Biology subjects

Ruiz-Moreno, A.

Publications and source records attributed to Ruiz-Moreno, A..

3 recordsLinked to original sources

bioRxiv2026

Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort:Origin, Persistence, Influencing Factors and Health Implications

The human gut virome is a key modulator of gut microbial ecology and function, yet its role in early gut ecosystem development remains poorly understood. Here, we profiled the DNA virome from 4,523 fecal and 91 breastmilk metagenomes from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT. This analysis generated a catalog of 31,205 unique vOTUs, with 31,019 detected in fecal and 248 in breastmilk samples, including 16,540 not previously reported in other databases. We find that the maternal virome is largely stable, in contrast to the infant viromes rapid diversification over time. We also identify delivery and feeding modes as major drivers of infant virome developmental trajectories, with additional influences of maternal parity, infections during pregnancy, socioeconomic factors, gestational age and infant birth weight. Notably, increased viral diversity was associated with the infant developing a food allergy. Strain-level virome profiling confirmed the maternal gut as the primary source of viruses for the infant gut, with increased sharing rates in vaginally delivered infants and with breastmilk as a secondary reservoir. We demonstrate that temperate phages frequently co-transmit with their bacterial hosts and identify multiple protein families associated with anti-defense functions enriched among maternally shared viruses. Finally, we show that DNA adenine N6-methyltransferase hin1523, together with widely active diversity-generating retroelements, promote long-term viral persistence in the infant and maternal gut. Together, these findings establish the origin, dynamics and modulating factors of the infant gut virome, along with the genetic strategies supporting its persistence in the gut ecosystem.

microbiology↗

bioRxiv2026

Gut microbiome changes over the course of multiple sclerosis differentially influence autoimmune neuroinflammation

Multiple sclerosis (MS) is the leading inflammatory and demyelinating disease of the central nervous system (CNS). MS begins with systemic inflammation and over time is compartmentalized within the CNS. Studies in humans, supported by animal experiments, suggest that the gut microbiome plays an important role in MS development. However, despite the dynamic nature of the disease, little is known on how the microbiome evolves over the course of MS and how these microbiome changes influence immune responses and disease progression. Here, using high-throughput sequencing, we identified distinct gut microbial communities with differential functional potential in MS patients stratified by time since disease onset. Importantly, using a humanized mouse model, we demonstrate that differences in microbial composition significantly impact disease outcomes. Microbiota from more recently diagnosed MS patients induced severe neuroimmune disease in mice, whereas microbiota from long-term MS patients and healthy individuals elicited only mild disease. Accordingly, we found that microbiota from earlier diagnosed MS patients exhibit a higher inflammatory potential. This was characterized by a reduced capacity to induce regulatory T cells in mice and an increased induction of pro-inflammatory cytokines in human peripheral blood mononuclear cells. Together, our results suggest that the ability of the gut microbiome to promote systemic inflammation and trigger MS pathology shifts over the course of the disease and is primarily critical during its early stages. These findings indicate that a limited therapeutic window should be considered when designing microbiome-based interventions for MS.

immunology↗

bioRxiv2024

High response diversity and conspecific density-dependence, not species interactions, drive dynamics of coral reef fish communities

Species-to-species and species-to-environment interactions are key drivers of community dynamics. Disentangling these drivers in species-rich assemblages is challenging due to the high number of potentially interacting species (the "curse of dimensionality"). We develop a process-based model that quantifies how intraspecific and interspecific interactions, and species covarying responses to environmental fluctuations, jointly drive community dynamics. We fit the model to reef fish abundance time series from 41 reefs of Australias Great Barrier Reef. We found that fluctuating relative abundances are driven by species heterogenous responses to environmental fluctuations, whereas interspecific interactions are negligible. Species differences in long-term average abundances are driven by interspecific variation in the magnitudes of both conspecific density-dependence and density-independent growth rates. This study introduces a novel approach to overcoming the curse of dimensionality, which reveals highly individualistic dynamics in coral reef fish communities that imply a high level of niche structure.

ecology↗