Inflammatory bowel disease (IBD), a chronic relapsing inflammatory disorder of the gastrointestinal tract, significantly increases the risk of progression to colorectal cancer (CRC). Emerging studies highlight the critical roles of gut microbial dysbiosis and sustained intestinal inflammation in driving this pathological transformation. Probiotics and prebiotics, as modulators of gut microbial ecology, have attracted considerable attention as potential interventions to restore microbial balance, regulate immune responses, and mitigate carcinogenic processes. In this review, we integrate the interplay mechanisms among inflammation, microbiota, and immunity in IBD-associated colorectal carcinogenesis (IBD-CRC), with a focus on the roles of probiotics and prebiotics in microbial remodeling, enhancement of epithelial barrier integrity, inhibition of inflammatory signaling, and activation of antitumor immunity. Furthermore, we discuss preclinical and clinical evidence supporting their efficacy in delaying or preventing IBD-CRC. The review also provides perspectives on future customized synbiotic strategies in microbiota-targeted therapy and cancer prevention.
Darby Steinman, Alyssa P. Petersen, Yasmi Chibber
et al.
Abstract The composition of the vaginal microenvironment has significant implications for gynecologic and obstetric outcomes. Where a Lactobacillus-dominated microenvironment is considered optimal, a polymicrobial environment is associated with increased risk for female reproductive diseases. Recent work examined bacteria-derived extracellular vesicles (bEVs) as an important mode of microbe-host communication that may influence reproductive outcomes. However, in order to communicate with female reproductive tissues, bEVs must penetrate the protective cervicovaginal mucus barrier. We demonstrate increased diffusion of bEVs compared to whole bacteria. Additionally, we evaluate the uptake of bEVs by, and the resulting effects on, human vaginal epithelial, endometrial, and placental cells, highlighting potential mechanisms of action by which vaginal dysbiosis contributes to gynecologic and obstetric diseases. Taken together, our work demonstrates the ability of bEVs to mediate female reproductive outcomes and highlights their potential as therapeutic modalities for treating dysbiosis and dysbiosis-associated diseases in the female reproductive tract.
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is the design of reliable feedback strategies to regulate cellular behavior and collective biological functions. In this article, we review recent advances in multicellular feedback control, where sensing, computation, and actuation are distributed across different cell populations within synthetic microbial consortia, giving rise to biological multiagent control systems governed by molecular communication. From a control-theoretic perspective, these consortia can be interpreted as distributed biomolecular control systems, where coordination among populations replace embedded regulation. We survey theoretical frameworks, control architectures, and modeling approaches, ranging from aggregate population-level dynamics to spatially aware agent-based simulations, and discuss experimental demonstrations in engineered \textit{Escherichia coli} consortia. We highlight how distributing control functions across populations can reduce metabolic burden, mitigate retroactivity, improve robustness to uncertainty, and enable modular reuse of control components. Beyond regulation of gene expression, we discuss the emerging problem of population composition control, where coordination among growing and competing cell populations becomes an integral part of the control objective. Finally, we outline key open challenges that must be addressed before multicellular control strategies can be deployed in real-world applications such as biomanufacturing, environmental remediation, and therapeutic systems. These challenges span modeling and simulation, experimental platform development, coordination and composition control, and long-term evolutionary stability.
Mackenzie B. Best, Zohreh Kazemi Motlagh, Virginia T. McLemore
et al.
ABSTRACT Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries, since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here, we combined microbial cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in south-central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that are related to inorganic nitrogen- and organic carbon-oxidizing taxa. Generally, rRNA transcript libraries contain many of the same organisms as rRNA gene libraries, indicating that most of these populations are active. Differences among total and active microbial communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.IMPORTANCENew Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine waste. However, the deposits did contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine wastes.
