Medicine-food homology (MFH) substances constitute a distinctive category of functional food ingredients deeply rooted in traditional dietary wisdom. Although their therapeutic potential is increasingly acknowledged, a comprehensive framework that mechanistically links their ecological roles in the gut to systemic health benefits remains necessary to advance modern food science and precision nutrition. This review synthesizes evidence from multi-omics studies, in vitro models, and animal and human research to establish MFH substances as dietary-derived ecological engineers of the gut microbiota. We focus on three core mechanisms of action: niche construction, metabolic reprogramming, and symbiosis induction. Furthermore, we evaluate emerging strategies—such as AI-driven formulation, phage-assisted delivery, and CRISPR-engineered probiotics—designed to overcome bioavailability challenges and enable personalized applications. Our analysis confirms that MFH substances reshape the gut ecosystem, enriching keystone taxa (e.g., Akkermansia , Bifidobacterium ) and stimulating bioactive metabolites (SCFAs, indoles, secondary bile acids). These metabolites activate host receptors (GPR43, AhR, FXR) to orchestrate multi-organ homeostasis, explaining their beneficial roles in metabolic disorders (e.g., obesity, NAFLD) via the gut–liver axis and neurological conditions (e.g., cognitive decline, depression) via the gut–brain axis. This provides a scientific basis for the ancient "preventive treatment" principle. Integrating this ecological insight with modern food technology positions MFH as a cornerstone for next-generation, microbiota-targeted functional foods, shifting dietary practice from passive intake to active health management. Beyond enriching well-recognized keystone taxa such as Akkermansia and Bifidobacterium , MFH interventions consistently modulate a broader spectrum of beneficial commensals, including Lactobacillus , Lachnospiraceae , Blautia , Romboutsia , and Prevotella , thereby supporting a more resilient and functionally diverse gut ecosystem. • Repositions MFH as dietary ecological engineers of gut microbiota. • Proposes AI/phage/CRISPR tools to boost MFH bioavailability. • Mechanistically links ancient preventive wisdom to food science. • Orchestrates multi-organ health via microbiota-derived metabolites. • Establishes a scientific basis for the "preventive treatment" principle.

Evolutionary "fitness" is operationalized in many different ways in models. Its role is to quantify that which is favored by natural selection. Generally, short-term ability to survive and reproduce (e.g. expected number of surviving offspring) is assigned to genotypes or phenotypes and used to non-trivially derive longer-term quantities (e.g. invasion rate or fixation probability) that provide insight as to which organismal strategies tend to evolve due to natural selection. Assigned fitness operationalizations either explicitly or implicitly specify organismal vital rates (i.e. births, deaths, organismal growth). Derived operationalizations also depend on assumptions regarding demographic stochasticity; environmental stochasticity; feedbacks whereby births, deaths, and organismal growth cause environmental change; and the impact of migration and niche construction on which environment is experienced. The choice of derived operationalization can impact conclusions, as we illustrate for the evolution of bet hedging when treated by invasion probability vs expected Malthusian parameter within an adaptive dynamics approach. After reviewing existing derived fitness operationalizations, we propose a new one that meets the particular challenges posed by balancing selection. Population genetic models generally sidestep ultra-high-dimensional phenotype and genotype spaces by deriving the long-term evolutionary fate/fitness of a lower-dimensional set of genetically encoded "strategies." Strategies (e.g. costly developmental commitment to producing armaments) are causally upstream from realized phenotypes (e.g. armament size), but downstream from how an organism's early environment (e.g. maternal effects) might inform developmental commitments. While selection is best understood in terms of differences in organismal vital rates, its derived outcomes are most easily understood as properties of genetic lineages.

