Rapid turnover and short-term blooms of Escherichia coli in the human gut

Abstract

Escherichia coli (E. coli ) is a common microorganism that is widely present in the environment and closely related to human health. The extent of E. coli presence in the human gut has been a subject of ongoing debate. Through whole-genome shotgun metagenomic sequencing, our study revealed that E. coli exists in the human body at a low abundance (average abundance 1.21%), with occasional short-term bursts leading to temporary increases in abundance, with the highest recorded at 50.91%. Further investigations into the factors contributing to these short-term blooms of E. coli showed significant variations in strain types and genomes within fecal samples collected from the same individuals at different time points. Evolutionary tree analysis indicated that samples from different individuals crossed, suggesting a change in the dominant E. coli strains within the human gut. Therefore, it can be inferred that E. coli in the human body are more likely to be transient bacteria rather than permanent residents in the gut. The rapid rate of turnover among months (87.5% within a month) and short-term blooms of E. coli in the human body can establish "latent infections" of nonpathogenic strains in healthy individuals while also posing a potential risk of introducing pathogenic strains, thereby impacting human health. In summary, our study revealed the variation in E. coli abundance and strains within the human gut, influenced by geographic area and temporal factors. These findings contribute to a better understanding of the relationship between E. coli , the gut microbiota, and human health. IMPORTANCE Escherichia coli (E. coli ) is a microorganism closely linked to human health, and its presence in the human gut has been a topic of debate. Our study, using whole-genome shotgun metagenomic sequencing, revealed that E. coli exists at a low abundance in the human body, with occasional short-term bursts leading to temporary increases. Strain and genome variations were observed within fecal samples from the same individuals at different time points, suggesting transient rather than permanent residence of E. coli in the gut. The rapid turnover rate and short-term blooms of E. coli can establish latent infections while also posing a risk of introducing pathogenic strains. These findings enhance our understanding of the relationship between E. coli , the gut microbiota, and human health.

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health

“…The 5-year longitudinal study revealed that Prevotella copri (Segatella copri) was consistently present in samples from P6 (March 2017 to November 2018), with genomic analysis indicating the same strain, without a turnover at the strain level. This finding is in contradiction with our previous finding based on Escherichia coli ( Han et al, 2024 ), as this species experiences a rapid monthly turnover rate (87.5% within a month), whereas Prevotella persists in the gut for a longer duration. We refer to Escherichia coli and other rapidly turning over bacteria, similar to it, as transient gut microbes.…”

“…In the original classification framework, the longitudinal study of up to 5 years demonstrated short-term blooms or decreases in the abundance of Prevotella over time ( Figures 1C , 2A ). Short-term blooms, defined as instances where the abundance of Prevotella exceeded 5 times the individual’s average abundance, and short-term decreases, defined as abundance dropping to more than 5 times lower than the previous time point ( Zhang et al, 2022 ; Han et al, 2024 ), were observed. These fluctuations were recorded at 17 time points over the 5 years and were distributed among 7 individuals ( Supplementary Figure S1 ).…”