Environment Animals Pets Dogs Pet dogs can help teens' mental health Breakthroughs, discoveries, and DIY tips sent every weekday. It's old news that having a dog provides a lot of benefits. Playing with a pooch can help our brains concentrate and relax, a family dog can help prevent food allergies in children, and even fulfill our primal need to nurture. They also may have some sway over some of the tiniest organisms around--the microbes that live in our bodies. A study published December 3 in the journal found that the family dog prompts changes in our gut microbiome that result in better mental health.

Aging is a highly complex and heterogeneous process that progresses at different rates across individuals, making biological age (BA) a more accurate indicator of physiological decline than chronological age. While previous studies have built aging clocks using single-omics data, they often fail to capture the full molecular complexity of human aging. In this work, we leveraged the Human Phenotype Project, a large-scale cohort of 10,000 adults aged 40-70 years, with extensive longitudinal profiling that includes clinical, behavioral, environmental, and multi-omics datasets spanning transcriptomics, lipidomics, metabolomics, and the microbiome. By employing advanced machine learning frameworks capable of modeling nonlinear biological dynamics, we developed and rigorously validated a multi-omics aging clock that robustly predicts diverse health outcomes and future disease risk. Unsupervised clustering of the integrated molecular profiles from multi-omics uncovered distinct biological subtypes of aging, revealing striking heterogeneity in aging trajectories and pinpointing pathway-specific alterations associated with different aging patterns. These findings demonstrate the power of multi-omics integration to decode the molecular landscape of aging and lay the groundwork for personalized healthspan monitoring and precision strategies to prevent age-related diseases.

The gut contents act like a microscopic time machine into pre-Hispanic Mexico. Breakthroughs, discoveries, and DIY tips sent every weekday. Underneath the remains of an ancient young adult man and his preserved feces lies a microscopic world. These microorganisms beneath the cloth hold clues to what the world may have looked like hundreds of years ago. Now, a new look at a 1,000-year-old mummy called the Zimapán man could tell us what ancient Mesoamericans ate, where they lived, and show us how much our world has changed since.

Detecting anomalies in irregularly sampled multi-variate time-series is challenging, especially in data-scarce settings. Here we introduce an anomaly detection framework for irregularly sampled time-series that leverages neural jump ordinary differential equations (NJODEs). The method infers conditional mean and variance trajectories in a fully path dependent way and computes anomaly scores. On synthetic data containing jump, drift, diffusion, and noise anomalies, the framework accurately identifies diverse deviations. Applied to infant gut microbiome trajectories, it delineates the magnitude and persistence of antibiotic-induced disruptions: revealing prolonged anomalies after second antibiotic courses, extended duration treatments, and exposures during the second year of life. We further demonstrate the predictive capabilities of the inferred anomaly scores in accurately predicting antibiotic events and outperforming diversity-based baselines. Our approach accommodates unevenly spaced longitudinal observations, adjusts for static and dynamic covariates, and provides a foundation for inferring microbial anomalies induced by perturbations, offering a translational opportunity to optimize intervention regimens by minimizing microbial disruptions.

Synthetic molecular communication (SMC) is a key enabler for future healthcare systems in which Internet of Bio-Nano-Things (IoBNT) devices facilitate the continuous monitoring of a patient's biochemical signals. To close the loop between sensing and actuation, both the detection and the generation of in-body molecular communication (MC) signals is key. However, generating signals inside the human body, e.g., via synthetic nanodevices, poses a challenge in SMC, due to technological obstacles as well as legal, safety, and ethical issues. Hence, this paper considers an SMC system in which signals are generated indirectly via the modulation of a natural in-body MC system, namely the gut-brain axis (GBA). Therapeutic GBA modulation is already established as treatment for neurological diseases, e.g., drug refractory epilepsy (DRE), and performed via the administration of nutritional supplements or specific diets. However, the molecular signaling pathways that mediate the effect of such treatments are mostly unknown. Consequently, existing treatments are standardized or designed heuristically and able to help only some patients while failing to help others. In this paper, we propose to leverage personal health data, e.g., gathered by in-body IoBNT devices, to design more versatile and robust GBA modulation-based treatments as compared to the existing ones. To show the feasibility of our approach, we define a catalog of theoretical requirements for therapeutic GBA modulation. Then, we propose a machine learning model to verify these requirements for practical scenarios when only limited data on the GBA modulation exists. By evaluating the proposed model on several datasets, we confirm its excellent accuracy in identifying different modulators of the GBA. Finally, we utilize the proposed model to identify specific modulatory pathways that play an important role for therapeutic GBA modulation.

