Knowledge of microbiology-related issues in dentistry is fundamental to clinical practice and patient care. The purpose of this literature review is to comprehensively describe the roles microbes play in pediatric dental practice, with a special focus on eight continuing and emerging microbiological issues related to waterline safety, dental material contamination, effects of oral bacteria on systemic health, antibiotic resistance, continuing COVID-19 findings and risks associated with animal-assisted therapies. Key points are highlighted on each topic, with current reports demonstrating microbial impacts on human health and clinical settings. Advice and risk management strategies related to patient care and clinical practice are provided.