Human collective intelligence (CI)-the capacity of groups to solve problems, make decisions and acquire knowledge beyond individual capabilities-is here understood as an emergent phenomenon that evolved in our lineage from a distinct trajectory of epistemic niche construction (ENC), and progressively sustained the latter. Humans systematically alter their informational landscapes in materially visible ways by creating enduring spatial and artefactual scaffolds for improved cognitive performance and social coordination. In this paper, we propose a set of criteria to define ENC and track its emergence in the archaeological record. These criteria highlight the importance of persistent, publicly accessible and evolutionarily incremental modifications that sustained behavioural coordination among individuals in space and time. We apply this framework to three major domains of material culture: the structuring of space for collective action, the culturalization of the human body and the emergence of exosomatic artefacts to store coded information. We argue that these practices did not merely externalize knowledge but progressively transformed material culture and environments into targeted epistemic infrastructures able to scaffold and amplify group-level performances characteristic of CI, thus shedding light on the evolution of human cognition and social organization. This article is part of the theme issue 'The evolution of collective intelligence'.

ABSTRACT Miranda Fricker’s concept of “epistemic injustice” has been crucial in revealing how identity prejudice can wrong individuals in their capacity as knowers. Yet this framework implicitly presupposes neurotypical norms of social communication and interaction as the baseline of epistemic exchange. In this paper, we argue that such presuppositions obscure how epistemic injustices against neurodivergent people often emerge not through identity prejudice but rather through socio-material environments that privilege certain neurotypes over others. Drawing on frameworks such as the neurodiversity paradigm and niche construction theory, we reframe the concept of epistemic injustice as a distributed phenomenon that is enacted through the interaction of cognitive agents, cultural practices, and material affordances to accommodate these more structural forms of epistemic injustice. In particular, we argue that José Medina’s concept of “meta-lucidity” can be used as a methodological resource for reconstructing epistemic niches such that neurodivergent perspectives are given a role in co-constituting the fabric of a “neurodiversified” social imagination.

Ecosystem Disturbance as a Niche Construction Strategy for Invasive Species

Evolutionary mechanisms have enabled humans to transform Earth systems. Because the resulting Anthropocene systems are highly interdependent and dynamically evolving, often with accelerating rates of cultural and technological evolution, One Earth and One Health must be framed and addressed in a holistic fashion. An agile, evolutionary, system-of-systems, convergence paradigm, which is based on a partially quantifiable, scientifically falsifiable theoretical framework, can be used to systematically identify, decompose, characterize, and then converge a nested, evolutionary ensemble of geophysical, biophysical, sociocultural, and sociotechnical systems. The paradigm includes individual organisms (spanning plants, fungi, and animals) engaging in niche construction in a global meta-ecosystem that integrates the deep evolutionary history of all Anthropocene systems. To coherently span the vast range of scales, the paradigm is divided into a somatic realm (externally oriented with respect to individual organisms) that can be applied at global, regional, urban, and local scales, as well as a visceral realm (internally oriented with respect to individual organisms) that includes organs, cells, organelles, genes, and molecules. The paradigm requires a causally coherent evolutionary framework, cross-scale, modular, and hierarchical conceptual models (based on a common language and reconciled ontology), with agile, extensible, and scalable computational frameworks, an associated decision-support system, and an educational pedagogy.

To present Ze Theory as an interpretive framework for quantum mechanics, reformulating known quantum phenomena in the language of Ze-observers—quantum systems by construction that possess proper time and act under conditions of struggle for existence. A Ze-observer is defined as a tuple (H, ρ_Z, {M_i}, τ_Z, θ_Z), where H is a Hilbert space, ρ_Z is a belief state, {M_i} is a POVM, τ_Z is a proper time counter, and θ_Z is a prediction threshold. The dynamics of τ_Z follow the rule: for a correct prediction (S-event), τ_Z is preserved; for an incorrect prediction (T-event), τ_Z decreases by 1. Two fundamental survival strategies of Ze are derived: internal adaptation (filtering of rare events) and external adaptation (niche construction). Within the proposed framework: (1) the arrow of time emerges from the decrease of τ_Z during T-events; (2) aging is interpreted as the dominance of the filtering strategy; (3) quantum entanglement corresponds to Ze generated by a common parent; (4) the double-slit experiment is reinterpreted through strategy choice; (5) spacetime is constructed from partial order and the commutation matrix of POVMs. Ze Theory offers a coherent interpretive framework for quantum mechanics, consistent with evolutionary epistemology. Open problems include deriving the Born rule from selection pressure, Lorentz invariance from Ze network dynamics, and the emergence of gravity.

