Naturally occurring antibiotic resistances in plant microbiomes
Published in Microbiology
The plant microbiome often harbors highly competitive microorganisms that can shield of pathogens and contribute to the host’s health. In our latest study we have focused on antibiotic resistances in a common salad plant and found that the indigenous enterobacterial community contributes to the highly interesting profile.
The fatal implications of various infections by opportunistic human pathogens were thought of as a burden of the past, especially after several generations of highly effective antibiotics were developed. With the increased occurrence of antibiotic-resistant microorganisms (mostly bacteria), this perception is changing and we are facing once again a problem that requires a long-lasting solution.
This solution will most likely not arise from a new generation of classic antibiotics. In fact, it will require to overthink how we administer antimicrobial agents and how to avoid the natural response of microorganisms when they are attacked. The world health organization (WHO; https://www.who.int) provides frequently updated lists of microorganisms for which antibiotic treatments are urgently required.
Interestingly, many of the bacteria that are found on these lists have close relatives that either occur in our bodies or in natural environments that we use for our food production. Often the only difference is strain-specific and only given by certain genes that can be also located on plasmids.
Previous studies have already shown that many plant-associated bacteria have many similarities with opportunistic human pathogens, mostly due to the fact that they require similar functional repertoires for their survival (Berg et al., 2005). These findings provide the basis to study how these microorganisms are controlled in their natural environments and how this might be transferred to environments that are relevant for our health.
These environments are not only restricted to the clinical field, but also agricultural production and the indoor environment in general. In order to further decipher the occurrence of antibiotic resistances in natural environments, we have selected a common salad plant as a model for our study that included metagenomic profiling and cultivation-based studies in order to confirm the presence of multi-resistant bacteria.
Eruca vesicaria var. sativa (Mill.) Thell., commonly known as arugula, is a popular raw-eaten ingredient in salads due to its peppery, pungent taste. Similar to other leafy green plants, E. sativa is colonized by a vast diversity of microbes, which complement the holobiont’s functioning.
We analyzed the structure, abundance and functioning of the plant-associated microbiota in the arugula phyllosphere, rhizosphere and the corresponding bulk soil in an integrative approach. When compared to the rhizosphere, higher proportions of Gammaproteobacteria, including Enterobacteriaceae were observed in aerial plant parts. Metagenomic profiling of the bacterial population indicated a higher prevalence of antibiotic resistances in plant-derived samples.
We found general resistance mechanisms including various efflux pumps in the datasets, but also specific resistance mechanisms against fluoroquinolone, chloramphenicol and other antibiotics. Our overall findings suggest that antibiotic resistance is common in distinct raw-eaten plants. This provides the basis to further explore how these resistances are formed and how carriers, which are rarely pathogens in such environments, can be controlled in the future.
Berg, G., Eberl, L., and Hartmann, A. (2005). The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environmental Microbiology, 7, 1673-1685.
Follow the Topic
-
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.
Harnessing plant microbiomes to improve performance and mechanistic understanding
This is a Cross-Journal Collection with Microbiome, Environmental Microbiome, npj Science of Plants, and npj Biofilms and Microbiomes. Please click here to see the collection page for npj Science of Plants and npj Biofilms and Microbiomes.
Modern agriculture needs to sustainably increase crop productivity while preserving ecosystem health. As soil degradation, climate variability, and diminishing input efficiency continue to threaten agricultural outputs, there is a pressing need to enhance plant performance through ecologically-sound strategies. In this context, plant-associated microbiomes represent a powerful, yet underexploited, resource to improve plant vigor, nutrient acquisition, stress resilience, and overall productivity.
The plant microbiome—comprising bacteria, fungi, and other microorganisms inhabiting the rhizosphere, endosphere, and phyllosphere—plays a fundamental role in shaping plant physiology and development. Increasing evidence demonstrates that beneficial microbes mediate key processes such as nutrient solubilization and uptake, hormonal regulation, photosynthetic efficiency, and systemic resistance to (a)biotic stresses. However, to fully harness these capabilities, a mechanistic understanding of the molecular dialogues and functional traits underpinning plant-microbe interactions is essential.