We studied a generalized question: chronic diseases like ME/CFS and long COVID exhibit high heterogeneity with multifactorial etiology and progression, complicating diagnosis and treatment. To address this, we developed BioMapAI, an explainable Deep Learning framework using the richest longitudinal multi-omics dataset for ME/CFS to date. This dataset includes gut metagenomics, plasma metabolome, immune profiling, blood labs, and clinical symptoms. By connecting multi-omics to a symptom matrix, BioMapAI identified both disease- and symptom-specific biomarkers, reconstructed symptoms, and achieved state-of-the-art precision in disease classification. We also created the first connectivity map of these omics in both healthy and disease states and revealed how microbiome-immune-metabolome crosstalk shifted from healthy to ME/CFS.

With all the advances in both the science of aging and artificial intelligence (AI), we are in a propitious position to accurately and precisely determine who is at high risk of developing Alzheimer's disease years before signs of even mild cognitive deficit. It takes at least 20 years for aggregates of misfolded β-amyloid and tau proteins to accumulate in the brain along with neuroinflammation that they incite. This provides a long window of opportunity to get ahead of the pathobiological process, both for prediction and prevention. A family history of Alzheimer's and the presence of genetic variants in the APOE4 (apolipoprotein E4) allele indicate an increased risk, as does a polygenic risk score that is based on the combined influence of many genetic variants. However, each of these clues provides little insight about when initial symptoms would likely present.

This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a computationally efficient inference algorithm based on variational inference to approximate the posterior distribution. We demonstrate the potential of the new approach on various synthetic datasets and for predicting human health status based on microbiome profile. Our analysis incorporates data pooled from multiple microbiome studies, along with a comprehensive comparison with other benchmark methods. Results in synthetic datasets show that the proposed approach has superior support recovery property when the underlying regression coefficients share a common sparsity structure across different tasks. Our experiments on microbiome classification demonstrate the utility of the method in extracting informative taxa while providing well-calibrated predictions with uncertainty quantification and achieving competitive performance in terms of prediction metrics. Notably, despite the heterogeneity of the pooled datasets (e.g., different experimental objectives, laboratory setups, sequencing equipment, patient demographics), our method delivers robust results.

The Alzheimer's Disease Analysis Model Generation 1 (ADAM) is a multi-agent large language model (LLM) framework designed to integrate and analyze multi-modal data, including microbiome profiles, clinical datasets, and external knowledge bases, to enhance the understanding and detection of Alzheimer's disease (AD). By leveraging retrieval-augmented generation (RAG) techniques along with its multi-agent architecture, ADAM-1 synthesizes insights from diverse data sources and contextualizes findings using literature-driven evidence. Comparative evaluation against XGBoost revealed similar mean F1 scores but significantly reduced variance for ADAM-1, highlighting its robustness and consistency, particularly in small laboratory datasets. While currently tailored for binary classification tasks, future iterations aim to incorporate additional data modalities, such as neuroimaging and biomarkers, to broaden the scalability and applicability for Alzheimer's research and diagnostics.

Understanding the complex interactions within the microbiome is crucial for developing effective diagnostic and therapeutic strategies. Traditional machine learning models often lack interpretability, which is essential for clinical and biological insights. This paper explores the application of symbolic regression (SR) to microbiome relative abundance data, with a focus on colorectal cancer (CRC). SR, known for its high interpretability, is compared against traditional machine learning models, e.g., random forest, gradient boosting decision trees. These models are evaluated based on performance metrics such as F1 score and accuracy. We utilize 71 studies encompassing, from various cohorts, over 10,000 samples across 749 species features. Our results indicate that SR not only competes reasonably well in terms of predictive performance, but also excels in model interpretability. SR provides explicit mathematical expressions that offer insights into the biological relationships within the microbiome, a crucial advantage for clinical and biological interpretation. Our experiments also show that SR can help understand complex models like XGBoost via knowledge distillation. To aid in reproducibility and further research, we have made the code openly available at https://github.com/swag2198/microbiome-symbolic-regression .