Enteric fermentation in ruminants is the largest agricultural source of methane (CH₄) and contributes to global warming. Practical mitigation strategies are therefore needed for sustainable dairy production. This study evaluated a silage inoculant composed of bacteriocin-producing lactic acid bacteria (LAB) strains, Lactococcus lactis subsp. lactis SL242 and Lactiplantibacillus plantarum LP58 in late-lactation, spring-calving Holstein cows. Thirty cows were housed indoors and fed inoculated or control silage for 7 weeks. Daily milk yield and CH₄ emissions were measured, milk composition was analysed weekly and body weight and body condition scores (BCSs) were recorded biweekly. Dry matter intake (DMI) was determined using the n-alkane technique in week 4 of the experimental period to allow the animals to be fully adapted to the experimental diets, with estimated LAB intake of ∼1011 CFU/cow per day. Treatment had no effect on DMI (12.4 ± 0.34 kg/cow per day), concentrate intake (4.3 kg/cow per day), milk yield or BCSs. However, a significant treatment-by-week interaction was observed for milk composition, with transient increases in milk fat concentration and milk solids production in the LAB group during weeks 4 and 5. Rumen microbiota analysis (16S rRNA sequencing) revealed distinct beta diversity clustering between groups at weeks 4 and 7. No overall reduction in CH₄ was observed, but emissions were numerically lower (5.8%) during weeks 4–7, with the greatest decrease (7.7%) at week 5 in the LAB group. These findings suggest that bacteriocin-producing LAB may transiently influence rumen microbial communities and reduce CH₄ output. Further research is warranted to optimise delivery strategies and maximise their potential to support sustainable dairy production.

In light of global sustainability challenges and the limited availability of conventional protein sources for livestock, it became essential to find alternative protein sources. In this context, the reintroduction of grain legumes into crop production systems may represent a promising strategy. Therefore, the aim of this study was to evaluate the replacement of soybean meal by Lupinus albus, on gut microbiota modulation in weaned piglets’ diet. Twenty weaned piglets (Landrace x Large White) were involved in the trial for 28 days. Animals were divided into two experimental groups balanced per weight and sex: the control (CTRL, n = 10) receiving basal diet with 7.3 % soybean meal and the treatment (LUP, n = 10) receiving 10 % of Lupinus albus (L. albus) meal. Microbiota analysis showed a limited modulation in terms of richness and evenness in LUP group compared to CTRL group. However, the dietary inclusion of lupin seed meal resulted in changes in the relative abundance of several bacterial genera, with higher abundances of Methanobrevibacter, a hydrogenotrophic methanogen associated with microbial fermentation, as well as Allobaculum and Romboutsia, which have been associated with the utilization of fibre and complex carbohydrates. In conclusion, the inclusion of L. albus as a replacement for soybean meal, in piglets’ diets could represent a viable strategy to reduce dependence on soybean protein by supporting local protein production systems, particularly suitable for organic farming as well as for extensive livestock systems supplying local markets.

This report summarizes key takeaways from the 11th International Yakult Symposium held in Amsterdam, the Netherlands, in October 2024. It provides an overview of insights obtained by the latest basic and clinical research, meta-analyses, and omics research, underscoring the relevance of the exposome, the outer and inner factors to which our bodies are exposed throughout our entire lifespan, in shaping the microbiota. The symposium addressed external factors such as diet (including probiotics and novel fermented foods), additives, pharmacologic agents, and physical environment, as well as the internal crosstalk between tissue or organ-specific microbial communities and their interactions with immune mediators, metabolic and neuroendocrine hormones, and their receptors. Collectively, the data presented during the symposium reinforced the understanding that health and disease are the result of the (im)balance of a tightly interconnected network rather than isolated axes. This was illustrated using examples of inflammatory and infectious diseases of the brain, mouth, gynaecologic tract, lungs, as well as of metabolic and mental states. Finally, a roundtable discussion on the current state of clinical trials in nutrition, including challenges and solutions was featured. The conclusion indicated that there is room for new developments and that hurdles need to be overcome, requiring continued collaboration across scientific disciplines.

