Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability

The ISME Journal, Год журнала: 2023, Номер 17(12), С. 2370 - 2380

Опубликована: Окт. 27, 2023

Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions coexisting genotypes. Despite the importance of auxotrophies, their distribution impact on diversity function human gut microbiome remain poorly understood. This study performed first systematic analysis amino using a combined metabolomic, metagenomic, modeling approach. Results showed that ubiquitous colon microbiome, with tryptophan auxotrophy being most common. Auxotrophy frequencies were higher for those acids also essential to host. Moreover, overall abundance was associated greater stability, auxotrophs found be related host's metabolome, including trimethylamine oxide, small aromatic acids, secondary bile acids. Thus, our results suggest important factors contributing ecology host-microbiome interactions.

Язык: Английский

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Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Global Change Biology, Год журнала: 2023, Номер 30(1)

Опубликована: Дек. 22, 2023

Abstract Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution communities their feedback mechanisms on SOC dynamics helps embed ecology soil microbiome into cycling, which serves to improve biodiversity conservation management strategy under global change. Here, croplands with a gradient were used understand how metabolisms decomposition linked diversity, composition, co‐occurrence networks encompassing archaea, bacteria, fungi, protists, invertebrates. As decreased, diversity prokaryotes eukaryotes also but network complexity showed contrasting patterns: increased due intensified niche overlap, while that decreased possibly because greater dispersal limitation owing breakdown macroaggregates. Despite decrease stocks, capacity was enhanced as indicated by enzyme activity enzymatic stoichiometric imbalance. This could, turn, expedite loss through respiration, particularly slow‐cycling pool. The dominantly driven multitrophic negative (competitive predator–prey) associations, fostered stability metacommunity. Interestingly, abiotic conditions including pH, aeration, nutrient exhibited less significant role. Overall, this study reveals need for C resources across levels maintain functionality declining results loss. Our researchers highlight importance integrating biological processes models turnover, agroecosystem functioning face intensifying anthropogenic land‐use climate

Язык: Английский

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Global prediction of soil microbial growth rates and carbon use efficiency based on the metabolic theory of ecology

Soil Biology and Biochemistry, Год журнала: 2024, Номер 190, С. 109315 - 109315

Опубликована: Янв. 10, 2024

Язык: Английский

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Sparse species interactions reproduce abundance correlation patterns in microbial communities

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(5)

Опубликована: Янв. 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.

Язык: Английский

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Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review

Microbiological Research, Год журнала: 2024, Номер 282, С. 127660 - 127660

Опубликована: Фев. 28, 2024

Язык: Английский

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