Food systems are usually discussed in terms of nutrition, food safety, productivity, sustainability or emissions. Less attention is given to the microbial dimension of the farm-to-fork pathway and to the way food systems shape the dietary substrates, food matrices and microbial exposures that reach the gut. Soils, plants, foods, processing environments, animals and the human gut all host microbial communities that influence nutrient cycling, plant performance, food characteristics, metabolism, immune regulation and ecological resilience. This review examines how food systems may modulate gut microbiota and microbiome resilience within a One Health framework. Evidence from soil, crop and food microbiome studies suggests that local conditions and farming practices can leave detectable microbial signatures on plants and edible tissues. However, the soil-food-gut continuum should not be understood as a simple transfer route. Microorganisms and microbial products are repeatedly filtered by plant traits, farming systems, animal-production interfaces, harvesting, processing, storage, preparation and host physiology. The review also considers how this continuity may be weakened or redirected. Agricultural intensification, pollutants, post-harvest processing, antimicrobial use, ultra-processed foods, additive mixtures, low-fibre diets, early-life microbial disruption and reduced contact with environmental biodiversity may alter microbial communities at different points of the food system. Antimicrobial resistance is also discussed as a functional microbial trait that can circulate across human, animal, food and environmental interfaces. One Health approaches to food systems should therefore combine microbial risk control with microbial stewardship: protecting useful microbial diversity and function while preserving food safety. The aim is not to maximise microbial exposure, but to understand which microbial functions matter and how food systems can support gut microbiota resilience across environments, foods and hosts.

Cheese is a widely consumed fermented dairy product with a long history of human consumption dating back several millennia, which justifies a brief historical introduction in this review. Beyond its cultural and gastronomic relevance, cheese presents a complex nutritional and microbial matrix that may confer neutral or even beneficial effects on cardiometabolic health, despite concerns related to its saturated fat and sodium content. This review first explores the key components of the cheese matrix and several mechanisms potentially involved in its metabolic impact, including the presence of polar lipids, the production of short-chain fatty acids (SCFAs) and alpha-linolenic acid (ALA) by the cheese microbiota, and the high calcium content that may reduce fat absorption, among others. Additional bioactive compounds formed during fermentation, such as angiotensin-converting enzyme (ACE)-inhibitory peptides, are also discussed for their potential health effects. We also include a comprehensive survey of most European Protected Designation of Origin (PDO) cheeses and their microbiota. Finally, to assess the most recent evidence in human health, we analyzed a sample of studies published on PubMed in the last 2.5 years, including observational studies and randomized controlled trials. This selection highlights the latest research trends and supports a growing body of evidence suggesting that cheese, particularly in its intact matrix form, is not associated with adverse cardiometabolic outcomes-and may even exert protective effects. These findings call for more robust, long-term trials to confirm causality and support updated dietary guidance.

Background: The gut microbiota is increasingly recognized as a key modulator in obesity management, influencing host energy balance, lipid metabolism, and inflammatory pathways. With obesity prevalence continuing to rise globally, dietary interventions that promote beneficial microbial shifts are essential for enhancing weight loss outcomes and long-term health. Objective: This study investigated the effects of the multicomponent Weight Loss Maintenance 3 Phases Program (WLM3P), which integrates caloric restriction, a high-protein low-carbohydrate diet, time-restricted eating (10h TRE), dietary supplementation (prebiotics and phytochemicals), and digital app-based support on gut microbiota composition compared to a standard low-carbohydrate diet (LCD) in adults with obesity. The analysis focused exclusively on the 6-month weight loss period corresponding to Phases 1 and 2 of the WLM3P intervention. Methods: In this sub-analysis of a randomized controlled trial (ClinicalTrials.gov Identifier: NCT04192357), 58 adults with obesity (BMI 30.0–39.9 kg/m2) were randomized to the WLM3P (n = 29) or LCD (n = 29) groups. Stool samples were collected at baseline and 6 months for 16S rRNA sequencing. Alpha and beta diversity were assessed, and genus-level differential abundance was determined using EdgeR and LEfSe. Associations between microbial taxa and clinical outcomes were evaluated using regression models. Results: After 6-month, the WLM3P group showed a significant increase in alpha diversity (p = 0.03) and a significant change in beta diversity (p < 0.01), while no significant changes were observed in the LCD group. Differential abundance analysis revealed specific microbial signatures in WLM3P participants, including increased levels of Faecalibacterium. Notably, higher Faecalibacterium abundance was associated with greater reductions in fat mass (kg, %) and visceral adiposity (cm2) in the WLM3P group compared to LCD (p < 0.01). Conclusions: These findings suggest a potential microbiota-mediated mechanism in weight loss, where Faecalibacterium may enhance fat reduction effectiveness in the context of the WLM3P intervention.

