A5024009158- Evolution and Genetic Dynamics
- Evolutionary Game Theory and Cooperation
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Plant and animal studies
- Ecosystem dynamics and resilience
- Ginseng Biological Effects and Applications
- Clostridium difficile and Clostridium perfringens research
- Stochastic processes and statistical mechanics
- Genetic diversity and population structure
- Species Distribution and Climate Change
- RNA and protein synthesis mechanisms
- Algorithms and Data Compression
- Cellular Automata and Applications
- Epigenetics and DNA Methylation
- Evolutionary Algorithms and Applications
- Gene expression and cancer classification
- Vector-borne infectious diseases
- Adolescent and Pediatric Healthcare
- Insect symbiosis and bacterial influences
- Aquaculture disease management and microbiota
- Mathematical and Theoretical Epidemiology and Ecology Models
- Sustainability and Ecological Systems Analysis
The Abdus Salam International Centre for Theoretical Physics (ICTP)
2022-2024
International Centre for Theoretical Sciences
2024
University of California, Los Angeles
2020-2023
Indiana University Bloomington
2015-2022
Indiana University
2020
James Madison University
2016
Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders magnitude 105 y. Our...
The human gut microbiome harbors substantial ecological diversity at the species level as well strain within species. In healthy hosts, abundance fluctuations in are thought to be stable, and these can described by macroecological laws. However, it is less clear how abundances change over time. An open question whether individual strains behave like themselves, exhibiting stability following relationships known hold level, or have different dynamics, perhaps due relatively close phylogenetic...
The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history their constituents. This is typically captured through taxonomic assignment phylogenetic reconstruction, sources information that frequently used group microbes into higher levels organization in experimental natural communities. Connecting community joint ecological dynamics abundances these groups a central problem ecology. However, how depends on scale observation at...
Amphibian populations worldwide are being threatened by the disease chytridiomycosis, which is caused Batrachochytrium dendrobatidis To mitigate effects of B. dendrobatidis, bioaugmentation antifungal bacteria has been shown to be a promising strategy. One way implement through indirect horizontal transmission, defined as transfer from host environment and another host. In addition, direct transmission among individuals can facilitate spread probiotic in population. this study, we tested...
Genetic variation in the human gut microbiome is responsible for conferring a number of crucial phenotypes like ability to digest food and metabolize drugs. Yet, our understanding how this arises maintained remains relatively poor. Thus, largely untapped resource, as large coexisting species presents unique opportunity compare contrast evolutionary processes across identify universal trends deviations. Here we outline features that, while not isolation, an assemblage make it system with...
Abstract Dormancy is an adaptation to living in fluctuating environments. It allows individuals enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. can also influence species interactions providing organisms with refuge from predators and parasites. Here we test the hypothesis that, generating seed bank protected individuals, dormancy modify patterns processes antagonistic coevolution. We conducted factorially designed experiment where passaged...
While the human gut microbiome has been intensely studied, we have yet to obtain a sufficient understanding of genetic diversity that it harbors. Research efforts demonstrated considerable fraction within-host variation in is driven by ecological dynamics co-occurring strains belonging same species, suggesting an lens may provide insight into empirical patterns diversity. Indeed, model self-limiting growth and environmental noise known as Stochastic Logistic Model (SLM) was recently shown...
We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The provides insight into the ecological strategies this bacterium in free-living and host-associated environments.
Abstract Fluctuations in the availability of resources constrain growth and reproduction individuals, which subsequently affects evolution their respective populations. Many organisms contend with such fluctuations by entering a reversible state reduced metabolic activity, phenomenon known as dormancy. This pool dormant individuals (i.e. seed bank) does not reproduce is expected to act an evolutionary buffer, though it difficult observe this effect directly over extended timescale. Through...
The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history their constituents. This is typically captured through taxonomic assignment phylogenetic reconstruction, sources information that frequently used group microbes into higher levels organization in experimental natural communities. Connecting community joint ecological dynamics abundances these groups a central problem ecology. However, how depends on scale observation at...
Abstract The structure and diversity of microbial communities is intrinsically hierarchical due to the shared evolutionary history their constituents. This typically captured through taxonomic assignment phylogenetic reconstruction, sources information that are frequently used group microbes into higher levels organization in experimental natural communities. Connecting community joint ecological dynamics abundances these groups a central problem ecology. However, how depends on scale...
Abstract Ecology has historically benefited from the characterization of statistical patterns biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal diversity abundance that can be captured by effective models. Experimentation simultaneously played a crucial role, advent high-replication community time-series allowed researchers to investigate underlying ecological forces. However, there...
We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from agricultural soil. The provides insight into the strategies that spp. use to contend with environmental stressors such as desiccation and starvation in host-associated ecosystems.
Microorganisms are the most abundant, diverse, and functionally important organisms on Earth. Over past decade, microbial ecologists have produced largest ever community datasets. However, these data rarely used to uncover law-like patterns of commonness rarity, test theories biodiversity, or explore unifying explanations for structure communities. Using a global-scale compilation >20,000 samples from environmental, engineered, host-related ecosystems, we power competing predict...
As the most abundant and diverse form of life on Earth, microorganisms commonly inhabit energy-limited environments where cellular maintenance growth is highly constrained. To gain insight into how persist under such conditions, we derived demographic parameters from a collection bacteria by censusing 100 populations in closed system for 1,000 days. All but one taxon survived prolonged resource scarcity, yielding estimated times-to-extinction ranging over four orders magnitude 10 0 – 5...
There is currently no framework for identifying genes that contribute to molecular divergence between microbial populations in different environments. To address this absence, we developed a null modeling approach describe the distribution of mutation counts among genes.
Abstract Microorganisms have the unique ability to survive extended periods of time in environments with extremely low levels exploitable energy. To determine extent that energy limitation affects microbial evolution, we examined molecular evolutionary dynamics a phylogenetically diverse set taxa over course 1,000 days. We found periodic exposure affected rate accumulation genetic diversity, and extinction. then determined degree spectrum mutations as well direction evolution at gene level....
An ecological theory of microbial biodiversity has yet to be developed. This shortcoming leaves patterns abundance, distribution, and diversity for the most abundant diverse organisms on Earth without a predictive framework. However, because their high abundance complex dynamics, communities may underpinned by lognormal i.e., synergistic interactions among stochastic variables. Using global-scale compilation 20,456 sites from set natural host-related environments, we test whether model...
Abstract The human gut microbiome harbors substantial ecological diversity at the species level, as well strain level within species. In healthy hosts, abundance fluctuations in are thought to be stable, and these can described by macroecological laws. However, it is less clear how abundances change over time. An open question whether individual strains behave like themselves, exhibiting stability following relationships known hold or have different dynamics, perhaps due relatively close...
Abstract Variation in the structure of host-associated microbial communities has been correlated with occurrence and severity disease diverse host taxa, suggesting a key role microbiome pathogen defense. However, whether these correlations are typically cause or consequence exposure remains an open question, requires experimental approaches to disentangle. In amphibians, infection by fungal Batrachochytrium dendrobatidis (Bd) alters skin community some species, whereas other appears mediate...