Moderate and transient impact of antibiotic use on the gut microbiota in a rural Vietnamese cohort

Bich, Vu Thi; Le, Ngoc-Giang; Barnett, David J.M.; Chan, Jiyang; Best, Niels van; Tien, Tran Dac; Anh, Nguyen Thi Hien; Hoang, Tran Huy; Doorn, H. Rogier van; Wertheim, Heiman; Penders, John

doi:10.1038/s41598-022-24488-9

Cited by 3 publications

(1 citation statement)

References 52 publications

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“…On the other hand, ‘additive’ measures creating new sources of clearance, such as antibiotics, should favor the best colonizers at the expense of the resident clones. This could explain the resilience of the microbiota in settings with high antibiotic use [55]. Conversely, a reduction in disturbances of the microbiota could explain an increase in the frequency of phylogroup B2, as observed in France [21, 47].…”

Section: Discussionmentioning

confidence: 99%

Residence-colonization trade-off and niche differentiation enable the coexistence ofEscherichia coliphylogroups in healthy humans

Morel-Journel,

Lehtinen,

Cotto

et al. 2023

Preprint

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Despite the extensive literature on the pathogenicity and virulence of the commensal bacterial species and major pathogen Escherichia coli, much less is known about its natural ecological and evolutionary dynamics in populations of healthy hosts. Based on remarkably detailed longitudinal data on the gut microbiota of eight healthy individuals over months to years, we identified a trade-off between colonization and persistence, with major E. coli strains (phylogroups) exhibiting a diversity of strategy from strong colonizers persisting for a few days, to poor colonizers persisting for years in the gut. All phylogroups exhibited similar fitness along the trade-off. Moreover, the persistence time was reduced more strongly when a focal strain competed with other strains of the same phylogroups than of different phylogroups, suggesting niche differentiation within the host. To derive the dynamical consequences of the trade-off and niche differentiation for coexistence between strains, we developed a discrete-state Markov model describing the dynamics of E. coli in a population of hosts. The trade-off and niche differentiation act together as equalizing and stabilizing mechanisms enabling the stable coexistence of phylogroups over extended periods of time. Strains with the largest number of virulence genes and highest pathogenicity are those persisting for longer in hosts. Our model predicts that a reduction in transmission (e.g., through better hygiene) would not alter the balance between phylogroups, while less disturbance of the microbiome favors persisters, such as those belonging to the pathogenic phylogroup B2.3. More generally, the trade-off between colonization and persistence could play a role in the diversification of other bacterial species of the microbiome.

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Section: Discussionmentioning

confidence: 99%

Residence-colonization trade-off and niche differentiation enable the coexistence ofEscherichia coliphylogroups in healthy humans

Morel-Journel,

Lehtinen,

Cotto

et al. 2023

Preprint

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Population-specific differences in the human microbiome: Factors defining the diversity

Govender,

Ghai

2025

Gene

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A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome

John,

Michael,

Dabcheva

et al. 2024

Front. Microbiomes

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The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome’s composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.

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Moderate and transient impact of antibiotic use on the gut microbiota in a rural Vietnamese cohort

Cited by 3 publications

References 52 publications

Residence-colonization trade-off and niche differentiation enable the coexistence ofEscherichia coliphylogroups in healthy humans

Residence-colonization trade-off and niche differentiation enable the coexistence ofEscherichia coliphylogroups in healthy humans

Population-specific differences in the human microbiome: Factors defining the diversity

A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome

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