Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth DOI Open Access
William R. Shoemaker, Jacopo Grilli

Published: Dec. 21, 2023

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 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 by Diversity Begets (DBD) hypothesis. richness estimates assuming independence members.Contrastingly, only including correlations members consequence interactions) predict results this study novel patterns establish sharp demarcation recently proposed not affected interactions.

Language: Английский

Sparse species interactions reproduce abundance correlation patterns in microbial communities DOI Creative Commons
José Camacho-Mateu, Aniello Lampo, Matteo Sireci

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(5)

Published: Jan. 24, 2024

During the last decades, macroecology has identified broad-scale patterns of abundances and diversity microbial communities put forward some potential explanations for them. However, these advances are not paralleled by a full understanding dynamical processes behind In particular, abundance fluctuations different species found to be correlated, both across time in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem points sparse interactions as necessary mechanism account Specifically, we discuss several possibilities include recognize Lotka-Volterra constants successful ansatz. For this, design Bayesian inference algorithm extract sets interaction able reproduce empirical probability distributions pairwise diverse biomes. Importantly, inferred still well-known single-species macroecological concerning communities. Endorsed agreement with empirically observed phenomenology, our analyses provide insights into properties networks interactions, revealing that sparsity is crucial feature.

Language: Английский

Citations

16
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth DOI Creative Commons
William R. Shoemaker, Jacopo Grilli

eLife, Journal Year: 2024, Volume and Issue: 12

Published: Jan. 22, 2024

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

Citations

7
The characteristics of intestinal microflora in infants with rotavirus enteritis, changes in microflora before and after treatment and their clinical values DOI Creative Commons
Qingpi Yan, Yuanyuan Chen,

E-Bin Gao

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 5, 2025

Rotavirus (RV) is a leading pathogen causing diarrhea in children. In this study, total of 51 fecal samples from children with RV enteritis, 29 post-treatment samples, and 38 age-matched healthy controls were collected. Microbial DNA was isolated the followed by high throughput Illumina sequencing targeting 16 S rRNA gene. Compared to group, RV-infected group exhibited reduced microbial diversity. Both groups shared Firmicutes as dominant phylum. Additionally, abundance Proteobacteria increased significantly group. At genus level, among top 50 most abundant genera, 34 showed significant differences, these differential genera correlating certain clinical indicators such dehydration levels C-reactive protein (CRP). Notably, there no differences microbiota before after treatment Only 8.82% (3/34) recovery trend towards state. This study enhances understanding how infection alters gut structure provides scientific basis for improving diagnosis strategies.

Language: Английский

Citations

0
Macroecological patterns in experimental microbial communities DOI Creative Commons
William R. Shoemaker,

Álvaro Sánchez,

Jacopo Grilli

et al.

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(5), P. e1013044 - e1013044

Published: May 8, 2025

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 found 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

Citations

0
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth DOI Creative Commons
William R. Shoemaker, Jacopo Grilli

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

Citations

6
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth DOI Creative Commons
William R. Shoemaker, Jacopo Grilli

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

Published: March 2, 2023

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 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 by Diversity Begets (DBD) hypothesis. richness estimates assuming independence members.Contrastingly, only including correlations members consequence interactions) predict results this study novel patterns establish sharp demarcation recently proposed not affected interactions.

Language: Английский

Citations

5
Macroecological patterns in experimental microbial communities DOI Creative Commons
William R. Shoemaker,

Álvaro Sánchez,

Jacopo Grilli

et al.

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

Citations

5
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth DOI Open Access
William R. Shoemaker, Jacopo Grilli

Published: Dec. 21, 2023

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 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 by Diversity Begets (DBD) hypothesis. richness estimates assuming independence members.Contrastingly, only including correlations members consequence interactions) predict results this study novel patterns establish sharp demarcation recently proposed not affected interactions.

Language: Английский

Citations

0