Somatic embryogenesis (SE) is a process by which somatic cells reprogram, acquire totipotency and embark on embryo formation. Although SE is a valuable tool for micropropagation in many crops, it presents specific challenges in woody species due to some bottlenecks, such as loss of embryogenic competence during subcultures and the often-low somatic embryo conversion into plantlets. Hence, great interest exists in exploring the regulatory networks involved on SE. As transcription modulators, long non-coding RNAs (lncRNAs) have been found essential in a wide range of biological processes. This work aimed to identify lncRNAs related to the embryogenic competence in Solanum betaceum Cav. (tamarillo). Nanopore® long-read sequencing was conducted in cell lines with distinct cell fates and, based on their coding potential, 60 transcripts were selected as lncRNA candidates. Similar expression patterns were found among embryogenic cell lines (EC) and cells that lost their embryogenic potential (herein long-term callus, LTC), whereas non-EC (NEC) showed differentially expressed lncRNAs. Whereas lncRNAs upregulated in EC and LTC were predicted to target embryogenesis-related genes, such as AGAMOUS-like 15 and WUSCHEL-related HOMEOBOX 2, lncRNAs upregulated in NEC were predicted to target mainly genes involved in carbohydrate metabolism, cell wall formation, auxin and ethylene signalling pathways. Altogether, these results show the involvement of lncRNA in the process of somatic embryogenesis in S. betaceum, indicating that EC present a pattern of lncRNA expression that suggests its action on genes that directly modulate the morphogenic response in vitro, while in NEC the modulation through this type of RNAs seems to be predominantly reflected in genes more related to cellular physiology. LncRNAs upregulated in EC/LTC were predicted to target embryogenesis-related genes, while lncRNAs upregulated in NEC were predicted to target genes involved in auxin and ethylene signalling and carbohydrate metabolism.

In Portugal, the Cova da Beira region is well-known for the production of Prunus spp. and is considered the main peach production area in the country. In the spring of 2021 and 2022, field surveys in peach and nectarine orchards showed symptoms of decline such as cankers, gummosis, dry branches, abortion of flowers, mummified fruits and the partial or total death of some plants. Brown rot is caused by three species of the genus Monilinia, M. fructigena, M. laxa and M. fructicola, the last is an OEPP/EPPO A2 quarantine organism on peach trees. Brown rot disease had previously been described in the Cova da Beira region, however, the recent high mortality and severity of symptoms raised doubts as to the species involved. Symptomatic plant material was collected from thirteen orchards and used for fungal isolation and molecular detection according to the OEPP/EPPO standard. M. fructicola was confirmed morphologically and molecularly in two orchards, and molecularly (duplex real-time PCR) detected in two others. Whole genome sequencing using Oxford Nanopore MinION was also carried out to confirm the identification. Pathogenicity tests were performed on peach, nectarine and sweet cherry fruit according to Koch's postulates. Based on all the results obtained, we report the first detection of M. fructicola in P. persica in Portugal.

