is critical to host development and health. Much research has focused on the microbiota biodiversity during the host life, however, empirical data on the basic ecological principles that govern microbiota assembly is lacking. Here we quantify the contribution of colonizer order, arrival time and colonization history to microbiota assembly on a host. We established the freshwater polyp Hydra vulgaris and its dominant colonizer Curvibacter as a model system that enables the visualization and quantification of colonizer population size at the single cell resolution, in vivo, in real time. We estimate the carrying capacity of a single Hydra polyp as 2 × 105 Curvibacter cells, which is robust among individuals and time. Colonization experiments reveal a clear priority effect of first colonizers that depends on arrival time and colonization history. First arriving colonizers achieve a numerical advantage over secondary colonizers within a short time lag of 24 h. Furthermore, colonizers primed for the Hydra habitat achieve a numerical advantage in the absence of a time lag. These results follow the theoretical expectations for any bacterial habitat with a finite carrying capacity. Thus, Hydra colonization and succession processes are largely determined by the habitat occupancy over time and Curvibacter colonization history. Our experiments provide empirical data on the basic steps of host-associated microbiota establishment – the colonization stage. The presented approach supplies a framework for studying habitat characteristics and colonization dynamics within the host–microbe setting.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    Format: other
    DOI: 10.3389/fmicb.2018.00443
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Emerging Sponge Models of Animal-Microbe Symbioses (2016)
    Frontiers
    In:  Frontiers in Microbiology, 7 . p. 2102.
    Details
    Publication Date: 2019-02-01
    Description: Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.3389/fmicb.2016.02102
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 5
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    Microorganism: Culture and single cell analysis (2019)
    In:  [Poster] In: 71. Annual Conference of the German Society for Hygiene and Microbiology (DGHM), 25.-27.02.2019, Göttingen, Germany .
    Details
    Publication Date: 2020-02-28
    Type: Conference or Workshop Item , NonPeerReviewed
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    OceanRep: Poster
  • 6
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    Bdellovibrio and Like Organisms Are Predictors of Microbiome Diversity in Distinct Host Groups (2020)
    Springer
    Details
    Publication Date: 2023-02-08
    Description: Biodiversity is generally believed to be a main determinant of ecosystem functioning. This principle also applies to the microbiome and could consequently contribute to host health. According to ecological theory, communities are shaped by top predators whose direct and indirect interactions with community members cause stability and diversity. Bdellovibrio and like organisms (BALOs) are a neglected group of predatory bacteria that feed on Gram-negative bacteria and can thereby influence microbiome composition. We asked whether BALOs can predict biodiversity levels in microbiomes from distinct host groups and environments. We demonstrate that genetic signatures of BALOs are commonly found within the 16S rRNA reads from diverse host taxa. In many cases, their presence, abundance, and especially richness are positively correlated with overall microbiome diversity. Our findings suggest that BALOs can act as drivers of microbial alpha-diversity and should therefore be considered candidates for the restoration of microbiomes and the prevention of dysbiosis.
    Type: Article , PeerReviewed
    Format: text
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 7
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    Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches (2019)
    Elsevier
    In:  Zoology, 133 . pp. 81-87.
    Details
    Publication Date: 2022-01-31
    Description: Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve metaorganism identities and to disclose the various roles that microorganisms play in the biology of their hosts.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.zool.2019.02.007
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 8
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    Molecular techniques and their limitations shape our view of the holobiont (2019)
    Elsevier
    In:  Zoology, 137 . Art.Nr. 125695.
    Details
    Publication Date: 2022-01-31
    Description: It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.zool.2019.125695
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 9
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    Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms (2019)
    Nature Research
    In:  Microbiome, 7 (1). Art.Nr. 133.
    Details
    Publication Date: 2022-01-31
    Description: Background The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms.” The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. Methods In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. Conclusion While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    Format: archive
    DOI: 10.1186/s40168-019-0743-1
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    Neutrality in the Metaorganism (2019)
    Public Library of Science (PLoS)
    Details
    Publication Date: 2023-03-09
    Description: Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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