Studies characterising the immunoglobulin (Ig)-bound microbiota apply varying methodologies, making comparisons difficult. This scoping review synthesised evidence on Ig–microbiota binding patterns in maternal and infant contexts, identified recurrent Ig-bound and -unbound bacteria across studies, and highlighted knowledge gaps for further study. Nine articles investigating Ig–microbiota binding patterns in stool or breastmilk samples in mothers or infants were included. Ig–microbiota associations were influenced by sample type, Ig-subclass, genetics, and diet. The most important antibody was IgA, with partial functional redundancy with IgM, while IgG appeared more selective for pathobionts. Ig-bound taxa in early life included important commensals and pathobionts, with high levels of individuality. Ig–microbiota associations shifted with microbiome maturation, environmental and host factors, resembling adults at around 2 years of age. Transfer of Ig-bound Bifidobacterium through breastmilk may contribute to vertical transmission from mother to infant. Ig–microbiota associations also differed between health and disease states, beyond the overall microbiota. Results were limited by study numbers and a lack of methodological consistency. We propose the standardised term “Ig-Seq” in referring to the technique to study Ig–microbiota binding patterns, and suggest standardisation of laboratory protocols, bioinformatic pipelines, and statistical analyses to improve consistency in Ig-Seq.

We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.

Microplastics are widespread in aquatic environments and support surface-associated microbial communities. Although antimicrobial resistance in the plastisphere has been reported, the organization of resistance genes across plasmid types and mobility categories on microplastic surfaces remains incompletely characterized. In this study, we analyzed published microplastic biofilm metagenomes to examine microbial community structure, plasmid replicon diversity, predicted mobility, and antimicrobial resistance genes (ARG) distributions across microplastics from various global locations. Phylum-level taxonomic profiles varied by geography, but most plastisphere communities were dominated by Pseudomonadota. Core microbiome analysis revealed several genera within the Pseudomonadota (Paracoccus, Pseudomonas, Sphingomonas, Sulfitobacter, Vibrio, Mesorhizobium, Rhizobium, Bradyrhizobium, Roseovarius, and Hyphomonas) as members of the plastisphere core. Plasmid reconstruction revealed differences in predicted mobility profiles, with conjugative plasmids frequently identified in the polyethylene, polypropylene, and polyvinyl chloride samples. A co-occurrence analysis of plasmid mobility, replicons, and ARG showed that conjugative plasmids connected a broader range of replicons to multiple ARG classes than mobilizable or non-mobilizable plasmids. IncFIB and IncFII replicons were prominent with high ARG co-occurrence. Additionally, several less-characterized rep_cluster replicons were detected across microplastic types, indicating diverse and understudied plasmid backbones within plastisphere communities, underscoring the importance of considering plasmid context when evaluating plastisphere resistomes.

Not only do politics and society struggle to make sense of current and future existential challenges, but science, especially in inter- and transdisciplinary endeavours, tackles the multifarious and often inextricably linked emergencies of our time. This contribution explores the intersection of cutting-edge microbiome science and literary works of art and its vital role in Public Humanities agendas. By the example of Adam Dickinson’s unique poetry collection Anatomic (2018), the paper demonstrates how the emerging, rapidly growing, and paradigm-shifting knowledge of the microbiome is a symbol for the porousness of science and literature, which not only fuels scientific and aesthetic innovation by enabling manifold exchanges beyond disciplinary and academic boundaries but also points towards its specific precariousness. As not only the borders of science and literature become porous as a prerequisite and result of circulatory processes of collaborative knowledge production but also the borders of (human) bodies as the sites of this knowledge-making do, there seems to be nothing less to negotiate than what it means to be human per se pointing towards modes of being human yet to be imagined by science and literature, within and beyond Academia alike.

