title: Building the microbiome in health and disease: niche construction and social conflict in bacteria.
abstract: Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of 'niche construction'. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.
authors.affiliation: Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK luke.mcnally@ed.ac.uk.
authors.forename: Luke
authors.initials: L
authors.lastname: McNally
authors.affiliation: Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK sam.brown@ed.ac.uk.
authors.forename: Sam P
authors.initials: SP
authors.lastname: Brown
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D018407:Bacterial Physiological Phenomena; D005075:Biological Evolution; D016360:Clostridioides difficile / Q000472:pathogenicity / Q000502:physiology; D003013:Clostridium / Q000502:physiology; D003550:Cystic Fibrosis / Q000150:complications / Q000382:microbiology; D004761:Enterocolitis, Pseudomembranous / Q000382:microbiology / Q000517:prevention & control; D000069196:Gastrointestinal Microbiome / Q000502:physiology; D054884:Host-Pathogen Interactions / Q000276:immunology / Q000502:physiology*; D006801:Humans; D008168:Lung / Q000382:microbiology; D064307:Microbiota / Q000502:physiology*; D008954:Models, Biological; D010641:Phenotype; D011552:Pseudomonas Infections / Q000150:complications / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000472:pathogenicity; D012486:Salmonella typhimurium / Q000276:immunology; D014774:Virulence
keywords: community ecology; cooperation; microbiota; niche construction; social evolution