Collective social niche construction shaping adaptive social networks.

Phenotypic variation within a single genotype under the same environment (intragenetic variation), the biologically meaningful part of , is frequently treated as a statistical nuisance rather than a biological reality, yet it represents an evolutionary driver of fitness that remains poorly integrated into evolutionary theory. The mechanism that translates such stochasticity into deterministic developmental phenotypic outcomes is not well understood. Here, we test a cumulative stochasticity model using wing polyphenism of the pea aphid (Acyrthosiphon pisum), where asexual mothers produce winged instead of wingless offspring in response to tactile cues. The model predicts that stochastic variation in maternal locomotor behavior alters the rate of tactile cue accumulation and thereby influences the probability of producing winged offspring. We demonstrate that maternal locomotor activity acts as a "stochastic pacemaker", where an individual's movement determines the rate at which it actively constructs its environment and accumulates environmental cues. Our results reveal that genotypes differ significantly in both mobility and the temporal pattern of wing induction, with behavioral variation explaining approximately 20% of the total phenotypic variance across genotypes. Crucially, we show that maternal mobility increases progressively during crowding, accompanied by significant temporal heteroscedasticity. This expanding variance and increase in mean suggest that initial, trivial stochasticity is magnified into systematic behavioral divergence through the integration of environmental signals. By demonstrating that total accumulated locomotor activity predicts offspring phenotype, we provide a mechanistic bridge between transient behavioral noise and stable morphological shifts. More broadly, our work reveals that is a dynamic product of behavioral history, suggesting a fundamental role for individual-level niche construction in generating macro-phenotypic diversity.

The present study examined the strategies of personal niche construction among Hungarian physicians at the workplace through basic psychological needs satisfaction and territoriality, within the socio-physical context of their workplace. The study aimed to delineate the latent patterns underlying participants’ organization, to characterize the attributes differentiating each subgroup, and to examine how these distinctive configurations contributed to strategies of niche construction within the workplace. A cross-sectional online survey was conducted among Hungarian physicians who have at least a degree in medicine and are currently pursuing medical practice (N = 261). Participants completed validated instruments assessing basic psychological needs satisfaction, workplace territoriality, and occupational well-being. Exploratory factor analysis identified underlying dimensions of need fulfillment and territoriality, followed by latent profile analysis to classify physicians into subgroups based on these patterns. Multinomial logistic regression and ANOVAs assessed demographic predictors and group differences in work satisfaction, fulfillment, interpersonal disengagement, exhaustion, and turnover intention. A three-profile solution emerged, reflecting distinct personal niche construction strategies: (1) Effortful self-expression (2), “Effortless self-expression”, and (3) “Low engagement in self-expression”. The profiles were named based on the quality of person-environment fit. Profiles differed significantly in basic psychological needs satisfaction, professional fulfillment, and interpersonal disengagement (p < 0.01). Profiles also differed significantly in work satisfaction, professional fulfillment, and interpersonal disengagement, with the “Low engagement in self-expression” group reporting the least favorable outcomes. The findings highlight the relevance of socio-ecological perspectives in occupational health, demonstrating that physicians’ capacity to construct, claim, and maintain their professional niches serves as a central mechanism of resilience in complex healthcare systems. Supporting autonomy, competence, and balanced ownership of workspace may sustainably foster physicians’ well-being and engagement.

