BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration

The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as blind docking or site-specific targeting, which are invaluable in applications ranging from drug repositioning to the exploration of new allosteric binding sites and toxicity assessments. BioProtIS has been designed with modularity at its core. This inherent flexibility empowers users to make custom modifications directly within the source code, tailoring the pipeline to their specific research needs. Moreover, it lays the foundation for seamless integration of diverse docking algorithms in future iterations, promising ongoing advancements in the field of computational biology. This pipeline is available for free distribution and can be download at: https://github.com/BBMDO/BioProtIS.

Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan

The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.

Invited review: Muscle protein breakdown and its assessment in periparturient dairy cows

Mobilization of body reserves including fat, protein, and glycogen is necessary to overcome phases of negative nutrient balance typical for high-yielding dairy cows during the periparturient period. Skeletal muscle, the largest internal organ in mammals, plays a crucial role in maintaining metabolic homeostasis. However, unlike in liver and adipose tissue, the metabolic and regulatory role of skeletal muscle in the adaptation of dairy cows to the physiological needs of pregnancy and lactation has not been studied extensively. The functional integrity and quality of skeletal muscle are maintained through a constant turnover of protein, resulting from both protein breakdown and protein synthesis. Thus, muscle protein breakdown (MPB) and synthesis are intimately connected and tightly controlled to ensure proper protein homeostasis. Understanding the regulation of MPB, the catabolic component of muscle turnover, and its assessment are therefore important considerations to provide information about the timing and extent of tissue mobilization in periparturient dairy cows. Based on animal models and human studies, it is now evident that MPB occurs via the integration of 3 main systems: autophagy-lysosomal, calpain Ca²⁺-dependent cysteine proteases, and the ubiquitin-proteasome system. These 3 main systems are interconnected and do not work separately, and the regulation is complex. The ubiquitin-proteasomal system is the most well-known cellular proteolytic system and plays a fundamental role in muscle physiology. Complete degradation of a protein often requires a combination of the systems, depending on the physiological situation. Determination of MPB in dairy cows is technically challenging, resulting in a relative dearth of information. The methods for assessing MPB can be divided into either direct or indirect measurements, both having their strengths and limitations. Available information on the direct measures of MPB primarily comes from stable isotopic tracer methods and those of indirect measurements from assessing expression and activity measures of the components of the 3 MPB systems in muscle biopsy samples. Other indirect approaches (i.e., potential indicators of MPB), including ultrasound imaging and measuring metabolites from muscle degradation (i.e., 3-methylhistidine and creatinine), seem to be applicable methods and can provide useful information about the extent and timing of MPB. This review presents our current understanding, including methodological considerations, of the process of MPB in periparturient dairy cows.

Investigating circulating miRNA in transition dairy cows: What miRNAomics tells about metabolic adaptation

In the current study, we investigated dairy cows’ circulating microRNA (miRNA) expression signature during several key time points around calving, to get insights into different aspects of metabolic adaptation. In a trial with 32 dairy cows, plasma samples were collected on days −21, 1, 28, and 63 relative to calving. Individually extracted total RNA was subjected to RNA sequencing using NovaSeq 6,000 (Illumina, CA) on the respective platform of IGA Technology Services, Udine, Italy. MiRDeep2 was used to identify known and novel miRNA according to the miRbase collection. Differentially expressed miRNA (DEM) were assessed at a threshold of fold-change > 1.5 and false discovery rate < 0.05 using the edgeR package. The MiRWalk database was used to predict DEM targets and their associated KEGG pathways. Among a total of 1,692 identified miRNA, 445 known miRNA were included for statistical analysis, of which 84, 59, and 61 DEM were found between days −21 to 1, 1 to 28, and 28 to 63, respectively. These miRNA were annotated to KEGG pathways targeting the insulin, MAPK, Ras, Wnt, Hippo, sphingolipid, T cell receptor, and mTOR signaling pathways. MiRNA-mRNA network analysis identified miRNA as master regulators of the biological process including miR-138, miR-149-5p, miR-2466-3p, miR-214, miR-504, and miR-6523a. This study provided new insights into the miRNA signatures of transition to the lactation period. Calving emerged as a critical time point when miRNA were most affected, while the following period appeared to be recovering from massive parturition changes. The primarily affected pathways were key signaling pathways related to establishing metabolic and immune adaptations.

