Biology subjects

Spreckels, J. E.

Publications and source records attributed to Spreckels, J. E..

4 recordsLinked to original sources

bioRxiv2026

Comprehensive profiling of infant gut virome assembly reveals associations with eczema and wheeze

Infancy is a critical developmental window during which the gut ecosystem assembles and helps train the immune system, thereby setting trajectories for lifelong health. Bacteria and viruses are equally numerous in this early ecosystem, yet the gut viromes composition, dynamics, and health relevance remain poorly understood. Here, we show that the infant gut virome is diverse, dynamic, and linked to health outcomes. We performed comprehensive virome profiling of 1,110 longitudinal fecal samples from 314 mother-infant pairs from the Dutch birth cohort Lifelines NEXT using both virus-like particle enrichment (VLP) and total metagenomic sequencing (MGS). We find only 18.9% compositional overlap between the VLP- and MGS-metaviromes, with VLP recovering the active virome and most novel species and MGS predominantly capturing temperate phages. By combining both methods, we identified 8,348 novel virus species spanning diverse hosts, from bacteria to humans, and all major viral genome types (dsDNA, ssDNA, and RNA). We find that bacteriophages frequently encode metabolic functions, including genes related to B vitamin metabolism. We further observe that the development of the infant gut virome is shaped by both host factors, including delivery mode and feeding practices, and continuous switching of temperate phage lifecycles. Notably, the relative abundance of induced temperate phages is also associated with eczema development within the first year of life. Together, these findings establish the infant gut virome as a dynamic and clinically relevant component of early-life microbial development and highlight how comprehensive dual-method profiling is a necessary framework for future virome research.

microbiology↗

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↗

bioRxiv2025

Vaginal microbiota changes during a natural menstrual cycle in the Women4Health cohort highlights specific features of the Italian population.

Large sex hormonal fluctuations are thought to influence vaginal microbiota, but little is known about the impact of small, physiological variations. Here we tracked changes in vaginal microbiota during four key menstrual cycle phases in 61 healthy, naturally menstruating Italian women from the Women4Health cohort. The microbiota, characterized using a high depth 16S rRNA amplicon sequencing approach covering four hypervariable regions, was primarily composed of Lactobacillus species, with Lactobacillus iners being the most abundant (average relative abundance 40%) and the most prevalent (prevalence 98%). Individual microbiota were generally stable, but beta diversity was higher during the follicular phase (p=0.007). Only 11 women exhibited compositional shifts, mostly occurring between follicular and ovulatory phases. Finally, using linear mixed models we assessed the association between taxa relative abundance and five sex-hormones along the menstrual cycle. Among these, 17-beta estradiol showed the largest number of significant associations, linking its increase to a decrease in relative abundance of taxa that are more common after menopause. Our study highlights specific features of the Italian population and points to the resilience of the vaginal microbiota to physiological hormonal changes. Noteworthy, the observed high abundance of L. iners contrasts with previous studies in European populations, challenging its proposed pathogenic role and suggesting distinct microbiota profiles within Europe. IMPORTANCEThe vaginal microbiota plays an important role in womens health, yet we know little about how it responds to normal hormonal fluctuations. In this study, we followed 61 healthy Italian women over a natural menstrual cycle to explore microbiota changes across different hormonal phases. We found that Lactobacillus iners was the most common species, unlike previous findings in Northern Europe, suggesting population-specific patterns. The common hypothesis that L. iners is invariably linked with poor health is called into question by our findings. They emphasize the importance of considering population context and hormonal status when assessing vaginal health. The vaginal microbiota was generally stable, with only a few changes observed between the follicular and ovulatory phases. When evaluating association between five sex hormones and taxa abundances, we found that 17-beta estradiol levels had the largest number of significant associations. These highlight an association between increase levels of 17-beta estradiol and increased relative abundance of rare bacterial taxa rather than dominant species like Lactobacillus. Our findings help define what constitutes a "healthy microbiota" in generally healthy Italian women of reproductive age and may inform future strategies for diagnosing or preventing womens health conditions.

microbiology↗

bioRxiv2023

Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. We longitudinally assessed the composition of gut viruses and their bacterial hosts in 322 total metagenomes and 205 metaviromes from 30 mothers during and after pregnancy and from their 32 infants during their first year of life. While the maternal gut virome composition remained stable during late pregnancy and after birth, the infant gut virome was dynamic in the first year of life and contained a higher abundance of active temperate phages compared to the maternal gut viromes. The infant gut virome composition was also influenced by infant feeding mode and place of delivery. Lastly, we provide evidence of viral-bacterial strains co-transmission from mothers to infants, demonstrating that infants acquire some of their virome from their mothers gut. Highlights- Longitudinal characterisation of the gut microbiome and virome in 30 mothers during pregnancy, at birth and 3 months after birth and in 32 infants from birth across the first year of life. - The maternal gut bacteriome changes from the first to the second trimester and then remains stable through birth and the first 3 months after birth. - The maternal gut virome remains stable during late pregnancy, birth and the first 3 months after birth. - The infant gut virome is highly dynamic during the first year of life and is shaped by infant feeding mode and place of delivery. - The infant gut harbours more temperate bacteriophages than the maternal gut, but their relative abundance decreases with increasing infant age. - Gut viral strains and their bacterial host strains are co-transmitted from mothers to their infants. - Gut viral strains are transferred from mother to infant around birth directly or via transfer of their bacterial hosts followed by the induction of prophages.

microbiology↗