A5020503237- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Evolution and Genetic Dynamics
- Evolutionary Game Theory and Cooperation
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Escherichia coli research studies
- Gastrointestinal motility and disorders
- Bacteriophages and microbial interactions
- Vibrio bacteria research studies
- Antibiotic Resistance in Bacteria
- Plant Virus Research Studies
- Building materials and conservation
- Fungal Biology and Applications
- Dermatology and Skin Diseases
- Childhood Cancer Survivors' Quality of Life
- Nail Diseases and Treatments
- Conservation Techniques and Studies
- Neutropenia and Cancer Infections
- Ecosystem dynamics and resilience
- Tryptophan and brain disorders
- Genomics and Phylogenetic Studies
- Bacterial biofilms and quorum sensing
- Microbial Metabolic Engineering and Bioproduction
- Microbial Fuel Cells and Bioremediation
University of Manchester
2020-2025
Genomics (United Kingdom)
2024-2025
Boston Children's Hospital
2018-2022
University of Oxford
2015-2021
Boston University
2018-2019
Harvard University
2018-2019
Memorial Sloan Kettering Cancer Center
2016-2018
What makes the gut microbiome stable? Classically, we think of our as stable, benign, and cooperative. Recent experimental work is beginning to unpick essential functions that can be attributed stable microbiota humans. To able manipulate improve health, need understand community structure composition models quantify predict stability. Coyte et al. applied concepts tools from ecology assembly. Independently developed converged on a surprising answer: A high diversity species likely coexist...
A randomized clinical trial demonstrates that autologous fecal microbiota transplant can reconstitute the gut of patients undergoing intensive antibiotic treatment.
Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order identity incoming symbionts is critical for health, but what determines the success assembly process remains poorly understood. Here we develop ecological theory to identify factors important microbial assembly. Our method maps out all feasible pathways given microbiome—with analogies mutational underlying fitness landscapes in evolutionary biology. Building these “assembly maps”...
The bacterial type 6 secretion system (T6SS) is a toxin-injecting nanoweapon that mediates competition in plant- and animal-associated microbial communities. Bacteria can evolve de novo resistance against T6SS attacks, but far from universal natural communities, suggesting key features of weaponry may act to limit its evolution. Here, we combine ecoevolutionary modeling experimental evolution examine how toxin multiplicity Acinetobacter baylyi attackers shape susceptible Escherichia coli...
Significance The overwhelming majority of bacteria live in porous environments, like soil, aquifers, and sediments, where they facilitate many important processes. Despite their importance, we understand little about how these complex environments shape the composition microbial communities that within them. Here, combine two diverse bodies theory—fluid dynamics game theory—to shed light on evolve habitats. We show face a fundamental dilemma: rely flow for nutrients dispersal; however, as...
Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of genes and mobility upon dynamics microbial communities remains largely unknown. Here we develop eco-evolutionary theory explore how alter stability diverse microbiomes in response stressors. We show that adding a microbiome typically increases its overall stability, particularly for...
Abstract What drives the stability, or instability, of complex ecosystems? This question sits at heart community ecology and has motivated a large body theoretical work exploring how properties shape ecosystem dynamics. However, overwhelming majority current theory assumes that species interactions are instantaneous, meaning changes in abundance one will lead to immediate abundances its partners. In practice, time delays respond another widespread across ecological contexts, yet impact these...
Abstract Understanding stability—whether a community will eventually return to its original state after perturbation—is major focus in the study of various complex systems, particularly ecosystems. Here, we challenge this focus, showing that short-term dynamics can be better predictor outcomes for Using random matrix theory, how ecosystems behave immediately small perturbations. Our analyses show many communities are expected ‘reactive’, whereby some perturbations amplified initially and...
The gut microbiota is known to play an important role in maintaining health through a symbiotic relationship with the host. Altered common feature of several diseases gastrointestinal tract; however, causal between and disease pathogenesis poorly understood. Necrotising enterocolitis (NEC) inflammatory bowel (IBD) are both severe affecting tract. Although they affect very different patient populations, NEC primarily being prematurity IBD predominantly adults although children can be...
Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors thus increasing the fitness their hosts (lysogens). Despite prevalence, however, key characteristics an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes weapon. We find that effectiveness is controlled by life history traits-in...
Dramatic deterioration of Hellenistic-Roman limestone remains recently excavated at Dülük Baba Tepesi (Southern Turkey) has been observed following the cold, wet winter 2011/2012. A conceptual model is presented to explain dramatic in which case hardening develops and initially strengthens stone against deterioration, but then makes it more prone exfoliation blistering. Data collected using non-destructive techniques (Equotip surface hardness tester Karsten tube for water uptake) on Fırat...
Abstract The bacterial Type 6 Secretion System (T6SS) is a toxin-injecting nanoweapon that mediates competition in plant- and animal-associated microbial communities. Bacteria can evolve de novo resistance against T6SS attacks, but far from universal natural communities, suggesting key features of weaponry may act to limit its evolution. Here, we combine eco-evolutionary modelling experimental evolution examine how toxin type multiplicity Acinetobacter baylyi attackers shape susceptible...
In healthy adults, the gastrointestinal tract harbours a diverse community of microbes that play critical roles in health and wellbeing. However, we are not born with this microbiome. Over first months years life gut microbiome gradually develops, undergoing process akin to classic primary succession. We here develop ecological theory order study factors drive these assembly processes. find interactions between species can enforce on development, interspecies dependencies driving...
Background Survival after allogeneic hematopoietic stem cell transplantation (ASCT) has significantly improved with early recognition of sepsis and prompt empiric antibiotic (AB) therapy during periods neutropenia. However, AB treatment prophylaxis practices have increased the duration exposure in ASCT patients. Recent studies adult patients shown that perturbations intestinal microbiome diversity are associated development acute graft vs. host disease (aGVHD). Furthermore, even brief to...
The infant gut microbiota develops remarkably predictably 1–7 , with pioneer species colonizing after birth, followed by an ordered succession of other microbes. This predictable assembly is vital to health 8,9 yet the forces underlying it remain unknown. environment, host and microbe-microbe interactions are all likely shape dynamics, but in such a complex ecosystem identifying specific role any individual factor has remained major challenge 10–14 . Here we use multi-kingdom absolute...
Abstract The human scalp hosts an unusually low diversity microbiota dominated by three species: Cutibacterium acnes , Staphylococcus epidermidis and Malassezia restricta where characteristic shifts in species’ frequencies are associated with seborrheic dermatitis dandruff. In order to better understand this important community, here we study the ecological interactions between these species. We establish a new experimental model system that supports growth of all species vitro allows one...
Abstract Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors thus increasing the fitness their hosts (lysogens). Despite prevalence, however, key characteristics an effective temperate phage weapon remain unclear. Here we use systematic mathematical analyses coupled with experimental tests to understand what makes weapon. We find that effectiveness is controlled by life history traits –...