Abstract Background Most winter-active mammals experience protein restriction. Gut microbiota is a key regulator of host energy homeostasis during nutrient deficiency, yet cross talk between microbiota and factors (e.g., hormones, signaling molecules) that regulate host energy metabolism in a low-protein (LP) context has not been studied sufficiently. Result The LP diet triggered the hepatic FGF21 adaptive metabolic pathway, which increased thermogenesis and reduced body weight, and this adaptive response was dependent on the composition and function of gut microbiota. Specifically, the LP diet induced a reshaping of the gut microbiota, altering its metabolic profile to increase deoxycholic acid levels and thereby increasing UCP1-induced thermogenesis of brown adipose tissue in an FGF21-dependent manner. Fecal transplantation with LP-associated microbiota increased thermogenesis through activation of GCN2-eIF2α-FGF21 signaling. Supplementation of the LP diet with yak fecal bacteria in plateau pika reduced UCP1-associated thermogenesis by altering the gut microbiome, decreasing deoxycholic acid production, suppressing activation of GCN2-eIF2α-FGF21 signaling, and alleviating LP-induced weight loss. Conclusions Our study reveals an association between the gut microbiota and LP diet-associated regulation of FGF21 signaling and thermogenesis and further demonstrates that this relationship is influenced by interspecies microbial transfer, indicating a critical mechanism whereby horizontal microbial exchange between sympatric species enhances host energy homeostasis. These findings provide novel insights into our understanding of the adaptations of mammals to high-elevation environments. Video Abstract
Lionfishes (Pterois spp.), originally native to the Indo-Pacific and Red Sea, have become one of the most invasive marine species globally, including the recent establishment in the Mediterranean Sea. This study investigates the microbiota of lionfish to explore its potential role in their invasion success and establishment. Using high-throughput sequencing and microbiota analyses, we characterized the species-specific core microbiome and identified habitat-specific markers across different regions (Red Sea, Mediterranean Sea, Caribbean, and aquarium populations) and organs. Focusing on the Mediterranean invasion, we tracked lionfish distribution and population dynamics along the Israeli coastline from 2017 to 2023, monitoring size, seasonal trends, and depth preferences. Our findings reveal that lionfish initially established themselves in deeper waters before expanding to shallower habitats, with a gradual increase in population size and body length over time. From a microbial aspect, we compared the microbiota of lionfish organs and identified a similar pattern (Photobacterium), to Earlier Lessepsian migrants fish species. This study provides novel insights into the interactions between microbiota and host ecology, shedding light on the mechanisms that may support the successful invasion. This study contributes to the understanding of lionfish invasion dynamics in the Mediterranean. It highlights the microbiota as an integral component for studying the ecological and biological mechanisms underpinning invasive species’ success and establishment of lionfish.
Robert Fontan, Christopher M. Perez, Ashish Adhikari
et al.
1. Expert knowledge elicitation provides information to characterize ecological systems and management options. Linking expert knowledge elicitation with a curated question catalog supports a community of practice for ongoing improvement of question quality. 2. The MetaQuestion web app we introduce here draws on the PlantQuest catalog of questions addressing applied plant ecology and management options, making the catalog available in a flexible form for organizers of expert knowledge elicitation. Organizers can select among questions in the catalog, modify them as needed, and generate an instrument customized to their elicitation project. MetaQuestion makes available PlantQuest questions specialized for the study of invasive species such as pathogens and arthropod pests, such as geographic analyses of prevalence and network analysis of the movement of plant materials. 3. Experts answer questions in the customized instrument and their responses are compiled. For settings where internet access may be sporadic, there are options to download the instrument for experts' work and then upload responses later. MetaQuestion provides the resulting dataset in a CSV file for analysis in users' choice of software 4. Development of the PlantQuest catalog and the MetaQuestion app is ongoing, incorporating lessons learned from applications of the app. The MetaQuestion app could also be adapted to address questions from other subject areas.