Limiting factors for milk production in dairy cows: perspectives from physiology and nutrition

Milk production in dairy cows increases worldwide since many decades. With rising milk yields, however, potential limiting factors are increasingly discussed. Particularly, the availability of glucose and amino acids is crucial to maintain milk production as well as animal health. Limitations arise from feed sources, the rumen and digestive tract, tissue mobilization, intermediary metabolism and transport, and the uptake of circulating nutrients by the lactating mammary gland. The limiting character can change depending on the stage of lactation. Although physiological boundaries are prevalent throughout the gestation-lactation cycle, limitations are aggravated during the early lactation period when high milk production is accompanied by low feed intake and high mobilization of body reserves. The knowledge about physiological constraints may help to improve animal health and make milk production more sustainably. The scope of this review is to address contemporary factors related to production limits in dairy cows from a physiological perspective. Besides acknowledged physiological constraints, selected environmental and management-related factors affecting animal performance and physiology will be discussed. Potential solutions and strategies to overcome or to alleviate these constraints can only be presented briefly. Instead, they are thought to address existing shortcomings and to identify possibilities for optimization. Despite a scientific-based view on physiological limits, we should keep in mind that only healthy animals could use their genetic capacity and produce high amounts of milk.

Expression of specific signaling components related to muscle protein turnover and of branched-chain amino acid catabolic enzymes in muscle and adipose tissue of preterm and term calves

Postnatal metabolism depends on maturation of key metabolic pathways around birth. In this regard, endogenous glucose production is impaired in calves born preterm. Concerning protein metabolism, the rates of protein turnover are greater during the neonatal period than at any other period of postnatal life. The mammalian target of rapamycin (mTOR) and the ubiquitin-proteasome system (UPS) are considered as the major regulators of cellular protein turnover. The objectives of this study were to investigate (1) the changes in plasma AA profiles, (2) the mRNA abundance of mTOR signaling and UPS-related genes in skeletal muscle, and (3) the mRNA abundance of branched-chain AA (BCAA) catabolic enzymes in skeletal muscle and adipose tissue in neonatal calves with different degree of maturation during the transition to extrauterine life. Calves (n = 7/treatment) were born either preterm (PT; delivered by cesarean section 9 d before term) or at term (T; spontaneous vaginal delivery) and were left unfed for 1 d. Calves in treatment TC were also spontaneously born but were fed colostrum and transition milk for 4 d. Blood samples were collected from all calves at birth and at 24 h of life. Additional blood samples were taken 2 h after feeding (26 h of life) for PT and T calves, and on d 4 of life for TC, to determine plasma glucose, urea, and AA. Tissue samples from 3 muscles [M. longissimus dorsi (MLD), M. semitendinosus (MST), and M. masseter (MM)], and kidney fat were collected following euthanasia at 26 h after birth (PT, T) or on d 4 of life (TC) at 2 h after feeding. The concentrations of the majority of plasma AA (Ala, Gln, Asn, Cit, Lys, Orn, Thr, and Tyr), nonessential AA, and total AA were greater during the first 24 h and also before and 2 h after feeding in PT than in T. The ratio of plasma BCAA to the aromatic AA (Tyr and Phe) was greatest in TC, followed by T, and least in PT. The mRNA abundance of mTOR and ribosomal protein S6 kinase 1 (S6K1) in MLD and MM was greater in PT and T than in TC. The mRNA abundance of muscle-specific ligases FBXO32 (F-box only protein 32) in the 3 different skeletal muscles and TRIM63 (tripartite motif containing 63) in MLD was greater in PT and T than in TC; in MM, TRIM63 mRNA was greatest in PT. The mRNA for BCKDHA and BCKDHB (the α and β polypeptide of branched-chain α-keto acid dehydrogenase) in kidney fat was elevated in PT and T compared with TC, suggesting a possible enhancement of BCAA oxidation as energy source to cover the energetic and nutritional postnatal demands in PT and T in a starved state. The increased abundances of mTOR-associated signaling factors and muscle-specific ligase mRNA indicate a greater rate of protein turnover in muscles of PT and T in a starved state. Elevated plasma concentrations of several AA may result from enhanced muscle proteolysis and impaired conversion to glucose in the liver of PT calves.

