Abstract:
The human gut microbiome plays a critical role in health and diseases. This complex
community of microorganisms is established early in life and undergoes significant
changes during infancy, a period crucial for long-term health. In infants, the gut
microbiome is particularly dynamic, with the mode of delivery being one of the initial
factors influencing it. Despite ongoing research, there are gaps in understanding the
dynamics of ARG acquisition, evolution and associations to environmental factors such as
diet, mode of delivery, maternal antibiotic exposures, infant’s antibiotic exposure, and
water type used by infants. This thesis aims to characterize ARGs in infants during first
year of life and investigate their associations with metadata variables including mode of
delivery, maternal antibiotic consumption, and environmental factors.
One way to explore these resistome dynamics is through the study of antibiotic resistome
analysis and how these ARGs are associated with mode of delivery and environmental
factors. This study combine metagenomics techniques with gene prediction and gene
catalogue construction tools like Prodigal and MMseqs2. ARGs were identified through
CARD database by using DIAMOND, according to the results infants delivered via Csection delivery had a higher abundance of ARGs which clear pattern of ARG prevalence
associated with delivery techniques. Notably, infants exposed to antibiotics whether
directly or through maternal source exhibited a disrupted microbiome and increased risk of
harboring ARGS potentially lead them to immunological dysregulation and illness like
obesity, inflammatory bowel disease, and cardiovascular disorders. This study emphasizes
the complex interactions between environmental variables and infant gut microbiome
xiv
underscoring the gut microbiota, underscoring the necessity for focused approaches to slow
the spread of ARGs. This study will help to prevent antibiotic resistance and its effects on
human health by deepening our understanding of antibiotic resistome dynamics their
relationship to early life exposures.
