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

Bacterial defences: mechanisms, evolution and antimicrobial resistance DOI
William P. J. Smith, Benjamin R. Wucher, Carey D. Nadell

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(8), P. 519 - 534

Published: April 24, 2023

Language: Английский

Citations

175
Metabolic exchanges are ubiquitous in natural microbial communities DOI
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(12), P. 2244 - 2252

Published: Nov. 23, 2023

Language: Английский

Citations

89
Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms DOI Creative Commons
Paul J. Weimer

Microorganisms, Journal Year: 2022, Volume and Issue: 10(12), P. 2345 - 2345

Published: Nov. 27, 2022

As major structural components of plant cell walls, cellulose and hemicellulose are degraded fermented by anaerobic microbes in the rumen to produce volatile fatty acids, main nutrient source for host. Cellulose degradation is carried out primarily specialist bacteria, with additional contributions from protists fungi, via a variety mechanisms. Hemicelluloses hydrolyzed cellulolytic bacteria generalist, non-cellulolytic microbes, largely extracellular enzymes. hydrolysis follows first-order kinetics its rate limited available substrate surface area. Nevertheless, at least an order magnitude more rapid than digesters, due near-obligatory adherence microbial cells surface, lack downstream inhibitory effects; host animal, fiber also enhanced unique process rumination. Cellulolytic hemicellulolytic exhibit intense competition amensalism, but they display mutualistic interactions other trophic levels. Collectively, fiber-degrading community displays functional redundancy, partial niche overlap, convergence catabolic pathways that all contribute stability ruminal fermentation. The superior hydrolytic fermentative capabilities degraders make them promising candidates several fermentation technologies.

Language: Английский

Citations

88
Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers DOI
Tingting Cao, Yunchao Luo, Man Shi

et al.

Soil Biology and Biochemistry, Journal Year: 2023, Volume and Issue: 188, P. 109215 - 109215

Published: Oct. 24, 2023

Language: Английский

Citations

86
Emergent coexistence in multispecies microbial communities DOI
Chang‐Yu Chang, Djordje Bajić, Jean C. C. Vila

et al.

Science, Journal Year: 2023, Volume and Issue: 381(6655), P. 343 - 348

Published: July 20, 2023

Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on coexistence has largely focused species pairs, but it unclear whether pairwise isolation required for multispecies community. To address this question, we conducted hundreds of competition experiments among stably coexisting members 12 different enrichment communities vitro. determine outcomes these experiments, developed an automated image analysis pipeline to quantify abundances. We found competitive exclusion was most common outcome, and strongly hierarchical transitive. Because many coexist within stable community fail co-culture under identical conditions, concluded emergent phenomenon. This highlights importance context understanding origins complex ecosystems.

Language: Английский

Citations

82
Rhizosphere bacterial interactions and impact on plant health DOI Creative Commons

Jane Chepsergon,

Lucy Moleleki

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 73, P. 102297 - 102297

Published: March 30, 2023

The rhizosphere is a chemically complex environment that harbors strikingly diverse microbial community. past few decades have seen rapid growth in the body of literature on plant–microbe–microbe interactions and plant health. Thus, aim this paper to review current knowledge (specifically bacteria) how these influence microbiomes impact This article discusses (i) recruits beneficial bacteria ii) competition between mechanisms/weapons employed bacteria–bacteria shapes microbiome turn affects heath. discussion mainly focuses interference competition, characterized by production specialized metabolites (antibacterial compounds) exploitative where bacterial strain restricts competitor's access nutrients such as through secretion siderophores could allude cooperation. Understanding mechanisms plant–bacteria provide insights into manipulate for improved agricultural outcomes.

Language: Английский

Citations

79
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation DOI Creative Commons
Yuxiang Zhao, Zishu Liu, Baofeng Zhang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 5, 2023

Abstract Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress thought to promote microbial mutualism, there a paucity of research this area. Here, we monitor communities quasi-natural composting system, where temperature variation (20 °C–70 °C) the main stress. Genomic analyses and culturing experiments provide evidence that selects slow-growing stress-tolerant strains (i.e., Thermobifida fusca Saccharomonospora viridis ), mutualistic interactions emerge between them remaining through sharing cobalamin. Comparison 3000 pairings reveals mutualism common (~39.1%) competition rare (~13.9%) pairs involving T. S. . Overall, our work provides insights into how high can favour reduce at both community species levels.

Language: Английский

Citations

79
Microbiome composition modulates secondary metabolism in a multispecies bacterial community DOI Creative Commons
Marc G. Chevrette, Chris S. Thomas, Amanda Hurley

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(42)

Published: Oct. 10, 2022

Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions responses to environmental change. Despite the importance in human health ecology, little is known about their roles regulation context multispecies communities. simplified model rhizosphere composed Bacillus cereus , Flavobacterium johnsoniae Pseudomonas koreensis we show that dynamics metabolism depend on community species composition interactions. Comparative metatranscriptomics metametabolomics reveal abundance transcripts biosynthetic gene clusters (BGCs) metabolomic molecular features differ between monocultures or dual cultures tripartite community. both two- three-member cocultures, P. modified expression BGCs for zwittermicin, petrobactin, B. F. johnsoniae, whereas BGC transcriptional response itself was minimal. Pairwise cocultures with displayed unique appear be derivatives lokisin, suggesting metabolic handoffs species. Deleting koreenceine, another metabolite, altered transcript metabolite profiles across community, including substantial up-regulation petrobactin bacillibactin koreenceine represses siderophore production. Results from this bacterial chemical output identity capacity coculture partners, microbiome may shape nature.

Language: Английский

Citations

76
Deterministic Effect of pH on Shaping Soil Resistome Revealed by Metagenomic Analysis DOI
Zishu Liu, Yuxiang Zhao, Baofeng Zhang

et al.

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(2), P. 985 - 996

Published: Jan. 5, 2023

Soil is recognized as the major reservoir of antibiotic resistance genes (ARGs), harboring most diverse naturally evolved ARGs on planet. Multidrug are a class ARGs, and their high prevalence in natural soil ecosystems has recently raised concerns. Since these express proton motive force (PMF) driven efflux pumps, studying whether pH determinant for selection multidrug pump thus shaping resistome great interest. In this study, we collected 108 soils with values ranging from 4.37 to 9.69 multiple profiled composition metagenomes metagenome-assembled genomes. We observed enriched acidic resistome, abundances have significant dependence. This reflects benefits activity genes, especially PMF-driven inner membrane transferase. addition, preliminary indicate putative microbial participants by applying ecological analyzing tools such stepwise regression random forest model fitting. The decisive influence more impactful than any other examined factors, consequence, revisited edaphic factors resistome; i.e., deterministic mechanisms could lead bottom-up ARG composition. Such developing herein suggested be considered assessing human-driven transmissions.

Language: Английский

Citations

66
A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation DOI Creative Commons

Ziqi Ma,

Tao Zuo, Norbert Frey

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: Sept. 23, 2024

Language: Английский

Citations

26