Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population

Metagenomics has improved our understanding of commensal bacteria that colonize human intestines yet relies almost exclusively on fecal samples. Thus, spatial information about the niche range of these gut microbes and the level of specialized adaptation that they undergo has been inaccessible to fecal metagenomic studies. Here, we leveraged metagenomic data obtained through colonoscopy aspirates from three intestinal sites of healthy adults, and reconstructed metagenome-assembled genomes of several common gut bacteria to address intestinal site-specific evolution. We show that the genomes of bacterial strains at specific intestinal sites are clearly distinct yet are interrelated and are derived from a single founder strain colonizing multiple sites. We also reveal that within those intestinal sites, purifying selection is the dominant evolutionary force acting on Escherichia coli genomes within human hosts. Importantly, no site-specific adaptations at the level of accessory genes were detected, implying that these commensals are well-adapted to several host microniches and can therefore colonize multiple intestinal sites with high efficiency. Nevertheless, bacterial in situ growth rates differ markedly across different sections of the intestine. Metagenomics of aspirate samples can reveal unique strain- and intestinal tissue-specific genomic information. Such information may be critical for understanding bacterial contribution to gastrointestinal diseases, which involve only a part of the intestine, as is often the case in inflammatory bowel disease. IMPORTANCE By reconstructing bacterial genomes from samples taken from specific sites within the human intestines, via aspiration, we show that strains at specific intestinal sites are genetically distinct yet interrelated and are derived from a single founder population. Organ-specific metagenomic information represents a powerful tool to generate insights into gastrointestinal diseases, which involve only a part of the intestine, such as inflammatory bowel disease.