This article explores the historical development of evolutionary biology-from Natural Theology to the Modern Synthesis (MS)-and the ongoing debate around the Extended Evolutionary Synthesis (EES). Over the past 2,500 years, evolutionary thinking has emerged from the interplay between empirical discoveries and dominant philosophical paradigms. Beginning with Aristotle and Saint Augustine, we trace how Darwin and Wallace introduced a scientific framework grounded in natural mechanisms. In the early 20th century, the MS unified Mendelian genetics and Darwinian selection, forming a gene-centered model of evolution focused on mutations and population dynamics. In recent decades, discoveries in epigenetics, phenotypic plasticity, symbiosis, niche construction, and cultural inheritance have challenged the explanatory scope of MS. The EES seeks to incorporate these processes not by discarding Darwinian principles, but by reinterpreting them through a systems biology lens. This mostly represents a conceptual shift in focus: from linear, gene-driven causality to multilevel, reciprocal, and environmentally embedded dynamics. While gaining traction, the EES has been criticized for its lack of formal models and predictive frameworks, remaining a contested proposal. Ultimately, evolutionary biology continues to evolve as a powerful scientific tradition, driven by humanity's enduring quest to understand the origins and evolution of life on Earth.

There have been numerous attempts to examine Indigenous cultures from a scientific and evolutionary perspective. In this work, however, there has been little acknowledgment of how the study of biological evolution is changing. I examine evidence of the way Indigenous cultures think about nonhumans and examine concepts of creation and creator figures in relation to Niche Construction, a 21st century evolutionary concept that examines how organisms shape both their own environments and those of other species by studying how Natural Selection can act upon how most organisms impact the survival and existence of other species. I focus this comparison on how many Indigenous Plains cultures of North America regard wolves as being creator figures within the context of the way they experience their environments. Ecological studies revealed that in 30 years since wolf reintroduction to Yellowstone, this species has reshaped the ecology of many other species in the park ecosystem. I argue that in the belief systems of Indigenous peoples, this restructuring is tantamount to an Act of Creation, and that Indigenous Americans recognized that wolves filled both this role, as well as a role in helping Indigenous cultures adjust to the environments of North America as they arrived on this continent over the last 20,000 years. I also consider the relationship from the wolves’ perspective. This concept of creation is rooted in ecology and evolutionary biology, and does not involve supernatural anthropomorphic beings the way Western stories of creation do.

The combined effects of plateau pikas and yak grazing on the distribution or occupancy of endemic passeridae birds on the Qinghai-Tibetan plateau, China remain largely unknown. To assess habitat selection patterns within the frameworks of niche construction theory and the rivet hypothesis, we measured the occupancy rates of passeridae species along five sample strips of transects established in a treeless ecosystem. Each transect was surveyed three times within each seasonal sampling window (spring, summer, and autumn 2024), and repeated visits were treated as detection occasions for occupancy modeling. We used plateau pika density and yak grazing patterns as key variables to investigate their influence on the occupancy of alpine passeridae birds. We found that the occupancy of both the White-rumped and Rufous-necked Snowfinch was positively associated with proximity to yak bedding sites and high densities of plateau pika burrows. However, the occupancy of both species declined with increasing distance from yak bedding areas. In contrast, the Ground Tit showed no detectable association with these variables. This strong interspecific variation underscores the importance of disentangling mechanistic linkages among large herbivores, ecosystem engineers, and avian niche specialization in this fragile biome. Further research should explore how cross-taxa interactions mediate habitat availability and species resilience under ongoing environmental change.

