Robustness of microbiome function

Lee, Kiseok Keith; Park, Yeonwoo; Kuehn, Seppe

doi:10.1016/j.coisb.2023.100479

Cited by 7 publications

(3 citation statements)

References 83 publications

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“…From this perspective, we identified functional phases that qualitatively govern the community’s response to environmental changes. For example, we discovered a regime of functional robustness (the Nutrient-limiting phase, Phase II) [4], where the indigenous biomass activity is robust to pH changes, as well as a regime where the rare biosphere determines community response (Phase III) to large basic perturbations [55].…”

Section: Discussionmentioning

confidence: 99%

“…From this perspective, we identified functional regimes demarcated by whether active biomass or available nutrients dictate the metabolism of the system. For example, we discovered a nutrient-limiting regime (Regime II), where the indigenous biomass is robust to moderate pH changes [43] and metabolism is governed by carbon limitation. In contrast, metabolism in Regime III is governed by the growth of initially rare taxa perturbations [44].…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, characterizing how these communities respond to natural and anthropogenic environmental perturbations is of critical importance. Understanding how these responses are shaped by community composition [4] may translate into principles for controlling community metabolic processes or predicting future responses to environmental change. However, due to the complexity of natural communities, establishing a quantitative link between microbiome metabolism, community composition, and environmental perturbations has proven challenging [5, 6].…”

Section: Introductionmentioning

confidence: 99%

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Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

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A major challenge in microbiome research is understanding how natural communities respond to environmental change. The ecological, spatial, and chemical complexity of soils makes understanding how these communities respond metabolically to perturbations particularly challenging. Here we measure the dynamics of respiratory nitrate utilization in >1,500 soil microcosms from 20 soil samples subjected to pH perturbations. Despite the complexity of the soil microbiome a minimal mathematical model with two parameters, the quantity of active biomass and the availability of a limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. The model reveals three distinct functional phases that encode the low-dimensional dynamics of nitrate utilization in response to short and long-term pH perturbations: a phase where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting phase where nitrate utilization is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth phase in basic conditions, where nutrients are in excess and rare taxa rapidly outgrow dominant populations. The underlying functional mechanism of each phase is revealed by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. The long-term pH of the soil determines the size of pH changes necessary to drive transitions between functional phases. Our results unify decades of previous studies on nitrogen utilization and pH in soils under a single quantitative framework. A minimal mathematical formalism reveals the existence of a few qualitative phases that capture the mechanisms and dynamics of a community responding to environmental change.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

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Editorial overview: Systems biology of ecological interactions across scales

Kussell,

Takeuchi

2024

Current Opinion in Systems Biology

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Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway

Liu

Cheng

Zhou

et al. 2023

Preprint

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The arginine dihydrolase metabolic pathway (arc operon) is present in the genomes of diverse human gut bacterial species and can modulate environmental pH. We lack an understanding of the role of this pathway on community-level interactions. We investigated the role of the arc operon in the probiotic E. coli Nissle on the assembly and production of the beneficial metabolite butyrate in a human gut community in vitro and in the murine gut. The presence of the arc operon shapes the dynamics of community assembly. With arc operon expression, we observed reduced variability in community structure from environmental pH perturbations. In particular, the abundance of butyrate producers was altered either transiently or longer-term. The arc operon can enhance or reduce butyrate production depending on the environmental pH. Dynamic computational modeling of community assembly reveals the extent of pH-mediated inter-species interactions on community assembly. Several species are identified with significant beneficial or detrimental non-pH-mediated interactions. Overall, we demonstrated that a single specialized metabolic pathway could shape community assembly, species colonization of the mammalian gut and butyrate production.

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Robustness of microbiome function

Cited by 7 publications

References 83 publications

Functional regimes define the response of the soil microbiome to environmental change

Functional regimes define the response of the soil microbiome to environmental change

Editorial overview: Systems biology of ecological interactions across scales

Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway

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