Flash dietary methionine supply over growth requirements in pigs: Multi-facetted effects on skeletal muscle metabolism

Dietary methionine affects protein metabolism, lean gain and growth performance and acts in the control of oxidative stress. When supplied in large excess relative to growth requirements in diets for pigs, positive effects on pork quality traits have been recently reported. This study aimed to decipher the molecular and biochemical mechanisms affected by a dietary methionine supply above growth requirements in the loin muscle of finishing pigs. During the last 14 days before slaughter, crossbred female pigs (n = 15 pigs/diet) were fed a diet supplemented with hydroxy-methionine (Met5; 1.1% of methionine) or not (CONT, 0.22% of methionine). Blood was sampled at slaughter to assess key metabolites. At the same time, free amino acid concentrations and expression or activity levels of genes involved in protein or energy metabolism were measured in the longissimus lumborum muscle (LM). The Met5 pigs exhibited a greater activity of creatine kinase in plasma when compared with CONT pigs. The concentrations of free methionine, alpha-aminobutyric acid, anserine, 3-methyl-histidine, lysine, and proline were greater in the LM of Met5 pigs than in CONT pigs. Expression levels of genes involved in protein synthesis, protein breakdown or autophagy were only scarcely affected by the diet. Among ubiquitin ligases, MURF1, a gene known to target creatine kinase and muscle contractile proteins, and OTUD1 coding for a deubiquitinase protease, were up-regulated in the LM of Met5 pigs. A lower activity of citrate synthase, a reduced expression level of ME1 acting in lipogenesis but a higher expression of PPARD regulating energy metabolism, were also observed in the LM of Met5 pigs compared with CONT pigs. Principal component analysis revealed that expression levels of many studied genes involved in protein and energy metabolism were correlated with meat quality traits across dietary treatments, suggesting that subtle modifications in expression of those genes had cumulative effects on the regulation of processes leading to the muscle transformation into meat. In conclusion, dietary methionine supplementation beyond nutritional requirements in pigs during the last days before slaughter modified the free amino acid profile in muscle and its redox capacities, and slightly affected molecular pathways related to protein breakdown and energy metabolism. These modifications were associated with benefits on pork quality traits.

Effects of metabolizable protein concentration, amino acid profile, and fiber source on the messenger RNA expression of skeletal muscle in peripartum dairy cows

After parturition, dairy cows mobilize AA from skeletal muscle to meet metabolizable protein (MP) requirements. High mobilization may compromise cow health and longer-term milk production. Postpartum diets with higher MP concentrations, improved AA profiles, or MP increased at the expense of forages rather than nonforage fiber sources may attenuate muscle catabolism; however, the molecular mechanisms responsible need investigation. We evaluated mRNA expression in the longissimus dorsi of cows fed postpartum diets differing in MP concentration, AA profile, and fiber source. From 0 to 25 d after parturition, 40 multiparous cows received the following diets: (1) 13% deficient in MP (D-MP), (2) adequate in MP using primarily soy protein (A-MP), (3) adequate in MP using blends of proteins and individual AA to improve the AA profile (Blend), or (4) similar to Blend except additional protein replaced forage (Blend-fNDF). Biopsies were taken approximately -5, 7, and 25 d relative to parturition. Greater dietary MP concentration (D-MP vs. A-MP and Blend) decreased expression of genes related to protein synthesis (MTOR, RPS6KB1) and degradation (FOXO1), inflammation (IFNG, TLR4), and endoplasmic reticulum (ER) stress (HSPA5, DDIT) and increased genes associated with lipogenesis (PPARG) and glucose oxidation (LDH, MB). In Blend versus A-MP (i.e., effect of AA profile), expression related to apoptosis (CASP8) and inflammation (TNFA) decreased and genes associated with cell cycle progression (E2F1) and fast-twitch glycolytic muscle fiber type (MYH4) increased. Less forage (Blend-fNDF vs. Blend) decreased genes associated with lipogenesis (PPARG, ACACA) and ER stress (BCL2, DDIT3, EIF2AK3, PPP1R15A) and increased genes associated with inflammation (TNF), inhibition of myogenesis (MSTN), and autophagy (PEBP1). In summary and based on mRNA expression, increasing MP supply may attenuate muscle turnover and ER stress. However, an unbalanced AA supply reduced cell cycle progression and protein synthesis. Lower energy supplies may reduce cell growth and cause autophagy.

