325 research outputs found

    Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters

    Get PDF
    Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.We thank for the many inspiring discussions with Ulla Li Zweifel and Åke Hagström on taking advantage of microbial genetic blueprints for informing on the health status of natural waters. We gratefully acknowledge Martin Brusin for contributing drawings of Figure 1. Research on this subject was supported by the marine strategic research program EcoChange to J. P and the BONUS BLUEPRINT project, which has received funding from BONUS, the Joint Baltic Sea Research and Development Program (Art 185), and Swedish, German and Danish research councils to JP, AA, ML and LR.Peer reviewe

    “There’s no disenfranchisement when you’re sitting in that room”: Evaluating a South Australian loss and grief support group for foster and kinship carers

    No full text
    For foster or kinship carers who provide long-term care to children who are unable to live with their birth parents, a strong bond is often formed. Yet despite the best intentions of all parties, in some cases placements may be terminated, often leaving foster or kinship carers dealing with considerable loss and grief. This paper reports on the evaluation of a South Australian support group tailored to the needs of foster and kinship carers experiencing loss and grief following an unplanned placement termination. The paper provides an overview of the group, and reports on a thematic analysis of eight interviews with group attendees. The findings in regard to factors leading to placement termination and the impact of placement termination on foster families echo pre- vious research on the topic. The findings with regard to the benefits of group attendance emphasise the utility of its restorative practices approach, highlighting that the group created a space in which participants could acknowledge what had been achieved for the child, take perspective about their role as a foster parent, recognise the attachment they shared with the child, and the use of group activities gave presence to the grief and helped participants to honour their relationship to the child. The paper concludes with recommendations for future research and highlights the benefits of a restorative practice approach to addressing disenfranchised grief and ambiguous loss among foster and kinship carers who have experienced an unplanned placement termination.Damien W.Riggs, Tandanya Allain, Liz Browne, Fiona Endacott, Amanda Quinc

    Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters

    No full text
    Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change

    A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice

    No full text
    The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms

    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes

    Get PDF
    The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data

    Functional heterogeneity in senescence

    Get PDF
    Senescence is a tumour suppressor mechanism which is cell-intrinsically activated in the context of cellular stress. Senescence can further be propagated to neighbouring cells, a process called secondary senescence induction. Secondary senescence was initially shown as a paracrine response to the secretion of cytokines from primary senescent cells. More recently, juxtacrine Notch signalling has been implicated in mediating secondary senescence induction. Primary and secondary senescent induction results in distinct transcriptional outcomes. In addition, cell type and the stimulus in which senescence is induced can lead to variations in the phenotype of the senescence response. It is unclear whether heterogeneous senescent end-points are associated with distinct cellular function in situ, presenting functional heterogeneity. Thus, understanding senescence heterogeneity could prove to be important when devising ways of targeting senescent cells by senolytics, senostatics or senogenics. In this review, we discuss a role for functional heterogeneity in senescence in tissue- and cell-type specific manners, highlighting potential differences in senescence outcomes of primary and secondary senescence

    Diversity within species: interpreting strains in microbiomes

    No full text
    Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data

    A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice.

    Get PDF
    The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms

    Theoretical and practical analyses in metagenomic sequence classification

    No full text
    Metagenomics is the study of genomic sequences in a heterogeneous microbial sample taken, e.g. from soil, water, human microbiome and skin. One of the primary objectives of metagenomic studies is to assign a taxonomic identity to each read sequenced from a sample and then to estimate the abundance of the known clades. With ever-increasing metagenomic datasets obtained from high-throughput sequencing technologies readily available nowadays, several fast and accurate methods have been developed that can work with reasonable computing requirements. Here we provide an overview of the state-of-the-art methods for the classification of metagenomic sequences, especially highlighting theoretical factors that seem to correlate well with practical factors, and could therefore be useful in the choice or development of a new method in experimental contexts. In particular, we emphasize that the information derived from the known genomes and eventually used in the learning and classification processes may create several experimental issues—mostly based on the amount of information used in the processes and its uniqueness, significance, and redundancy,—and some of these issues are intrinsic both in current alignment-based approaches and in compositional ones. This entails the need to develop efficient alignment-free methods that overcome such problems by combining the learning and classification processes in a single framework
    • 

    corecore