TY - JOUR
T1 - Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria
AU - Seelbinder, Bastian
AU - Chen, Jiarui
AU - Brunke, Sascha
AU - Vazquez-Uribe, Ruben
AU - Santhaman, Rakesh
AU - Meyer, Anne Christin
AU - De Oliveira Lino, Felipe Senne
AU - Chan, Ka Fai
AU - Loos, Daniel
AU - Imamovic, Lejla
AU - Tsang, Chi Ching
AU - Lam, Rex Pui Kin
AU - Sridhar, Siddharth
AU - Kang, Kang
AU - Hube, Bernhard
AU - Woo, Patrick Chiu Yat
AU - Sommer, Morten Otto Alexander
AU - Panagiotou, Gianni
PY - 2020/9/12
Y1 - 2020/9/12
N2 - Background: Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. Results: While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. Conclusions: We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. [MediaObject not available: see fulltext.].
AB - Background: Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. Results: While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. Conclusions: We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. [MediaObject not available: see fulltext.].
U2 - 10.1186/s40168-020-00899-6
DO - 10.1186/s40168-020-00899-6
M3 - Journal article
C2 - 32919472
AN - SCOPUS:85090872814
VL - 8
JO - Microbiome
JF - Microbiome
SN - 2049-2618
IS - 1
M1 - 133
ER -