Population-level impacts of antibiotic usage on the human gut microbiome
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Population-level impacts of antibiotic usage on the human gut microbiome. / Lee, Kihyun; Raguideau, Sebastien; Sirén, Kimmo; Asnicar, Francesco; Cumbo, Fabio; Hildebrand, Falk; Segata, Nicola; Cha, Chang Jun; Quince, Christopher.
In: Nature Communications, Vol. 14, 1191, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Population-level impacts of antibiotic usage on the human gut microbiome
AU - Lee, Kihyun
AU - Raguideau, Sebastien
AU - Sirén, Kimmo
AU - Asnicar, Francesco
AU - Cumbo, Fabio
AU - Hildebrand, Falk
AU - Segata, Nicola
AU - Cha, Chang Jun
AU - Quince, Christopher
N1 - Publisher Copyright: © 2023, The Author(s).
PY - 2023
Y1 - 2023
N2 - The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
AB - The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
U2 - 10.1038/s41467-023-36633-7
DO - 10.1038/s41467-023-36633-7
M3 - Journal article
C2 - 36864029
AN - SCOPUS:85149298430
VL - 14
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 1191
ER -
ID: 340974086