Murphy, O. | Search bioRxiv

bioRxiv2025

The MicroMap is a network visualisation resource for microbiome metabolism

The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for diaerent microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.

systems biology↗

bioRxiv2023

Experienced Meditators Show Multifaceted Attention-Related Differences in Neural Activity

ObjectivesMindfulness meditation (MM) is suggested to improve attention. Research has explored this using the attentional-blink (AB) task, where stimuli are rapidly presented, and a second target stimulus (T2) is often missed if presented [~]300ms after an initial target stimulus (T1). This research showed improved task-accuracy and altered neural activity after an intensive 3-month MM retreat. We tested whether these results replicated in a community sample of typical meditators. MethodsThirty-one mindfulness meditators and 30 non-meditators completed an AB task while electroencephalography (EEG) was recorded. Between-group comparisons were made for task-accuracy, event-related potential activity (posterior-N2 and P3b), theta and alpha oscillatory phase synchronisation to stimuli presentation, and alpha-power. Primary aims examined effects within time windows reported by previous research. Additional exploratory aims assessed effects across broader time windows. ResultsNo differences were detected in task-accuracy or neural activity within our primary hypotheses. However, exploratory analyses showed posterior-N2 and theta phase synchronisation effects indicating meditators prioritised attending to T2 stimuli (p < 0.01). Meditators also showed more alpha-phase synchronisation, and lower alpha-power when processing T2 stimuli (p < 0.025). ConclusionsOur results showed multiple differences in neural activity that suggested enhanced attention in meditators. The neural activity patterns in meditators aligned with theoretical perspectives on activity associated with enhanced cognitive performance. These include enhanced alpha gating mechanisms, increased oscillatory synchronisation to stimuli, and more equal allocation of neural activity across stimuli. However, meditators did not show higher task-accuracy, nor did effects align with our primary hypotheses or previous research. PreregistrationThis study was not preregistered.

neuroscience↗