The increasing demand for sustainable feed ingredients in aquaculture has driven research into alternative protein sources to replace fishmeal. This study evaluated the nutritional, physiological, and microbiological impacts of housefly (Musca domestica) larvae meal as a replacement for fishmeal in the diets of rainbow trout (Oncorhynchus mykiss). Diets were formulated to replace fishmeal with larvae meal at 50% and 100% inclusion levels. Growth performance, body composition, intestinal health, and gut microbiota were assessed over a 16-week feeding trial. Fish fed larvae meal-based diets exhibited comparable growth metrics, muscle yield, and hepatosomatic index to those fed fishmeal and commercial diets, indicating no compromise in growth efficiency. Intestinal histological examination revealed no diet-induced morphological changes, with all parameters remaining within normal ranges, highlighting the compatibility of larvae meal with fish intestinal health. Analysis of gut microbiota showed a shift toward Firmicutes dominance and increased abundance of Clostridiales in larvae meal-fed fish, suggesting enhanced fermentation activity. Blood chemistry parameters were consistent across dietary groups, supporting the physiological suitability of larvae meal-based diets. These findings demonstrate that housefly larvae meal is a sustainable and nutritionally viable alternative to fishmeal in aquafeeds for rainbow trout. The results underscore its potential to reduce reliance on fishmeal while maintaining fish health and growth performance.

Cervical cancer remains a major global health burden. Despite standard-of-care therapies, 30–50% of locally advanced-stage patients develop treatment resistance, leading to recurrence and mortality. While tumour-intrinsic mechanisms (e.g., DNA methylation, cancer-associated fibroblasts) explain only partial resistance heterogeneity, emerging evidence identifies the microbiome as a critical modulator of therapeutic efficacy. This review synthesizes recent advances demonstrating that vaginal microbial dysbiosis, characterized by Lactobacillus iners enrichment and L. crispatus depletion, drives resistance through lactate-mediated metabolic rewiring, immune checkpoint stabilization and drug metabolism alteration. Longitudinal studies reveal dynamic microbiome trajectories during therapy, with geographic variations (notably HIV co-infection in sub-Saharan Africa) further modulating treatment responses. We critically evaluate microbiome-based interventions, from probiotics to engineered bacteria, including synthetic biology-driven precision microbiome therapies, and establishing standardized multi-centre trial protocols. Bridging mechanistic insights with clinical application represents a paradigm shift towards microbiome-informed cervical cancer management.

Current efforts to reduce the incidence of non-communicable disease (NCD) are slow, but increasing evidence highlights the microbiome as a potential target for prevention. The majority of microbial development occurs in the first 1,000 days of life, presenting opportunities for strategic intervention to reduce the prevalence of future NCDs. In this review, we explore the social, structural, and political barriers that may hinder physiological gut microbial development in the first 1,000 days in the context of current scientific knowledge, focusing on nutritional factors in pregnancy, and during the exclusive breastfeeding and complementary feeding periods. We summarise emerging evidence and explore obstacles to nutritional choices affecting microbial development, and unpack the rhetoric that healthy eating to develop a microbiome that supports optimum health is an individual choice. As evidence on the role of the microbiome in health and disease grows, specific attention must be applied to existing social, structural, and political barriers that may hinder optimal microbial development. Addressing the role of corporate actors and social determinants influencing dietary choices and barriers surrounding breastfeeding must be prioritised, alongside efforts to advance basic scientific research. Until a wider public health perspective is taken, the success of interventions and recommendations will be limited.

Microbial dysbiosis has been linked to environmental enteropathy (EE) and alterations in nutrient absorption; however, compositional modifications following exposure to supplementary nutrients are poorly understood. Here, we report the effect of amino acid and micronutrient supplementation on the gut microbiome of adults with EE.

In the AMAZE trial, adults with EE were randomized to amino acids (AA) and/or micronutrients (MM) for 16 weeks in a 2 × 2 factorial design against placebo. Endoscopy was performed before and after intervention, during which duodenal aspirates were collected as well as fecal samples. 16S rRNA amplicon sequencing was performed on both these samples, and differences in bacterial community composition before and after interventions were investigated using differential abundance analysis, corrected using false discovery rate, plus alpha and beta diversity measurements.

HIV seropositive participants exhibited lower alpha and beta diversity at baseline. AA and/or MM supplementation did not show significant changes in abundance or diversity of genera post-intervention compared to placebo. Micronutrient supplementation resulted in an increase in the pyruvate fermentation to acetone MetaCyc pathways compared to the placebo arm.

This study provides insights into the responsiveness of the gut microbiome to micronutrient and amino acid supplementation in adults with EE.

