Why the bad is not always bad
Published in Microbiology
Only recently, we have recognised the importance of microbe-to-host interactions. While before, bacterial, fungal and viral interactions with our cells were not really taken into account, nowadays it is seen as common knowledge that we are not sterile organisms. Indeed, bacteria was already found in our blood and only recently it was hypothesised to be potentially found in the brain.1
Many microbes were associated with certain diseases but now we know that it is not the number of bacteria which differentiates the healthy from the non-healthy but the shift of a prevalence of certain strains. Therefore, we understood that treating these diseases with antibiotics can cause more harm than good. Usually, we cannot select for those we want to keep and those we want to get rid of and we end up with killing all. Also, the wrong use of antibiotics by its patients has led to the occurrence of antibiotic resistant strains which will survive any treatment and therefore become the prevalent strain.
In this sense, it seems a promising approach to identify a healthy mixture and use it to engraft on the host. The same mechanism was already successfully implemented in our gut. Take the bacteria of an “healthy” donor and transplant it in an “unhealthy” one. This approach got famous under the term “fecal microbiome transplantation” - in short FMT. Also, recently it was suggested that there might be a direct link between ageing and gut-microbiome composition. Researchers found that verrucomicrobia Akkermansia muciniphila, found in centenarians, had a lifespan-enhancing effect when transplanted into a mouse-model.2 Another example describing the importance of interactions to the gut microbiome was the finding that Veillonella atypica abundance is responsible for the enhancement of performance in athletes due to its ability to metabolize lactate into propionate.3
So, why not using this transplantation approach on another site on our human body, for example the skin? We swapped multiple patients and we identified their skin microbial community, mainly focusing on Cutibacterium acnes- a major skin commensal, living in the sebaceous glands of the human body. This bacterium was negatively associated with the skin condition acne vulgaris and was long seen as a pathogen. Today, we understand the necessity of C. acnes on the healthy human skin and so we tried to modulate a recipient microbiome with a donor microbiome. We saw that with a certain combination of strains we could reach transplantation significant engraftment on the human recipient. This modulation would stabilise during application and return slowly to its original state when the application was stopped.
It is interesting to see how different populations can influence the health of the host. We should reconsider the way we see the human body and approach it as a whole and embrace the fact that we are inhabited by a community of organism which can contribute to our well-being.
2. Bárcena, C. et al. Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice. Nat. Med. (2019). doi:10.1038/s41591-019-0504-5
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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.
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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.
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