Frontiers in cellular and infection microbiology · 2026
Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.
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Huang Jinjie, Yan Xudong, Su Qian, Tu Huiying, Yu Zhangbin, Liu Dong, Wu Benqing
Аннотация
INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.
METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.
RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).
DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.
METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.
RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).
DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.