The gut microbiota influences intestinal barrier integrity through mechanisms that are incompletely understood. Here we show that the commensal microbiota weakens the intestinal barrier by suppressing epithelial neuropilin-1 (NRP1) and Hedgehog (Hh) signaling. Microbial colonization of germ-free mice dampens signaling of the intestinal Hh pathway through epithelial Toll-like receptor (TLR)-2, resulting in decreased epithelial NRP1 protein levels. Following activation via TLR2/TLR6, epithelial NRP1, a positive-feedback regulator of Hh signaling, is lysosomally degraded. Conversely, elevated epithelial NRP1 levels in germ-free mice are associated with a strengthened gut barrier. Functionally, intestinal epithelial cell-specific Nrp1 deficiency (Nrp1ΔIEC) results in decreased Hh pathway activity and a weakened gut barrier. In addition, Nrp1ΔIEC mice have a reduced density of capillary networks in their small intestinal villus structures. Collectively, our results reveal a role for the commensal microbiota and epithelial NRP1 signaling in the regulation of intestinal barrier function through postnatal control of Hh signaling.

Long-read sequencing methods allow a comprehensive analysis of transcriptomes in identifying full-length transcripts. This revolutionary method represents a considerable breakthrough for non-model species since it allows enhanced gene annotation and gene expression studies when compared to former sequencing methods. However, woody plant tissues are challenging to the successful preparation of cDNA libraries, thus, impairing further cutting-edge sequencing analyses. Here, a detailed protocol for preparing cDNA libraries suitable for high throughput RNA sequencing using Oxford Nanopore Technologies® is described. This method was used to prepare eight barcoded cDNA libraries from two Solanum betaceum cell lines: one with compact morphology and embryogenic competency (EC) and another with friable and non-embryogenic (NEC). The libraries were successfully sequenced, and data quality assessment showed high mean quality scores. Using this method, long-read sequencing will allow a comprehensive analysis of plant transcriptomes.

There is an academic tradition - national and international - which consists of marking the most important events with the publication of collective works, in which we join for some common purpose. The purpose of this Liber Amicorum is to pay tribute to a professor and researcher of the Law School of the University of Minho, who worked 21 years in the institution, gathering great admiration from the academic community. It brings together works by colleagues, from the UM and other Academies, focusing on the area of fundamental rights - from different perspectives - in dialogue with the work of Benedita Mac Crorie.

The gut microbiota is often mentioned as a “forgotten organ” or “metabolic organ”, given its profound impact on host physiology, metabolism, immune function and nutrition. A healthy diet is undoubtedly a major contributor for promoting a “good” microbial community that turns out to be crucial for a fine-tuned symbiotic relationship with the host. Both microbial-derived components and produced metabolites elicit the activation of downstream cascades capable to modulate both local and systemic immune responses. A balance between host and gut microbiota is crucial to keep a healthy intestinal barrier and an optimal immune homeostasis, thus contributing to prevent disease occurrence. How dietary habits can impact gut microbiota and, ultimately, host immunity in health and disease has been the subject of intense study, especially with regard to metabolic diseases. Only recently, these links have started to be explored in relation to lung diseases. The objective of this review is to address the current knowledge on how diet affects gut microbiota and how it acts on lung function. As the immune system seems to be the key player in the cross-talk between diet, gut microbiota and the lungs, involved immune interactions are discussed. There are key nutrients that, when present in our diet, help in gut homeostasis and lead to a healthier lifestyle, even ameliorating chronic diseases. Thus, with this review we hope to incite the scientific community interest to use diet as a valuable non-pharmacological addition to lung diseases management. First, we talk about the intestinal microbiota and interactions through the intestinal barrier for a better understanding of the following sections, which are the main focus of this article: the way diet impacts the intestinal microbiota and the immune interactions of the gut–lung axis that can explain the impact of diet, a key modifiable factor influencing the gut microbiota in several lung diseases.

