Weaning is a critical stage in the life of a pig, particularly in current animal production systems that hit the animals with a double whammy of feed transition in combination with social stress caused by separation from the mother and littermates. Stress and the shift in the intestinal microbiota makes piglets susceptible to diarrheal pathogens, particularly Escherichia coli. Smoothing that transition will benefit well-being of piglets and reduce the need for antibiotics to treat enteric infections. Our publication provides a detailed analysis of the transition of swine microbiota after weaning – the combination of quantification of enzymes that relate to carbohydrate degradation with metagenomic binning allowed us to identify the key players in carbohydrate and fibre metabolism in the intestinal microbiome of swine.
We initially hypothesized that the use of probiotics beneficially influences the piglet’s microbiome, and that reutericyclin, an antimicrobial produced by Lactobacillus reuteri, enhances this impact. The impact of reutericyclin was assayed by the use of isogenic reutericyclin positive and –negative strains.
This proved to be yet another beautiful hypothesis that was slain by ugly facts.
Initial analyses demonstrated that the influence of probiotics on the overall gut microbiome was very minor; we had to look hard and with strain- or species specific to detect their influence on specific bacterial taxa. The reduction of pathogenic Escherichia coli that was observed in previous studies, however, could be confirmed.
A more detailed analysis by metagenomic binning demonstrated that uncultured bacterial taxa represented most of the key organisms in the swine intestine – this indicates that much of the work that has been done for human intestinal microbiota, culturing of key bacteria to determine their physiological and metabolic properties – still remains to be done for swine intestinal communities. The “elephant in the room” explaining most of the changes in the microbiome was the diet – other factor were transient or did not matter. Consequently, our subsequent analyses focused on carbohydrate metabolism by gut microbiota. Because wheat and lactose were the major components of the feed, we focused on starch, fructans, and lactose as main dietary carbohydrates, and compared carbohydrate metabolism in the swine intestine to the corresponding organisms in the human intestine. The metagenomic assembly and binning that was performed by the collaborators from Huazhong Agricultural University provided an excellent and unprecedented foundation to analyse the metabolic networks for carbohydrate metabolism in the swine gut.
Comparable to human intestinal microbiota, starch degradation is dependent on metabolic cooperativity of diverse members of Firmicutes and Bacteroidetes. Surprisingly, the most abundant enzyme was not an amylase but a branching enzyme which likely functions to solubilise resistant starch and to make it accessible to hydrolytic enzymes.
Key players for fructan and lactose metabolism in swine differed from those in the human intestinal microbiota. Lactobacilli expressing extracellular fructanases were major contributors to fructan metabolism in swine. Database searches revealed that the corresponding enzyme, FruA, is present in lactobacilli from the swine intestine but absent in all other lactobacilli – we have yet to figure out why this enzyme is important in pig intestine but not in any other of the (intestinal) ecosystems that harbor lactobacilli.
In the human gut and particularly in infants, bifidobacteria are the main degraders of lactose. In swine, lactobacilli take over that role and are major contributors to β-galactosidase activity. Taken together these findings may enable manipulation of the piglet’s microbiome after weaning by the animal’s diet.
The relationship between swine microbiota and lactobacilli in food fermentations provided an interesting and surprising sidekick of the work. Lactobacilli from swine are commonly found in specific cereal fermentations – in one of these fermentations, lactobacilli expressing the exceptional extracellular fructan hydrolase dominate and contribute to the degradation fructans for production of low-FODMAP bread. We were also surprised to find Lactobacillus delbrueckii at weaning. This organisms is used globally to produce yoghurt and has adapted to lactose and milk environments, however, to date, it has not been associated with intestinal environments. To confirm this unexpected occurrence, we went back to older datasets from weaning piglets; these analyses confirmed that L. delbrueckii is present at weaning but quickly disappears after the transition to solid feed. If confirmed by culture, this unexpected finding may demonstrate that L. delbrueckii adapted to suckling mammals, which could open new perspectives with regards to probiotics and intestinal health in infants and suckling animals.
I sometimes point out - tongue in cheek - that swine are an “in vivo model for food fermentations”. This study shows indeed that knowledge on host-adapted lactobacilli that is derived from food fermentations helps to explain metabolism in intestinal ecosystems. Conversely, knowledge on the ecology of these lactobacilli in the intestine helps us to improve their use in food fermentations and as probiotics.
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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.
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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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