Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

MOTIVATION

Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations.

RESULTS

We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

AVAILABILITY AND IMPLEMENTATION

Microbiome Modelling Toolbox and tutorials are freely available as part of the COBRA Toolbox at https://git.io/microbiomeModelingToolbox.

Variation in follow-up for children born very preterm in Europe

BACKGROUND

Children born very preterm (<32 weeks of gestation) face high risks of neurodevelopmental and health difficulties compared with children born at term. Follow-up after discharge from the neonatal intensive care unit is essential to ensure early detection and intervention, but data on policy approaches are sparse.

METHODS

We investigated the characteristics of follow-up policy and programmes in 11 European countries from 2011 to 2022 using healthcare informant questionnaires and the published/grey literature. We further explored how one aspect of follow-up, its recommended duration, may be reflected in the percent of parents reporting that their children are receiving follow-up services at 5 years of age in these countries using data from an area-based cohort of very preterm births in 2011/12 (N = 3635).

RESULTS

Between 2011/12 and 22, the number of countries with follow-up policies or programmes increased from 6 to 11. The policies and programmes were heterogeneous in eligibility criteria, duration and content. In countries that recommended longer follow-up, parent-reported follow-up rates at 5 years of age were higher, especially among the highest risk children, born <28 weeks' gestation or with birthweight <1000 g: between 42.1% and 70.1%, vs. <20% in most countries without recommendations.

CONCLUSIONS

Large variations exist in follow-up policies and programmes for children born very preterm in Europe; differences in recommended duration translate into cross-country disparities in reported follow-up at 5 years of age.

Plant biochemical genetics in the multiomics era

Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.