The concept of heterogeneity among obese individuals in their risk for developing metabolic dysfunction and associated complications has been recognized for decades. At the origin of the heterogeneity idea is the acknowledgement that individuals with central obesity are more prone to developing type 2 diabetes and cardiovascular disease than those with peripheral obesity. There have been attempts to categorize subjects according to their metabolic health and degree of obesity giving rise to different obese and non-obese phenotypes that include metabolically unhealthy normal-weight (MUHNW), metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO). Individuals belonging to the MHO phenotype are obese according to their body mass index although exhibiting fewer or none metabolic anomalies such as type 2 diabetes, dyslipidemia, hypertension, and/or unfavorable inflammatory and fribinolytic profiles. However, some authors claim that MHO is only transient in nature. Additionally, the phenotype categorization is controversial as it lacks standardized definitions possibly blurring the distinction between obesity phenotypes and confounding the associations with health outcomes. To add to the discussion, the factors underlying the origin or protection from metabolic deterioration and cardiometabolic risk for these subclasses are being intensely investigated and several hypotheses have been put forward. In the present review, we compare the different definitions of obesity phenotypes and present several possible factors underlying them (adipose tissue distribution and cellularity, contaminant accumulation on the adipose tissue, dysbiosis and metabolic endotoxemia imposing on to the endocannabinoid tone and inflammasome, and nutrient intake and dietary patterns) having inflammatory activation at the center.

α-Linolenic acid (ALA) is well-known for its anti-inflammatory activity. In contrast, the influence of an ALA-rich diet on intestinal microbiota composition and its impact on small intestine morphology are not fully understood. In the current study, we kept adult C57BL/6J mice for 4 weeks on an ALA-rich or control diet. Characterization of the microbial composition of the small intestine revealed that the ALA diet was associated with an enrichment in Prevotella and Parabacteroides. In contrast, taxa belonging to the Firmicutes phylum, including Lactobacillus, Clostridium cluster XIVa, Lachnospiraceae and Streptococcus, had significantly lower abundance compared to control diet. Metagenome prediction indicated an enrichment in functional pathways such as bacterial secretion system in the ALA group, whereas the two-component system and ALA metabolism pathways were downregulated. We also observed increased levels of ALA and its metabolites eicosapentanoic and docosahexanoic acid, but reduced levels of arachidonic acid in the intestinal tissue of ALA-fed mice. Furthermore, intestinal morphology in the ALA group was characterized by elongated villus structures with increased counts of epithelial cells and reduced epithelial proliferation rate. Interestingly, the ALA diet reduced relative goblet and Paneth cell counts. Of note, high-fat Western-type diet feeding resulted in a comparable adaptation of the small intestine. Collectively, our study demonstrates the impact of ALA on the gut microbiome and reveals the nutritional regulation of gut morphology.

Protease‐activated receptors (PARs) are a unique class of G‐protein‐coupled transmembrane receptors, which revolutionized the perception of proteases from degradative enzymes to context‐specific signaling factors. Although PARs are traditionally known to affect several vascular responses, recent investigations have started to pinpoint the functional role of PAR signaling in the gastrointestinal (GI) tract. This organ is exposed to the highest number of proteases, either from the gut lumen or from the mucosa. Luminal proteases include the host's digestive enzymes and the proteases released by the commensal microbiota, while mucosal proteases entail extravascular clotting factors and the enzymes released from resident and infiltrating immune cells. Active proteases and, in case of a disrupted gut barrier, even entire microorganisms are capable to translocate the intestinal epithelium, particularly under inflammatory conditions. Especially PAR‐1 and PAR‐2, expressed throughout the GI tract, impact gut permeability regulation, a major factor affecting intestinal physiology and metabolic inflammation. In addition, PARs are critically involved in the onset of inflammatory bowel diseases, irritable bowel syndrome, and tumor progression. Due to the number of proteases involved and the multiple cell types affected, selective regulation of intestinal PARs represents an interesting therapeutic strategy. The analysis of tissue/cell‐specific knockout animal models will be of crucial importance to unravel the intrinsic complexity of this signaling network. Here, we provide an overview on the implication of PARs in intestinal permeability regulation under physiologic and disease conditions.