Targeted assessment of the metabolome in skeletal muscle and in serum of dairy cows supplemented with conjugated linoleic acid during early lactation

In the dairy cow, late gestation and early lactation are characterized by a complexity of metabolic processes required for the homeorhetic adaptation to the needs of fetal growth and milk production. Skeletal muscle plays an important role in this adaptation. The objective of this study was to characterize the metabolome in skeletal muscle (semitendinosus muscle) and in serum of dairy cows in the context of the physiological changes occurring in early lactation and to test the effects of dietary supplementation (from d 1 in milk onwards) with conjugated linoleic acids (sCLA; 100 g/d; supplying 7.6 g of cis-9,trans-11 CLA and 7.6 g of trans-10,cis-12 CLA per cow/d; n = 11) compared with control fat-supplemented cows (CTR; n = 10). The metabolome was characterized in skeletal muscle samples collected on d 21 and 70 after calving in conjunction with their serum counterpart using a targeted metabolomics approach (AbsoluteIDQ p180 kit; Biocrates Life Sciences AG, Innsbruck, Austria). Thereby 188 metabolites from 6 different compound classes (acylcarnitines, amino acids, biogenic amines, glycerophospholipids, sphingolipids, and hexoses) were quantified in both sample types. In both groups, dry matter intake increased after calving. It was lower in sCLA than in CTR on d 21, which resulted in reduced calculated net energy and metabolizable protein balances. On d 21, the concentrations of dopamine, Ala, and hexoses in the skeletal muscle were higher in sCLA than in CTR. On d 21, the changed metabolites in serum were mainly long-chain (>C24) diacyl phosphatidylcholine PC (PC-aa) and acyl-alkyl phosphatidylcholine (PC-ae), along with lysophosphatidylcholine acyl (lysoPC-a) C26:1 that were all lower in sCLA than in CTR. Supplementation with CLA affected the muscle concentrations of 22 metabolites on d 70 including 10 long-chain (>C22) sphingomyelin (SM), hydroxysphingomyelin [SM(OH)], PC-aa, and PC-ae along with 9 long-chain (>C16) lysoPC-a and 3 metabolites related to amino acids (spermine, citrulline, and Asp). On d 70, the concentrations of lysoPC-a C18:2 and C26:0 in serum were higher in the sCLA cows than in the CTR cows. Regardless of treatment, the concentrations of Ile, Leu, Phe, Lys, His, Met, Trp, and hydroxybutyrylcarnitine (C4-OH) decreased, whereas those of ornithine, Gln, and trans-4-hydroxyproline (t4-OH-Pro) increased from d 21 to 70 in muscle. The significantly changed metabolites in serum with time of lactation were 28 long-chain (>C30) PC-ae and PC-aa, 7 long-chain (>C16) SM and SM(OH), along with lysoPC-a C20:3 that were all increased. In conclusion, in addition to other significantly changed metabolites, CLA supplementation mainly led to changes in muscle and serum concentrations of glycerophospholipids and sphingolipids that might reflect the phospholipid compositional changes in muscle. The metabolome changes observed in sCLA on d 21 seem to be, at least in part, due to the lower DMI in these cows. The changes in the muscle concentrations of AA from d 21 to 70, which coincided with the steady energy and MP balances, might reflect a shift of protein synthesis/degradation balance toward synthesis.