Decreased gut microbial diversity is associated with greater depression symptoms in adults. Findings on the relationship between the gut microbiome and depression or anxiety in children and adolescents are mixed, and evidence syntheses are needed. Seven databases were searched for peer-reviewed studies on the gut microbiome and internalizing symptoms, depression, or anxiety, in children and adolescents (<19 years). Random-effects meta-analyses of alpha diversity indices were performed. Youth advisors validated the research findings’ relevance to their experiences and contributed to dissemination planning. Eight studies were included, representing 2,865 participants (mean age = 11.4 years, SD = 4.3). Study designs were cross-sectional (n = 5), longitudinal (n = 2), and interventional (n = 1). No association was found between alpha or beta diversity and internalizing problems, depression, or anxiety. Increased abundance of genera within phyla Bacillota (e.g., Fusicatenibacter) and Pseudomonadota (e.g., Escherichia), along with decreased abundance of other Bacillota genera (e.g., Faecalibacterium), were associated with depression and anxiety symptoms. This review identified preliminary associations between specific bacterial taxa and depression and anxiety in children and adolescents. Larger studies using comprehensive analytical approaches are needed to explore the role of the gut microbiome in the genesis and treatment of internalizing disorders.

Microbiomes are communities of microorganisms that form close associations with metazoan hosts and have important roles in host biological processes. With the advent of Next Generation Sequencing, the microbiomes of myriad animals and plants have been described. However, the microbiomes of parasites have received little attention, which is surprising considering their ecological and medical importance. This study characterizes, for the first time, the microbiome of Dujardinascaris helicina, a gastrointestinal nematode parasite of the American crocodile. Dujardinascaris helicina were isolated from crocodiles residing in two geographically separated habitats across Belize. Using 16S sequencing, we compare β-diversity between sampling locations using generalized linear mixed modeling. Our results show that D. helicina microbiomes differ in composition depending on location. We also show that D. helicina microbiomes show strong shifts toward consolidation of specific taxa when proximity to human modified environments increases.

Colorectal cancer (CRC) represents a relevant public health problem, with high incidence and mortality in Western countries. CRC can occur as sporadic (65%–75%), common familial (25%), or as a consequence of an inherited predisposition (up to 10%). While unravelling its genetic basis has been a long trip leading to relevant clinical implementation over more than 30 years, other contributing factors remain to be clarified. Among these, micro-organisms have emerged as critical players in the development and progression of the disease, as well as for CRC treatment response. Fusobacterium nucleatum (Fn) has been associated with CRC development in both pre-clinical models and clinical settings. Fusobacteria are core members of the human oral microbiome, while being less prevalent in the healthy gut, prompting questions about their localization in CRC and its precursor lesions. This review aims to critically discuss the evidence connecting Fn with CRC pathogenesis, its molecular subtypes and clinical outcomes.

The endocannabinoidome (eCBome) and the gut microbiota have been implicated in diet-induced obesity and impaired metabolism. While the eCBome and the gut microbiome are known to respond to diet macronutrient composition, interaction with micronutrient intake has been relatively unexplored. Iron (Fe) is an essential micronutrient for the function of enzymes involved in energy and lipid metabolism. Here, we evaluated how 28 days of Fe depletion and enrichment, in interaction with Low Fat-Low Sucrose (LFLS) or High Fat-High Sucrose (HFHS) diets, affect the host via the eCBome, and modulate intestinal gut microbial communities. Circulating levels of N-oleoyl-ethanolamine (OEA) showed an elevation associated with Fe-enriched LFLS diet, while the Fe-depleted HFHS diet showed an elevation of N-arachidonoyl-ethanolamine (anandamide, AEA) and a decrease of circulating linoleic acid. In parallel, the response of intestinal inflammatory mediators to Fe in the diet showed decreased levels of prostaglandins PGE1, PGE3, and 1a,1b-dihomo PGF2α in the caecum. Individual differences in microbial taxa were less pronounced in the ileum than in the caecum, where Eubacterium coprostanoligenes group showed an increase in relative abundance associated with Fe-depleted LFLS diets. In conclusion, our study shows that Fe intake modulates the response to the macronutrient composition of the diet in mice.

Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (Macaca mulatta), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (n = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14–30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6–8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify “co-abundance factors” describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (MaAsLin2) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high Prevotella and Lactobacillus (β = −0.88, p = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (β = −1.33, p = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: β = −3.13, p < 0.01; Shannon diversity model: β = −3.77, p < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.