A macroecological perspective on genetic diversity in the human gut microbiome

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(7), P. e0288926 - e0288926

Published: July 21, 2023

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 successfully predict temporal within single host. However, its ability across hosts be tested. In this manuscript I determine whether predictions SLM explain unrelated for 22 common microbial species. Specifically, stationary distribution explains allele frequencies predicts harboring given (i.e., prevalence) sites. The accuracy correlated with independent estimates strain structure, follow statistically similar forms due existence strain-level ecology.

Language: Английский

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Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Aug. 21, 2023

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 which defined has never been systematically examined. Here, we macroecological approach quantitatively characterize among disparate environments across scales. We found measures biodiversity given can be consistently predicted using minimal model ecology, Stochastic Logistic Model growth (SLM). result suggests SLM more appropriate null-model for than alternatives such as Unified Neutral Theory Biodiversity. Extending within-scale results, examined relationship between calculated different scales (e.g. genus vs. family), an empirical pattern previously evaluated context Diversity Begets (DBD) hypothesis (Madi et al., 2020). richness estimates assuming independence members, demonstrating DBD sufficiently explained null Contrastingly, only by including correlations members consequence interactions) predict results this study novel patterns establish sharp demarcation recently proposed not affected interactions.

Language: Английский

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Macroecological patterns in experimental microbial communities

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 26, 2023

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 remains gap between experiments performed in laboratory documented natural systems, we do not know whether these recapitulated lab experimental manipulations produce effects. This work aims at bridging ecology Using time-series, demonstrate observed nature exist setting, despite controlled conditions, unified under Stochastic Logistic Model growth (SLM). We find demographic (e.g., migration) impact patterns. By modifying SLM incorporate said alongside details sampling), obtain predictions are consistent with outcomes. combining models, macroecology viewed predictive discipline.

Language: Английский

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Interactions-based classification of a single microbial sample

Cell Reports Methods, Journal Year: 2024, Volume and Issue: 4(5), P. 100775 - 100775

Published: May 1, 2024

To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based interspecific microbial relationships. We verify, using both numerical simulations as well real and shuffled profiles from human oral cavity, method can classify their interactions. By analyzing gut microbiome people with autistic spectrum disorder, found our interaction-based improve classification subjects sample. These results demonstrate underlying be practically utilized facilitate microbiome-based diagnosis precision medicine.

Language: Английский

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Synthetic Ecosystems: From the Test Tube to the Biosphere

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(12), P. 3812 - 3826

Published: Nov. 21, 2024

The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. In this framework, quantifying numbers related variables (associated with metabolism or biological-environmental interactions) plays a central role in measuring predicting system-level properties. As we move toward advanced technological engineering cells organisms, the possibility bioengineering ecosystems (from gut microbiome to wildlands) opens several questions that will require quantitative models find answers. Here, present comprehensive survey modeling approaches for managing three kinds synthetic sharing presence engineered strains. These include test tube examples hosting relatively low number interacting species, mesoscale closed (or ecospheres), macro-scale, ecosystems. potential outcomes ecosystem designs their limits be relevant different disciplines, including biomedical engineering, astrobiology, space exploration fighting climate change impacts on endangered We propose possible captures broad range scenarios tentative roadmap open problems further exploration.

Language: Английский

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Synthetic Ecosystems: From the Test Tube to the Biosphere

Published: May 14, 2024

The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. In this framework, quantifying numbers related variables (associated with metabolism or biological-environmental interactions) plays a central role in measuring predicting system-level properties. As we move towards advanced technological engineering cells organisms, the possibility bioengineering ecosystems (from gut microbiome to wildlands) opens several questions that will require quantitative models find answers. Here, present comprehensive survey modelling approaches for managing three kinds synthetic sharing presence engineered strains. These include test tube examples hosting relatively low number interacting species, mesoscale closed (or ecospheres), macro-scale, ecosystems. potential outcomes ecosystem designs their limits be relevant different disciplines, including biomedical engineering, astrobiology, space exploration fighting climate change impacts on endangered We propose possible captures broad range scenarios tentative road map open problems further exploration.

Language: Английский

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