Objective: Recruitment of neutrophils and formation of neutrophil extracellular traps (NETs) contribute to lethality in acute mesenteric infarction. To study the impact of the gut microbiota in acute mesenteric infarction, we used gnotobiotic mouse models to investigate whether gut commensals prime the reactivity of neutrophils towards formation of neutrophil extracellular traps (NETosis). Approach and Results: We applied a mesenteric ischemia-reperfusion (I/R) injury model to germ-free (GF) and colonized C57BL/6J mice. By intravital imaging, we quantified leukocyte adherence and NET formation in I/R-injured mesenteric venules. Colonization with gut microbiota or monocolonization withEscherichia coliaugmented the adhesion of leukocytes, which was dependent on the TLR4 (Toll-like receptor-4)/TRIF (TIR-domain-containing adapter-inducing interferon-beta) pathway. Although neutrophil accumulation was decreased in I/R-injured venules of GF mice, NETosis following I/R injury was significantly enhanced compared with conventionally raised mice or mice colonized with the minimal microbial consortium altered Schaedler flora. Also ex vivo, neutrophils from GF and antibiotic-treated mice showed increased LPS (lipopolysaccharide)-induced NETosis. Enhanced TLR4 signaling in GF neutrophils was due to elevated TLR4 expression and augmented IRF3 (interferon regulatory factor-3) phosphorylation. Likewise, neutrophils from antibiotic-treated conventionally raised mice had increased NET formation before and after ischemia. Increased NETosis in I/R injury was abolished in conventionally raised mice deficient in the TLR adaptor TRIF. In support of the desensitizing influence of enteric LPS, treatment of GF mice with LPS via drinking water diminished LPS-induced NETosis in vitro and in the mesenteric I/R injury model. Conclusions: Collectively, our results identified that the gut microbiota suppresses NETing neutrophil hyperreactivity in mesenteric I/R injury, while ensuring immunovigilance by enhancing neutrophil recruitment.

The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan – from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation.

Bone mineral density (BMD) and microstructure depend on estrogens and diet. We assessed the impact of natural mineral-rich water ingestion on distal femur of fructose-fed estrogen-deficient female Sprague Dawley rats. Ovariectomized rats drank tap or mineral-rich waters, with or without 10%-fructose, for 10 weeks. A sham-operated group drinking tap water was included (n = 6/group). Cancellous and cortical bone compartments were analyzed by microcomputed tomography. Circulating bone metabolism markers were measured by enzyme immunoassay/enzyme-linked immunosorbent assay or multiplex bead assay. Ovariectomy significantly worsened cancellous but not cortical bone, significantly increased circulating degradation products from C-terminal telopeptides of type I collagen and receptor activator of nuclear factor-kappaB ligand (RANKL), and significantly decreased circulating osteoprotegerin and osteoprotegerin/RANKL ratio. In ovariectomized rats, in cancellous bone, significant water effect was observed for all microstructural properties, except for the degree of anisotropy, and BMD (neither a significant fructose effect nor a significant interaction between water and fructose ingestion effects were observed). In cortical bone, it was observed a significant (a) water effect for medullary volume and cortical endosteal perimeter; (b) fructose effect for cortical thickness, medullary volume, cross-sectional thickness and cortical endosteal and periosteal perimeters; and (c) interaction effect for mean eccentricity. In blood, significant fructose and interaction effects were found for osteoprotegerin (no significant water effect was seen). For the first time in ovariectomized rats, the positive modulation of cortical but not of cancellous bone by fructose ingestion and of both bone locations by natural mineral-rich water ingestion is described.

Autologous fat grafting is widely used for soft-tissue augmentation and replacement in reconstructive and aesthetic surgery providing a biocompatible, natural and inexpensive method. Multiple approaches have been developed in the past years, varying in the location of adipose tissue donor-sites, use of wetting solutions, harvesting, processing and placing techniques. Despite many advances in this subject, the lack of standardization in the protocols and the unpredictability of the resorption of the grafted tissue pose a significant limitation for graft retention and subsequent filling. In this review, we discuss several approaches and methods described over the last years concerning the harvesting of autologous fat grafts. We focus on contents such as the best donor-site, differences between existing harvesting techniques (namely tissue resection, hand aspiration or liposuction techniques), recommended harvesting cannula diameters, pressure application and volume of wetting solution injected prior aspiration. Results and comparisons between methods tend to vary according to the outcome measured, thus posing a limitation to pinpoint the most efficient methods to apply in fat grafting. Additionally, the lack of a standard assay to determine viability or volume augmentation of fat grafting remains another limitation to obtain universally accepted grafting procedures and protocols.