Abstract Intraspecific trait variation (ITV) can be important for population performance in a variable and changing environment because individuals with different traits have different fitness responses. Furthermore, there are three mechanisms via which individuals can interact with their environment to potentially improve fitness: niche conformance, niche construction and niche choice (NC 3 ). These processes become increasingly important in the presence of environmental change, but there is still no mathematical modelling framework that would unite the effects of ITV and the NC 3 mechanisms. In this paper, we build a general model incorporating ITV and two of the NC 3 mechanisms (niche conformance and niche construction, NC 2 ) to investigate how they affect populations in a changing and variable environment. We quantify their effects on average individual fitness using non‐linear averaging approaches. Our method allows us to answer the question of what would have happened if individuals in the study system did not have ITV or did not perform NC 2 mechanisms. The answer to this question depends on the shapes of the fitness function and the NC 2 functions and can be estimated via a Taylor approximation. We apply the method to two case studies: great tits adjusting their laying date to yearly changes in vegetation green‐up and a host–parasite system in which the parasite changes its environment by immunodepression of the host. In the great tits, we found a slight negative effect of ITV and a slight positive effect of niche conformance on the population fitness. In the host–parasite system, we found ITV to have no effect without niche construction, but with niche construction, ITV decreased virulence. Also, niche construction had a strong negative effect on virulence. Our extension of non‐linear averaging theory, combining intraspecific and environmental variation, niche conformance and niche construction, allowed us to assess average population performance with those mechanisms at play. However, how well one can estimate such performance depends on the type of data available. This framework can be extended further to niche choice and evolution; therefore, including all processes that can change the match between individuals and their environment.

Functional differentiation and niche construction: Divergent responses of bacterial communities in livestock manure co-composting to PAHs stress and potential mechanisms for contaminated soil remediation

Engineered nanovesicles amplify the crosstalk between neurogenesis and angiogenesis for pro-regenerative niche construction

Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.

Why should we still care what Herbert Spencer (1820–1903) had said about evolution? We should care about what Spencer had said, for one last time, when it comes to social evolution and social sciences, because Spencer had invented some of the most influential misunderstandings about biological and social evolution despite being a quasi-evolutionist at best and a pseudo-evolutionist at worst. His four key ideas about evolution include: 1) evolution as a universal phenomenon; 2) evolution produces “survival of the fittest”; 3) evolution is development as unfolding a design via differentiation and integration; 4) human society is a Super-organism that requires both a structure and functions. I show that none of them is valid, even though Spencer’s pseudo-evolutionism had penetrated deeply into our understanding of social evolution. In place of Spencer’s pseudo-evolutionary organicism and structural functionalism approach, we should adopt a social niche construction (SNC)-based approach toward human society, which is genuinely social evolutionary. I then single out Thorstein Veblen’s Theory of the Leisure Class and Norbert Elias’s The Court Society as quintessential SNC theories, and underscore that some key principles of SNC have been partially responsible for their explanatory power, even though SNC was not known during their time.

BackgroundObservational studies in vinegar fermentation suggested a temporal succession between Bacillus cereus and Acetilactobacillus jinshanensis. Here, we reinterpret this pattern in terms of facilitation and niche construction rather than classical competitive succession. We test this ecological model in a distinct biological context — stingless bee larval food — by combining organism-specific interactomes (GenPPI), hub topology (BriCe outliers), and genome-scale metabolic modeling.ResultsThe B. cereus interactome shows a diversified hub architecture enriched in environmental sensing, transport, stress response, and secreted effectors—consistent with a pioneer that probes and actively modifies a fresh niche. In contrast, the A. jinshanensis interactome is dominated by a cytoplasm-centric, translation-heavy super-hub—consistent with a fast-growth specialist optimized for efficient biomass production once resources are simplified and available. Flux analyses indicate capacities for xenobiotic processing and terpenoid precursor synthesis in both organisms, but the topological signatures and pathway enrichments align with complementary roles: niche construction and conditioning by B. cereus, followed by rapid exploitation by A. jinshanensis.conclusionOur findings support a facilitation-based ecological mechanism: B. cereus functions as an early colonizer and niche engineer—sensing, detoxifying, and depolymerizing complex substrates via secreted enzymes—while A. jinshanensis is a fast-growth specialist whose dominance emerges in the conditioned niche. This reframing resolves the apparent contradiction between a “fast-growth” profile and late-stage dominance and provides mechanistic, systems-level support for complementary roles across distinct environments.

Advancements and challenges in carrier-mediated enhancement of partial nitritation-anammox (PN/A): Mechanisms and optimisation strategies - a review.