Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Microbial Ecology, Год журнала: 2024, Номер 87(1)

Опубликована: Апрель 8, 2024

Abstract Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring these dynamic systems, one can begin to unravel role played by microbial species. Towards this, various methods have been developed decipher communities. The current review focuses on qualitative and quantitative that currently exist study interactions. Qualitative such co-culturing experiments are visualized using microscopy-based techniques combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative include construction networks network inference, computational models, development synthetic consortia. These provide valuable clue roles interacting partners, well possible solutions overcome pathogenic microbes cause life-threatening infections susceptible hosts. Studying will further our understanding less-studied ecosystems enable design effective frameworks for treatment infectious diseases.

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

---

Challenges and pitfalls of inferring microbial growth rates from lab cultures

Frontiers in Ecology and Evolution, Год журнала: 2024, Номер 11

Опубликована: Янв. 17, 2024

Introduction After more than 100 years of generating monoculture batch culture growth curves, microbial ecologists and evolutionary biologists still lack a reference method for inferring rates. Our work highlights the challenges estimating rate from curve data. It shows that inaccurate estimates rates significantly impact estimated relative fitness, principal quantity in evolution ecology. Methods results First, we conducted literature review found which methods are currently used to estimate These differ meaning parameter. Mechanistic models intrinsic µ , whereas phenomenological – both model-based model-free maximum per capita max . Using math simulations, show conditions is not good estimator Then, demonstrate absolute overcome by calculating values. Importantly, find poor approximations sometimes lead wrongly classifying beneficial mutant as deleterious. Finally, re-analyzed four published data sets, using most our review. We detected no single best-fitting model across all experiments within set Gompertz models, were among commonly used, often worst-fitting. Discussion study suggests how experimenters can improve their associated fitness neglected but fundamental problem nearly everyone who studies populations lab.

Язык: Английский

---

Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative

PLoS Biology, Год журнала: 2024, Номер 22(2), С. e3002482 - e3002482

Опубликована: Фев. 5, 2024

Knowing how species interact within microbial communities is crucial to predicting and controlling community dynamics, but interactions can depend on environmental conditions. The stress-gradient hypothesis (SGH) predicts that are more likely facilitate each other in harsher environments. Even if the SGH gives some intuition, quantitative modeling of context-dependency requires understanding mechanisms behind SGH. In this study, we show with both experiments a theoretical analysis varying concentration single compound, linoleic acid (LA), modifies interaction between 2 bacterial species, Agrobacterium tumefaciens Comamonas testosteroni, from competitive at low concentration, facilitative higher concentrations where LA becomes toxic for one species. We demonstrate mechanism facilitation able reduce reactive oxygen (ROS) produced spontaneously LA, allowing short-term rescue sensitive ROS longer coexistence serial transfers. our system, competition occur simultaneously, changing compound alter balance two.

Язык: Английский

---

Quantifying microbial interactions: concepts, caveats, and applications

Current Opinion in Microbiology, Год журнала: 2024, Номер 80, С. 102511 - 102511

Опубликована: Июль 13, 2024

Язык: Английский

---

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

Journal of Applied Microbiology, Год журнала: 2024, Номер 135(7)

Опубликована: Июнь 27, 2024

Abstract Microbiomes, the complex networks of micro-organisms and molecules through which they interact, play a crucial role in health ecology. Over at least past two decades, engineering biology has made significant progress, impacting bio-based industry, health, environmental sectors; but only recently begun to explore microbial ecosystems. The creation synthetic communities presents opportunities help us understand dynamics wild ecosystems, learn how manipulate interact with existing microbiomes for therapeutic other purposes, create entirely new capable undertaking tasks industrial biology. Here, we describe ecosystems can be constructed controlled, focusing on available methods interaction mechanisms facilitate regulation community composition output. While experimental decisions are dictated by intended applications, vast number tools suggests great opportunity researchers develop diverse array novel

Язык: Английский

---

Assembly Graph as the Rosetta Stone of Ecological Assembly

Environmental Microbiology, Год журнала: 2025, Номер 27(1)

Опубликована: Янв. 1, 2025

Ecological assembly-the process of ecological community formation through species introductions-has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non-theoreticians, they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool connect emerging theories. The visually represents dynamics, where nodes symbolise combinations edges represent transitions driven by introductions. Through lens graphs, review how processes reduce uncertainty in random arrivals (informational approach), identify graphical properties that guarantee coexistence examine class dynamical models constrain topology graphs (dynamical quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, also methods decompose complex into smaller, measurable components, well computational tools for deriving graphs. In sum, this math-light progress aims catalyse research towards predictive understanding assembly.

Язык: Английский

---

Detecting (the Absence of) Species Interactions in Microbial Ecological Systems

Studies in Applied Mathematics, Год журнала: 2025, Номер 154(2)

Опубликована: Фев. 1, 2025

ABSTRACT Microbial communities are complex ecological systems of organisms that evolve in time, with new variants created, while others disappear. Understanding how species interact within can help us shed light into the mechanisms drive ecosystem processes. We studied serial propagation, where community is kept alive by taking a subsample at regular intervals and replating it fresh medium. The data usually collected consist % population for each species, several time points. In order to utilize this type data, we formulated system equations (based on generalized Lotka–Volterra model) derived conditions noninteraction. This was possible achieve reformulating problem as finding feasibility domains, which be solved number efficient algorithms. methodology provides cost‐effective way investigate interactions microbial communities.

Язык: Английский

---

Coexistence Theory for Microbial Ecology, and Vice Versa

Environmental Microbiology, Год журнала: 2025, Номер 27(3)

Опубликована: Март 1, 2025

ABSTRACT Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross‐pollination. Here we explore opportunities stronger integration of ecological theory into research (and vice versa) through the lens so‐called “modern” coexistence theory. Coexistence can be used to disentangle contributions different mechanisms (e.g., resource partitioning, environmental variability) make species coexistence. We begin with a short primer on fundamental concepts theory, an emphasis relevance communities. next present systematic review, which highlights paucity empirical applications systems. In light this gap, then identify and discuss ways which: (i) help answer applied questions particularly spatio‐temporally heterogeneous environments, (ii) experimental systems leveraged validate advance Finally, address several unique often surmountable challenges posed by systems, as well some conceptual limitations. Nevertheless, thoughtful presents wealth advancement both ecology.

Язык: Английский

---

Full factorial construction of synthetic microbial communities

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 5, 2024

Abstract Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and find optimal consortia. At moment, this accomplished through either painstaking, labor intensive liquid handling procedures, or use state-of-the-art microfluidic devices. Here we present a simple, rapid, low-cost, highly accessible methodology for assembling all possible combinations library strains, which can be implemented with basic laboratory equipment. To demonstrate usefulness methodology, construct set consortia from eight Pseudomonas aeruginosa empirically measure community-function landscape biomass productivity, identify highest yield community, that lead its function. This easy implement, inexpensive will make assembly easily laboratories.

Язык: Английский

---