Sampling strategies for digestive system flora studies: current research and perspectives.

Area of Science:

• Microbiology
• Gastroenterology
• Genomics

Background:

• The digestive system's microbial community is linked to numerous diseases.
• Microbial composition varies significantly across organs, regions, and disease stages.
• Investigating these microbial communities aids in diagnosing and treating digestive pathologies.

Purpose of the Study:

• To systematically evaluate biological samples and collection methods in digestive system microbiota research.
• To guide future sample selection and collection strategies for microbial studies.
• To address the complexity of dynamic shifts in microbial composition during disease progression.

Main Methods:

• Comprehensive literature review using PubMed and Web of Science.
• Focused on high-throughput sequencing studies comparing different samples and sampling methods.
• Analyzed the impact of various sampling techniques on microbial community structure.

Main Results:

• A wide range of microbiological samples are available, including saliva, biopsies, luminal fluid, feces, bile, and tissues.
• Multiple techniques exist for specimen collection from identical locations, each with pros and cons.
• Diverse sampling methods can influence observed microbial community structures.

Conclusions:

• Selecting appropriate specimens and sampling methods is crucial for microbiota studies.
• Considerations include microbiota characteristics, research environment, and study objectives.
• Consensus on optimal sample types and collection methods for microbial studies is still lacking.