Agricultural and Veterinary Sciences

Supplementary files related to article entitled Evaluating in vitro nutritional strategies clusters for mitigating methane emissions in intensive dairy farms by a mechanistic model of in vitro rumen fermentation

This data is related to untargeted metabolomics of a published paper entitled "Exogenous syringic acid mitigates arsenic toxicity in lettuce plants: A physiological, antioxidant, and metabolomics investigation" in Physiologia plantarum.

Daily feeding behavior (FB) in ruminants emerges from interacting physiological, dietary, managerial, and environmental drivers (Albright, 1993). Systems thinking (ST) provides a methodological base to conceptualize this complex biological phenomenon by identifying the interaction between variables (Tedeschi et al., 2025). A preliminary causal loop diagram (CLD) had previously identified the main feedback structures underlying FB, but several dynamic structures were not fully explicated, particularly those linking FB with nutrient inflow, nitrogen efficiency, and nitrogen dynamics as well as recycling (Canossa et al., 2025). This limitation is relevant to move toward a mathematical formulation of the conceptual model. A systems thinking approach was applied through problem articulation, system boundary definition, literature review, and extraction of variables and causal relationships from more than 90 publications. The previous CLD was refined by integrating short-term ingestive regulation with medium-term metabolic responses and external constraints. Where available, variables and causal links were specified using literature-derived quantitative evidence, so that the feedback structure is aligned with measurable relationships among key variables. The refined CLD highlights that FB is a determinant of nutrient inflow, because meal pattern and eating rate regulate the timing and quantity of substrates entering rumen fermentation. This is relevant for nitrogen dynamics, since dietary N intake, ruminal ammonia production, microbial N synthesis, urea-N recycling, and urinary and fecal N excretion depend on nutrient entry and absorption/transformation within the digestive system (Li et al., 2019). Thus, the expanded CLD provides a conceptual basis for linking feeding behavior to intake dynamics and for developing a quantitative model of nutrient inflow and nitrogen flows, supporting the evaluation of strategies to improve nitrogen use efficiency and reduce N excretion.

Files generated by Vensim Professional software (version 10.3.2, Ventana System Inc., Harvard, MA) containing raw data for causal loop diagram (CLD) representing the conceptual model of feeding behavior. The variables influencing those shown in Fig. 1 and determining daily meal pattern are grouped (clockwise) into: physiology, metabolism and health status; environment and feed bunk management; feed characteristics; and animal traits. A total of 14 feedback loops were identified: R1: feeding behavior; R2: hunger hormones; R3: metabolic disorders and feed consumption; R4: metabolic disorders, energy requirements, and energy balance; R5: dynamics of fermentation products in the rumen-reticulum compartment; R6: animal physical activity and feed intake; R7: ruminal particle flow; R8: competition for feeding space; B1: DM content in the rumen; B2: gap in energy balance; B3: animal activity and feeding frequency; B4: fill effect; B5: management of the feed station; and B7: feed sorting. Among these, seven loops are highlighted as they represent key control mechanisms of feed intake: physiological (R2), physical (B4), and psychogenic (R3, R8, B1, B5, B7)

This study provides preliminary results on the changes of plasma analytes in dairy goats having a positive or negative bacteriological culture before dry-off and the use of intramammary tube of cephazolin. Goats having a positive bacteriological culture experienced dyslipidemia 5 days after dry-off and a greater inflammatory status around kidding. Antibiotic administration at dry-off did not affect plasma analytes trends. Plasma analytes could serve as effective diagnostic tools to improve the detection of intramammary infections in dairy goats. This dataset includes supplementary information supporting the main paper. In particular: Table s1. Intra- and inter-assay coefficient of variations, limit of quantification (LOQ), codes of commercial kits used, calibrators and quality controls used for plasma analytes included in the study. Values are reported based on bovine plasma, which represents the most frequently analyzed matrix in our laboratory and for which robust datasets are available. All assays were also verified for consistency and repeatability in goat plasma before use. Figure S2. Time course of plasma concentrations of creatinine and calcium in Alpine dairy goats having a healthy (HEAL) or infected (INFE) mammary gland 7 days before dry-off.

