A High Fraction of Oral Bacteria in the Feces Indicates Gut Microbiota Depletion with Implications for Human Health

Abstract

High relative abundance of oral bacteria in the gut is considered abnormal and has been linked to intestinal disorders. However, this reported association has two alternate explanations: ectopic oral bacteria may increase in absolute numbers in the intestine and drive disease (the driver hypothesis) or, instead, intestinal commensals may decrease in absolute numbers and the relative rise in oral bacteria is simply an indicator of this loss (the marker hypothesis). Here we use experiments in mice and clinical data from patients to provide evidence in favor of the marker hypothesis. We demonstrate that depletion of intestinal bacteria by antibiotics increases the relative abundance of oral bacteria in the host feces without increasing their absolute abundance, and the relative enrichment can indicate host health parameters such as stool consistency, pathogen overgrowth, and immunity. Our results reframe the conventional interpretation of microbiome sequencing data with implications for intestinal disorders and microbiome therapies.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

“…4b and 5b ). These findings are consistent with prior work showing that oral microbes are frequently transmitted into the gut 55 and can reach high relative abundances when gut commensals decrease in absolute abundance 56 . We also identified potential opportunistic pathogens 21,48,57 like Klebsiella pneumoniae , Citrobacter freundii , and Streptococcus gallolyticus ( Extended Data Fig.…”

Gut and oral microbial community characterization from women with breast cancer, women with ductal carcinoma in situ, and healthy women reveals differences in gut but not oral microbiota

“…While inflammatory bowel disease and colon cancer are both conditions where oral taxa are found to be enriched in the gut, recent improvements in quantifying the absolute bacterial load in oral and gut samples has revealed that oral taxa enrichment may be more a reflection of reduced gut bacterial loads. 63 We analyzed the oral-gut microbiota overlap, and found from Venn diagram analysis that 29%, 36%, and 27% of taxa overlapped across the three cohorts (BC, DCIS, healthy), respectively. These results suggest that oral-gut inter-organ translocation was similar across these cohorts.…”

Ectopic colonization by oral bacteria as an emerging theme in health and disease

“…Regarding community dynamics, it remains unclear whether the ectopic colonization by oral bacteria is leading to an expansion of oral bacteria at distant sites or if a decrease in the resident microbiota is leading to a relative increase in these oral bacteria, while the absolute count remains constant (Liao et al 2022 ). Liao et al ( 2022 ) have recently provided evidence that tips the balance in favor of the second option.…”

“…Regarding community dynamics, it remains unclear whether the ectopic colonization by oral bacteria is leading to an expansion of oral bacteria at distant sites or if a decrease in the resident microbiota is leading to a relative increase in these oral bacteria, while the absolute count remains constant (Liao et al 2022 ). Liao et al ( 2022 ) have recently provided evidence that tips the balance in favor of the second option. Indeed, displacement of autochthonous strains has been observed in several diseases, including IBDs (Metwaly et al 2020 ) or childhood undernutrition (Vonaesch et al 2018 , 2022 ) and it is thus not clear if the disappearance of these strains and/or the overrepresentation of oral strains are the main disease-inducing entities.…”

“…within the lower gastrointestinal (GI) tract (Schmidt et al 2019 , Gough et al 2020 ). Also, regarding community dynamics, it remains unclear whether the ectopic colonization by oral bacteria is leading to an expansion of oral bacteria at distant sites or if a decrease in the resident microbiota is leading to a relative increase in these oral bacteria, while the absolute counts remain constant (Liao et al 2022 ). Finally, to date microbiome research has often leaned towards the oral and intestinal microbiomes, because of their easier accessibility, leading to the identification of numerous strains in these extensively studied environments.…”