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Profiling of circulating microRNA and pathway analysis in normal- versus over-conditioned dairy cows during the dry period and early lactation

The objective of this study was to determine the circulating microRNA (miRNA) profile in over-conditioned (HBCS) versus normal-conditioned (NBCS) dairy cows in combination with pathway enrichment analyses during the transition period. Thirty-eight multiparous Holstein cows were selected 15 wk before anticipated calving date based on their current and previous body condition scores (BCS) for forming either a HBCS group (n = 19) or a NBCS group (n = 19). They were fed different diets during late lactation to reach the targeted differences in BCS and backfat thickness until dry-off. A subset of 15 animals per group was selected based on their circulating concentrations of nonesterified fatty acids (on d 14 postpartum) and β-hydroxybutyrate (on d 21 postpartum), representing the greater or the lower extreme values within their BCS group. Blood serum obtained at d -49 and 21 relative to parturition (3 pools with 5 cows per each group and time point) were used to identify miRNA that were differentially expressed (DE) between groups or time points using miRNA sequencing. No DE-miRNA were discovered between NBCS versus HBCS. Comparing pooled samples from d -49 and d 21 resulted in 7 DE-miRNA in the NBCS group, of which 5 miRNA were downregulated and 2 miRNA were overexpressed on d 21 versus -49. The abundance of 5 of these DE-miRNA was validated in all individual samples via quantitative PCR and extended to additional time points (d -7, 3, 84). Group differences were observed for miR-148a, miR-122 as well as miR-455-5p, and most DE-miRNA (miR-148a, miR-122, miR-30a, miR-450b, miR-455-5p) were downregulated directly after calving. Subsequently, the DE-miRNA was used for bioinformatics analysis to identify putative target genes and the most enriched biological pathways. The most significantly enriched pathways of DE-miRNA were associated with cell cycle and insulin signaling as well as glucose and lipid metabolism. Overall, we found little differences in circulating miRNA in HBCS versus NBCS cows around calving.

Mammalian target of rapamycin signaling and ubiquitin-proteasome-related gene expression in skeletal muscle of dairy cows with high or normal body condition score around calving

The objective of the current study was to investigate the effects of overconditioning around calving on gene expression of key components of the mammalian target of rapamycin (mTOR) pathway and ubiquitin-proteasome system (UPS) in skeletal muscle as well as the AA profiles in both serum and muscle of periparturient cows. Fifteen weeks antepartum, 38 multiparous Holstein cows were allocated to either a high body condition group (HBCS; n = 19) or a normal body condition group (NBCS; n = 19) and were fed different diets until dry-off (d -49 relative to calving) to amplify the difference. The groups were also stratified for comparable milk yields (NBCS: 10,361 ± 302 kg; HBCS: 10,315 ± 437 kg). At dry-off, the NBCS cows (parity: 2.42 ± 1.84; body weight: 665 ± 64 kg) had a body condition score (BCS) <3.5 and backfat thickness (BFT) <1.2 cm, whereas the HBCS cows (parity: 3.37 ± 1.67; body weight: 720 ± 57 kg) had a BCS >3.75 and BFT >1.4 cm. During the dry period and the subsequent lactation, both groups were fed identical diets but maintained the BCS and BFT differences. Blood samples and skeletal muscle biopsies (semitendinosus) were repeatedly (d -49, +3, +21, and +84 relative to calving) collected for assessing the concentrations of free AA and the mRNA abundance of various components of mTOR and UPS. The differences in BCS and BFT were maintained throughout the study. The circulating concentrations of most AA with the exception of Gly, Gln, Met, and Phe increased in early lactation in both groups. The serum concentrations of Ala (d +21 and +84) and Orn (d +84) were lower in HBCS cows than in NBCS cows, but those of Gly, His, Leu, Val, Lys, Met, and Orn on d -49 and Ile on d +21 were greater in HBCS cows than in NBCS cows. The serum concentrations of 3-methylhistidine, creatinine, and 3-methylhistidine:creatinine ratio increased after calving (d +3) but did not differ between the groups. The muscle concentrations of all AA (except for Cys) remained unchanged over time and did not differ between groups. The muscle concentrations of Cys were greater on d -49 but tended to be lower on d +21 in HBCS cows than in NBCS cows. On d +21, mTOR and eukaryotic translation initiation factor 4E binding protein 1 mRNA abundance was greater in HBCS cows than in NBCS cows, whereas ribosomal protein S6 kinase 1 was not different between the groups. The mRNA abundance of ubiquitin-activating enzyme 1 (d +21), ubiquitin-conjugating enzyme 1 (d +21), atrogin-1 (d +21), and ring finger protein-1 (d +3) enzymes was greater in HBCS cows than in NBCS cows, whereas ubiquitin-conjugating enzyme 2 was not different between the groups. The increased mRNA abundance of key components of mTOR signaling and of muscle-specific ligases of HBCS cows may indicate a simultaneous activation of anabolic and catabolic processes and thus increased muscle protein turnover, likely as a part of the adaptive response to prevent excessive loss of skeletal muscle mass during early lactation.

