Having recently finished a great period as Marie Sklodowska-Curie fellow working on viral Metagenomics, I was lucky enough to get an Assistant Professor position in my hometown. While the amount of bureaucratic and teaching work involved, especially in Spain, would surely take a toll in my scientific career, the opportunity was a godsend, as I had two kindergarten-aged girls, and a spouse that had already accompanied me previously overseas for a three years postdoc.
What interesting idea could I attack without much hope for initial funding or too much spare time, and on my own?. Actually, I knew exactly what I wanted to do, something that had been on the back of my mind for the last four years. During the last year of my first postdoc I analyzed human gut microbiota samples looking for bacterial groups present in all samples (i.e. core), something much en vogue at the time. I did not merely focus on a fixed OTU similarity clustering threshold or taxonomic rank, and indeed found various core groups. Not only did these core groups varied in phylogenetic depth, but their subsequent co-abundance network analysis revealed various intriguing features that did look to me (a likely biased observer) as hints of community assembly rules. Unfortunately, the results were based on too few samples and I finished my contract and was eager to move forth before we could find a larger dataset.
Now was the time to revisit those results. I carried out a similar analysis on large and comprehensive human gut datasets and found that they presented a preeminent compositional core comprised of discrete core groups of varying phylogenetic depth [1]. However, when I communicated my feeling that the existence of phylogenetic core groups in microbial ecosystems was a thread worth pulling from, many colleagues at conferences and meetings (and various reviewers) received the idea with a clear lack of enthusiasm and commonplace responses such as “the OTU is dead, you have to use ESVs”, “communities assemble based on functional genes, not bacterial groups” or “16S sequencing is the past, only shotgun metagenomics matters now”. I understood what they meant but felt that their commentaries were unrelated to my idea that given the fact that both microbial traits and ecological coherence show signs of phylogenetic conservation, the possible existence of phylogenetic core groups in microbial ecosystems was noteworthy. If I was a fool, what was I not seeing?
So, I set out to explain myself properly, read quite a bit, found inspiring papers (e.g. [2, 3]), and produced what I felt was a worthy conceptual framework for the assembly of microbial communities. The final factor that convinced me of its value was the discovery of Goldford et al. study of community assembly on single carbon and energy sources using complex microbial communities derived from different natural habitats [4]; my a priori theoretical predictions beautifully matched their experimental results!.
You can find my ideas on microbial community assembly published here:
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0754-y
1. Aguirre de Cárcer D. The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units. Scientific Reports. 2018;8:14069.
2. Cordero OX, Datta MS. Microbial interactions and community assembly at microscales. Current Opinion in Microbiology. 2016;31:227-34.
3. Kinnunen M, Dechesne A, Proctor C, Hammes F, Johnson D, Quintela-Baluja M et al. A conceptual framework for invasion in microbial communities. The Isme Journal. 2016;10:2773.
4. Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A et al. Emergent simplicity in microbial community assembly. Science. 2018;361:469-74.
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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.
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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:
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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
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