Recent advances in multi-omics technologies, synthetic biology, and high-throughput functional screening have accelerated our ability to dissect these interactions at molecular, cellular, and system levels. Yet, significant challenges remain in translating these mechanistic insights into robust microbiome-based applications for agriculture. Core knowledge gaps include identifying microbial functions that are conserved across environments and hosts, understanding the signaling networks and metabolic exchanges between partners, and predicting microbiome assembly and stability under field conditions.
This Research Topic welcomes Original Research, Reviews, Perspectives, and Meta-analyses that delve into the functional and mechanistic basis of plant-microbiome interactions. We are particularly interested in contributions that integrate molecular microbiology, systems biology, plant physiology, and computational modeling to unravel the mechanisms by which microbial communities enhance plant performance and/or mechanisms employed by plant hosts to assemble beneficial microbiomes. Studies ranging from controlled experimental systems to applied field trials are encouraged, especially those aiming to bridge the gap between fundamental understanding and translational outcomes such as microbial consortia, engineered strains, or microbiome-informed management practices.
Ultimately, this collection aims to advance our ability to rationally design and apply microbiome-based strategies by deepening our mechanistic insight into how plants select beneficial microbiomes and in turn how microbes shape plant health and productivity.
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.
Collection policies for Microbiome and Environmental Microbiome:
Please refer to this page. Please only submit to one journal, but note authors have the option to transfer to another participating journal following the editors’ recommendation.
Collection policies for npj Science of Plants and npj Biofilms and Microbiomes:
Please refer to npj's Collection policies page for full details.
Publishing Model: Open Access
Deadline: Jun 01, 2026
Microbiome and Reproductive Health
Microbiome is calling for submissions to our Collection on Microbiome and Reproductive Health.
Our understanding of the intricate relationship between the microbiome and reproductive health holds profound translational implications for fertility, pregnancy, and reproductive disorders. To truly advance this field, it is essential to move beyond descriptive and associative studies and focus on mechanistic research that uncovers the functional underpinnings of the host–microbiome interface. Such studies can reveal how microbial communities influence reproductive physiology, including hormonal regulation, immune responses, and overall reproductive health.
Recent advances have highlighted the role of specific bacterial populations in both male and female fertility, as well as their impact on pregnancy outcomes. For example, the vaginal microbiome has been linked to preterm birth, while emerging evidence suggests that gut microbiota may modulate reproductive hormone levels. These insights underscore the need for research that explores how and why these microbial influences occur.
Looking ahead, the potential for breakthroughs is immense. Mechanistic studies have the power to drive the development of microbiome-based therapies that address infertility, improve pregnancy outcomes, and reduce the risk of reproductive diseases. Incorporating microbiome analysis into reproductive health assessments could transform clinical practice and, by deepening our understanding of host–microbiome mechanisms, lay the groundwork for personalized medicine in gynecology and obstetrics.
We invite researchers to contribute to this Special Collection on Microbiome and Reproductive Health. Submissions should emphasize functional and mechanistic insights into the host–microbiome relationship. Topics of interest include, but are not limited to:
- Microbiome and infertility
- Vaginal microbiome and pregnancy outcomes
- Gut microbiota and reproductive hormones
- Microbial influences on menstrual health
- Live biotherapeutics and reproductive health interventions
- Microbiome alterations as drivers of reproductive disorders
- Environmental factors shaping the microbiome
- Intergenerational microbiome transmission
This Collection supports and amplifies research related to SDG 3, Good Health and Well-Being.
All submissions in this collection undergo the journal’s standard peer review process. As an open access publication, this journal levies an article processing fee (details here). 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.
Publishing Model: Open Access
Deadline: Jun 16, 2026
Please sign in or register for FREE
If you are a registered user on Research Communities by Springer Nature, please sign in