Supplementary materials. Table S1 Metabolomics dataset of Maize plants under normal, heat stress, and combination with organic matter Table S2 Metabolomics dataset of Sunflower plants under normal, heat stress, and combination with organic matter Table S3 Statistical analysis from AMOPLS-DA model for both Mazie and Sunflower, shared and separately Table S4 VIP markers name and values of the most significant contribution to pairwise comparisons Table S5 Statistical analysis from Random Forest model for both Mazie and Sunflower

Heavy metal (HM) contamination in agricultural soils poses a significant threat to soil health and plant productivity. This study investigates the impact of cadmium (Cd) and zinc (Zn) stress on tomato plants (Solanum lycopersicum) and explores the mitigation potential of microbial biostimulants (MBs), including arbuscular mycorrhizal fungi (AMF) and Pseudomonas fluorescens So_08 (PGPR), over a 52-day period using multi-omics ap-proaches. Root exudate profiling revealed distinct metabolic changes under HM stress, which compromised soil-plant interactions. Cd stress reduced the secretion of phe-nylpropanoids (sum LogFC: -45.18), lipids (sum LogFC: -27.67), and isoprenoids (sum LogFC: -11-67), key metabolites in antioxidative defense, while also suppressing rhi-zosphere fungal populations. Conversely, Zn stress enhanced lipid exudation (such as sphingolipids and sterols, as sum LogFC of 8,72 and 9.99, respectively) to maintain membrane integrity and reshaped rhizobacterial communities. The MBs application mitigated HM-induced stress by enhancing specialized metabolite syntheses, including cinnamic acids, terpenoids, and flavonoids, which promoted crop resilience. MBs also reshaped microbial diversity, fostering beneficial species like Portibacter spp., Alkalitalea saponilacus under Cd stress, and stimulating rhizobacteria like Aggregatilinea spp. under Zn stress. Specifically, under Cd stress, bacterial diversity remained relatively stable, suggesting their resilience to Cd. However, fungal communities exhibited greater sen-sitivity, with a decline in diversity in Cd-treated soils and partial recovery when MBs were applied. Conversely, Zn stress caused decline in bacterial α-diversity, while fungal diversity was maintained, indicating that Zn acts as an ecological filter that suppresses sensitive bacterial taxa and favors Zn-tolerant fungal species. Multi-omics data integration combined with network analysis highlighted key features associated with improved nutrient availability and reduced HM toxicity under MB treatments, including metabo-lites and microbial taxa linked to sulfur cycling, nitrogen metabolism, and iron reduction pathways. These findings demonstrate that MBs can modulate plant metabolic responses and restore rhizosphere microbial communities under Cd and Zn stress, with PGPR showing broader metabolomic recovery effects and AMF influencing specific metabolite pathways. This study provides new insights into plant-microbe interactions in HM-contaminated environments, supporting the potential application of biostimulants for sustainable soil remediation and plant health improvement. Version 2: The data was changed based on reviewer request

Supplementary table 1. Least squares means and associated SEM for reproductive parameters in lactating Holstein cows from 7 to 56 DIM (n = 10/group; Control = CTR; Mycotoxin = MTX; Mycotoxin-deactivating product = MDP). Three primiparous (P) and 7 multiparous (M) (lactation no.: CTR = 3.33±1.50, MTX = 3.67 ±1.33, MDP 3.5±1.15) cows were enrolled per group. The CTR diet was supplemented with a placebo (0.34% DM), the MTX ration was added a mycotoxin contaminated culture medium (0.19%) and placebo (0.19%), whereas the MDP was supplemented with the culture medium (0.19%) and MDP product (Mycofix, BIOMIN Holding, GmbH, Tulln, Austria; 0.15%), a mycotoxin-deactivating product. Different letters indicate statistical differences (a-b-c P  0.05).

Supplementary material of manuscript - A Pseudomonas Plant Growth Promoting Rhizobacterium and Arbuscular Mycorrhiza differentially modulate the growth, photosynthetic performance, nutrients allocation, and stress response mechanisms triggered by a mild Zinc and Cadmium stress in tomato

dataset of the manuscript "A new metabolomics insight for origin and processing authentication of thyme by comprehensive UHPLC-HRMS fingerprinting and chemometrics" by Araceli Rivera-Pérez, Pascual García-Pérez, Roberto Romero-González, Antonia Garrido Frenich, and Luigi Lucini The data are produced by LC-HRMS foodomics and include annotated features, Ms and MS/MS spectra, as well as individual abundance across samples and treatments.