Metabolomics meets machine learning: Longitudinal metabolite profiling in serum of normal versus overconditioned cows and pathway analysis

This study aimed to investigate the differences in the metabolic profiles in serum of dairy cows that were normal or overconditioned when dried off for elucidating the pathophysiological reasons for the increased health disturbances commonly associated with overconditioning. Fifteen weeks antepartum, 38 multiparous Holstein cows were allocated to either a high body condition (HBCS; n = 19) group or a normal body condition (NBCS; n = 19) group and were fed different diets until dry-off to amplify the difference. The groups were also stratified for comparable milk yields (NBCS: 10,361 ± 302 kg; HBCS: 10,315 ± 437 kg; mean ± standard deviation). At dry-off, the cows in the NBCS group (parity: 2.42 ± 1.84; body weight: 665 ± 64 kg) had a body condition score (BCS) <3.5 and backfat thickness (BFT) <1.2 cm, whereas the HBCS cows (parity: 3.37 ± 1.67; body weight: 720 ± 57 kg) had BCS >3.75 and BFT >1.4 cm. During the dry period and the subsequent lactation, both groups were fed identical diets but maintained the BCS and BFT differences. A targeted metabolomics (AbsoluteIDQ p180 kit, Biocrates Life Sciences AG, Innsbruck, Austria) approach was performed in serum samples collected on d -49, +3, +21, and +84 relative to calving for identifying and quantifying up to 188 metabolites from 6 different compound classes (acylcarnitines, AA, biogenic amines, glycerophospholipids, sphingolipids, and hexoses). The concentrations of 170 metabolites were above the limit of detection and could thus be used in this study. We used various machine learning (ML) algorithms (e.g., sequential minimal optimization, random forest, alternating decision tree, and naïve Bayes-updatable) to analyze the metabolome data sets. The performance of each algorithm was evaluated by a leave-one-out cross-validation method. The accuracy of classification by the ML algorithms was lowest on d 3 compared with the other time points. Various ML methods (partial least squares discriminant analysis, random forest, information gain ranking) were then performed to identify those metabolites that were contributing most significantly to discriminating the groups. On d 21 after parturition, 12 metabolites (acetylcarnitine, hexadecanoyl-carnitine, hydroxyhexadecenoyl-carnitine, octadecanoyl-carnitine, octadecenoyl-carnitine, hydroxybutyryl-carnitine, glycine, leucine, phosphatidylcholine-diacyl-C40:3, trans-4-hydroxyproline, carnosine, and creatinine) were identified in this way. Pathway enrichment analysis showed that branched-chain AA degradation (before calving) and mitochondrial β-oxidation of long-chain fatty acids along with fatty acid metabolism, purine metabolism, and alanine metabolism (after calving) were significantly enriched in HBCS compared with NBCS cows. Our results deepen the insights into the phenotype related to overconditioning from the preceding lactation and the pathophysiological sequelae such as increased lipolysis and ketogenesis and decreased feed intake.