The sustainable restoration of intermittent streams has become a critical priority in contemporary urban planning, particularly as cities confront the dual challenges of ecological degradation and climate change. In Tehran, decades of rapid urbanization and poor management practices have confined natural streams into rigid concrete channels, eroding their ecological value and disconnecting them from community life. This paper introduces an ecological and sustainability-oriented framework for the restoration of the Darband and Darabad river valleys, highlighting their potential to function as ecological corridors that support biodiversity, thermal regulation, cultural identity, and urban resilience. The study employs a systematic methodology that integrates ecological engineering, landscape design, hydrological modeling, and participatory planning. Findings suggest that restoring these river valleys through sustainable strategies, such as the creation of active green networks, multifunctional public spaces, and resilient hydrological systems, can transform them from degraded drainage corridors into life-giving urban landscapes. Moreover, the research emphasizes the necessity of linking restoration with sustainability goals to ensure long-term ecological balance, social well-being, and climate adaptation. This case study demonstrates that sustainable river restoration, when aligned with ecological design and community engagement, has the potential to reposition intermittent streams as essential infrastructures for sustainable urban development and resilience.
This paper asks whether our relationship with nature can move from human dominance to genuine interdependence, and whether artificial intelligence (AI) can mediate that shift. We examine a new ecological-design paradigm in which AI interacts with non-human life forms. Through case studies we show how artists and designers apply AI for data analysis, image recognition, and ecological restoration, producing results that differ from conventional media. We argue that AI not only expands creative methods but also reframes the theory and practice of ecological design. Building on the author's prototype for AI-assisted water remediation, the study proposes design pathways that couple reinforcement learning with plant-based phytoremediation. The findings highlight AI's potential to link scientific insight, artistic practice, and environmental stewardship, offering a roadmap for future research on sustainable, technology-enabled ecosystems.
Physics-Informed Neural Networks (PINNs) have become a popular way to infer interpretable interaction parameters from noisy microbial time series, but practitioners face many tunable design choices (loss weights, regularisers, scaling, training schedules) with little guidance, and uncertainty is rarely quantified. We present a two-part study using a DeepXDE PINN for a six-species generalised Lotka-Volterra (gLV) model with a known step input and fixed, species-specific step amplitudes, under synthetic noise. Part A: Accuracy ablation. Starting from a broad-init baseline, we systematically vary constrained initialisation, parameter scaling, L2 regularisation with loss-weighting, split training with auxiliary observations, function constraints, adaptive collocation, hyperparameter tuning, and optimisers (Adam,L-BFGS). The largest gains come from simple parameter scaling. Hyperparameter tuning and adaptive collocation achieve competitive pairwise interaction errors. Part B: Uncertainty quantification. We benchmark deep ensembles and Monte Carlo (MC) dropout and report multi-replicate fits with different initial conditions. An N=10 deep ensemble yields the best single-trajectory growth-rate accuracy, while MC-dropout provides predictive bands. Overall, scaling plus either tuning or ensembles delivers robust interaction inference; our loss-weight sweep and additional regularisation settings offer practical defaults. We release code, metrics, and figures to serve as baselines for accuracy and uncertainty quantification in microbiome PINNs.
Spencer Rugaber, Scott Bunin, Andrew Hornback
et al.
Conceptual modeling has been an important part of constructionist educational practices for many years, particularly in STEM (Science, Technology, Engineering and Mathematics) disciplines. What is not so common is using agent-based simulation to provide students feedback on model quality. This requires the capability of automatically compiling the concept model into its simulation. The VERA (Virtual Experimentation Research Assistant) system is a conceptual modeling tool used since 2016 to provide introductory college biology students with the capability of conceptual modeling and agent-based simulation in the ecological domain. This paper describes VERA and its approach to coupling conceptual modeling and simulation with emphasis on how a model's visual syntax is compiled into code executable on a NetLogo simulation engine. Experience with VERA in introductory biology classes at several universities and through the Smithsonian Institution's Encyclopedia of Life website is related.