Deterministic and stochastic processes generating alternative states of microbiomes

ISME Communications, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Abstract The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such “alternative states” microbiome compositions has been one major challenges ecology and microbiology. In a time-series analysis experimental microbiomes, we here show both deterministic stochastic ecological processes drive divergence alternative states. We introduced species-rich soil-derived eight culture media with 48 replicates, monitoring shifts community at six time points (8 × replicates 6 = 2304 samples). then confirmed microbial diverged few state each medium conditions as predicted presence processes. other words, was differentiated small number reproducible under same environment. This fact indicates not only selective forces leading to specific equilibria resource use but also influence demographic drift (fluctuations) on assembly. A reference-genome-based further suggested observed states differed ecosystem-level functions. These findings will help us examine how functions can be controlled by changing “stability landscapes” compositions.

Язык: Английский

---

Cooperative growth in microbial communities is a driver of multistability

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 3, 2024

Abstract Microbial communities often exhibit more than one possible stable composition for the same set of external conditions. In human microbiome, these persistent changes in species and abundance are associated with health disease states, but drivers alternative states remain unclear. Here we experimentally demonstrate that a cross-kingdom community, composed six relevant to respiratory tract, displays four each dominated by different species. pairwise coculture, observe widespread bistability among pairs, providing natural origin multistability full community. contrast common association between antagonism, experiments reveal many positive interactions within community members. We find multiple display cooperative growth, modeling predicts this could drive observed as well non-canonical outcomes. A biochemical screening reveals glutamate either reduces or eliminates cooperativity growth several species, confirm such supplementation extent across pairs Our findings provide mechanistic explanation how rather competitive can underlie microbial communities.

Язык: Английский

---

Metabolic complexity drives divergence in microbial communities

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(8), С. 1493 - 1504

Опубликована: Июль 2, 2024

Язык: Английский

---

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use

mLife, Год журнала: 2022, Номер 1(4), С. 382 - 398

Опубликована: Ноя. 3, 2022

Although the accomplishments of microbiome engineering highlight its significance for targeted manipulation microbial communities, knowledge and technical gaps still limit applications in biotechnology, especially environmental use. Addressing challenges refractory pollutants fluctuating conditions requires an adequate understanding theoretical achievements practical engineering. Here, we review recent cutting-edge studies on strategies their classical bioremediation. Moreover, a framework is summarized combining both top-down bottom-up approaches toward improved applications. A strategy to engineer microbiomes use, which avoids build-up toxic intermediates that pose risk human health, suggested. We anticipate highlighted will be beneficial address difficult such as degrading multiple sustain performance engineered situ with indigenous microorganisms under conditions.

Язык: Английский

---

Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 14, 2023

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, use thousands of microbial communities cultured in vitro from human feces uncover simple assembly rules develop a predictive model community composition upon addition single nutrients central carbon metabolism complex medium. Community membership was largely determined by donor feces, whereas relative abundances were supplemental source. The absolute abundance most taxa independent supplementing nutrient, due ability fast-growing organisms quickly exhaust their niche medium then exploit monopolize Relative dominant could be predicted nutritional preferences growth dynamics species isolation, exceptions consistent with strain-level variation capabilities. Our study reveals that follows utilization provides framework for manipulating commensal perturbations.

Язык: Английский

---

Microbial functional guilds respond cohesively to rapidly fluctuating environments

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 30, 2025

Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal climactic variations. Understanding how microbial populations respond these is critical for predicting the impact of perturbations, interventions, and climate change on communities. Since typically harbor tens hundreds distinct taxa, response abundances perturbations potentially complex. However, while taxonomic diversity high, many taxa can be grouped into functional guilds strains with similar metabolic traits. These effectively reduce complexity system by providing a physiologically motivated coarse-graining. Here, using combination simulations, theory, experiments, we show that nutrient depends timescale those fluctuations. Rapid drive cohesive, positively correlated abundance dynamics within guilds. For slower variation, members guild begin compete due resource preferences, driving negative correlations between same guild. Our results provide route understanding relationship community changing environments, as well an experimental approach discovering via designed

Язык: Английский

---

Dynamic coexistence driven by physiological transitions in microbial communities

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(16)

Опубликована: Апрель 17, 2025

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they forced out of the state into stressed, nongrowing Such dynamics typical ecological succession nature and serial-dilution cycles laboratory. Here, we introduce a phenomenological model, Community State Model, to gain insight dynamic coexistence due changes physiological states during cyclic succession. Our model specifies preference each along global coordinate, taken be biomass density community, but is otherwise agnostic specific (e.g., nutrient starvation, stress, aggregation), order focus on self-consistency conditions combinations states, “community states,” stable ecosystem. We identify three key features such dynamical communities contrast starkly with steady-state communities: enhanced community stability through staggered dominance different increased tolerance diversity fast growing dominating distinct requirement late-growing species. These features, derived explicitly for simplified models, proposed here as principles aiding understanding complex communities. shifts ecosystem from bottom–up studies based fixed, idealized interspecies interaction top–down accessible macroscopic observables rates total density, enabling quantitative examination community-wide characteristics.

Язык: Английский

---

Diauxic lags explain unexpected coexistence in multi‐resource environments

Molecular Systems Biology, Год журнала: 2022, Номер 18(5)

Опубликована: Май 1, 2022

Язык: Английский

---

Unravelling metabolic cross‐feeding in a yeast–bacteria community using ¹³C‐based proteomics

Molecular Systems Biology, Год журнала: 2023, Номер 19(4)

Опубликована: Фев. 13, 2023

Abstract Cross‐feeding is fundamental to the diversity and function of microbial communities. However, identification cross‐fed metabolites often challenging due universality metabolic biosynthetic intermediates. Here, we use 13 C isotope tracing in peptides elucidate co‐cultures Saccharomyces cerevisiae Lactococcus lactis . The community was grown on lactose as main carbon source with either glucose or galactose fraction molecule labelled C. Data analysis allowing for possible mass‐shifts yielded hundreds which could assign both species identity labelling degree. pattern showed that yeast utilized and, a lesser extent, lactic acid shared by L. sources. While provided essential amino acids bacterium expected, data also uncovered complex exchange. further supported metabolite co‐culture supernatant, diminished fitness galactose‐negative mutant community. Together, our results demonstrate utility C‐based proteomics uncovering interactions.

Язык: Английский

---

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(48)

Опубликована: Ноя. 22, 2023

Microbiome engineering offers the potential to leverage microbial communities improve outcomes in human health, agriculture, and climate. To translate this into reality, it is crucial reliably predict community composition function. But a brute force approach cataloging function hindered by combinatorial explosion number of ways we can combine species. An alternative parameterize using simplified, mechanistic models, then extrapolate these models beyond where have sampled. approaches remain data-hungry, as well requiring an priori specification what kinds mechanisms are included which omitted. Here, resolve both issues introducing mechanism-agnostic predicting compositions functions limited data. The critical step identification sparse representation landscape. We sparsity functions, drawing from techniques compressive sensing. validate on silico data, generated theoretical model. By sampling just ∼ 1% all possible communities, accurately out sample. demonstrate real-world application our applying four experimental datasets showing that recover interpretable, accurate predictions highly

Язык: Английский

---