Antibiotic treatment also affects the intestinal fungal microbiota

It is generally considered that following treatment with antibiotics, which reduces the bacterial population in the digestive tract, the fungal population present in the intestine will take advantage of these freed niches and proliferate... but our study proved the contrary!

Published in Microbiology

Antibiotic treatment also affects the intestinal fungal microbiota
Like

Share this post

Choose a social network to share with, or copy the URL to share elsewhere

This is a representation of how your post may appear on social media. The actual post will vary between social networks

Explore the Research

BioMed Central
BioMed Central BioMed Central

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem - Microbiome

Background Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal load increases in the gastrointestinal tract following antibiotic treatment, but better characterization is clearly needed of how antibiotics directly or indirectly affect the mycobiota and thus the entire microbiota. Design We used samples from humans (infant cohort) and mice (conventional and human microbiota-associated mice) to study the consequences of antibiotic treatment (amoxicillin-clavulanic acid) on the intestinal microbiota. Bacterial and fungal communities were subjected to qPCR or 16S and ITS2 amplicon-based sequencing for microbiota analysis. In vitro assays further characterized bacterial-fungal interactions, with mixed cultures between specific bacteria and fungi. Results Amoxicillin-clavulanic acid treatment triggered a decrease in the total fungal population in mouse feces, while other antibiotics had opposite effects on the fungal load. This decrease is accompanied by a total remodelling of the fungal population with the enrichment in Aspergillus, Cladosporium, and Valsa genera. In the presence of amoxicillin-clavulanic acid, microbiota analysis showed a remodeling of bacterial microbiota with an increase in specific bacteria belonging to the Enterobacteriaceae. Using in vitro assays, we isolated different Enterobacteriaceae species and explored their effect on different fungal strains. We showed that Enterobacter hormaechei was able to reduce the fungal population in vitro and in vivo through yet unknown mechanisms. Conclusions Bacteria and fungi have strong interactions within the microbiota; hence, the perturbation initiated by an antibiotic treatment targeting the bacterial community can have complex consequences and can induce opposite alterations of the mycobiota. Interestingly, amoxicillin-clavulanic acid treatment has a deleterious effect on the fungal community, which may have been partially due to the overgrowth of specific bacterial strains with inhibiting or competing effects on fungi. This study provides new insights into the interactions between fungi and bacteria of the intestinal microbiota and might offer new strategies to modulate gut microbiota equilibrium. Video Abstract

In our study, we were surprised to find that treatment with amoxicillin and clavulanic acid (Augmentin), a treatment regularly prescribed by doctors, also reduced the fungal population in the intestine in an in vivo mouse model.

The study of the effect of these antibiotics on the fungal and bacterial intestinal microbiota allowed us to show that there was a massive modification of the bacterial microbiota and in particular an increase in amoxicillin-resistant populations, including enterobacteria. In vitro analyses of strains isolated from these microbiotas after treatment with this cocktail of antibiotics allowed us to identify a strain of bacteria partly responsible for the fall in the fungal population: Enterobacter hormaechei. Indeed, E. hormaechei is able in vitro in co-culture and in vivo after gavage in mice to decrease the amount of fungi. To date, the mechanisms explaining these effects are not completely understood. We have been able to show a slight competition effect around the nutrients useful to the fungi to grow but not strong enough to explain the observed effect. On the other hand, we have also demonstrated a clear physical interaction between the cells of the fungi and the bacteria after specific co-culture of this bacterium using scanning microscopy images.

This study allowed us to show that the effect of a treatment with antibiotics has different effects on the fungal population depending on the type of antibiotic. We have also identified a new bacterial strain capable of having a negative effect on the growth of fungi in a complex context of the intestinal microbiota. The continuation of our research work will allow us to elucidate the mechanisms of action of this bacterium on fungi and to progress in our understanding of the interaction between these 2 microbiotas.

Article: https://doi.org/10.1186/s40168-023-01516-y

Video: https://youtu.be/UqlwxRJx5jE

Please sign in or register for FREE

If you are a registered user on Research Communities by Springer Nature, please sign in

Follow the Topic

Microbiology
Life Sciences > Biological Sciences > Microbiology
  • Microbiome Microbiome

    This journal hopes to integrate researchers with common scientific objectives across a broad cross-section of sub-disciplines within microbial ecology. It covers studies of microbiomes colonizing humans, animals, plants or the environment, both built and natural or manipulated, as in agriculture.

Related Collections

With Collections, you can get published faster and increase your visibility.

Oncobiome

This collection of papers delves into the burgeoning field of oncobiome research, exploring the intricate relationship between cancer and the microbiome. The oncobiome encompasses the diverse microbial communities residing in and on the human body, which influence cancer development, progression, and treatment responses. By examining these interactions, our aim is to unravel the complex mechanisms through which the microbiome impacts oncogenesis and therapeutic outcomes.

This compilation highlights cutting-edge research, offering insights into potential diagnostic markers and novel therapeutic strategies, thereby advancing our understanding of cancer biology and paving the way for innovative, microbiome-targeted cancer treatments.

This is a cross-journal collection between:

Biomarker Research

BJC Reports

Experimental Hematology and Oncology

Infectious Agents and Cancer

Microbiome

Articles will undergo the standard peer-review process of the journal to which they are submitted and are subject to either the BMC editorial policies or those of BJC Reports. Articles will be added to the Collection as they are published. The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.

Publishing Model: Open Access

Deadline: Ongoing

The Apple Microbiome

Microbiome and Environmental Microbiome are calling for submissions to our Collection on the Apple Microbiome.

With world apple production estimated at 84 million tons, the microbiome of the apple has significant implications for agriculture, food security, and human health. Understanding the complex interactions between apple plants and their associated microbial communities can lead to improved crop management strategies, enhanced fruit quality and longevity, and sustainable agricultural practices. Recent advances have highlighted the role of specific bacteria and fungi in promoting plant health and resilience against specific pathogens. Moreover, detailed profiling of these microbial communities, revealing their diversity and functional potential facilitate exciting future developments, such as the identification of beneficial microbial consortia for biocontrol and the formulation of tailored probiotic treatments for both plants and humans. By advancing our collective understanding in this area, we can work towards a more sustainable and resilient agricultural system.

Topics of interest include but are not limited to:

-Microbial diversity and function associated with apples

-Effects of soil health and rhizosphere interactions on apple production

-Impact of climate change on the apple microbiome

-Role of the apple microbiome in fruit quality

-Microbiome-driven strategies for disease resistance

This collection is open for submissions from all authors on the condition that the manuscript falls within both the scope of the collection and the journal it is submitted to.

All submissions in this collection undergo the relevant journal’s standard peer review process. Similarly, all manuscripts authored by a Guest Editor(s) will be handled by the Editor-in-Chief of the relevant journal. As an open access publication, participating journals levy an article processing fee (Microbiome, Environmental Microbiome). We recognize that many key stakeholders may not have access to such resources and are committed to supporting participation in this issue wherever resources are a barrier. For more information about what support may be available, please visit OA funding and support, or email OAfundingpolicy@springernature.com or the Editor-in-Chief of the journal where the article is being submitted.

Publishing Model: Open Access

Deadline: Sep 30, 2026