Ideal Animal Research Articles

Ideal animal models according to multifaceted mechanisms and peculiarities in neurological disorders: present and challenges.

Neurological disorders, encompassing conditions such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), pose a significant global health challenge, affecting millions worldwide. With an aging population and increased life expectancy, the prevalence of these disorders is escalating rapidly, leading to substantial economic burdens exceeding trillions of dollars annually. Animal models play a crucial role in understanding the underlying mechanisms of these disorders and developing effective treatments. Various species, including rodents, non-human primates, and fruit flies, are utilized to replicate specific aspects of human neurological conditions. However, selecting the ideal animal model requires careful consideration of its proximity to human disease conditions and its ability to mimic disease pathobiology and pharmacological responses. An Animal Model Quality Assessment (AMQA) tool has been developed to facilitate this selection process, focusing on assessing models based on their similarity to human conditions and disease pathobiology. Therefore, integrating intrinsic and extrinsic factors linked to the disease into the study's objectives aids in constructing a biological information matrix for comparing disease progression between the animal model and human disease. Ultimately, selecting an ideal animal disease model depends on its predictive, face, and construct validity, ensuring relevance and reliability in translational research efforts.

A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina

Heliocidaris crassispina is a tropical sea urchin that holds both ecological and economic value and serves as an ideal experimental animal. This study first employed a combination of PacBio HiFi and Hi-C sequencing data to present a high-quality, chromosome-level assembly of H. crassispina genome. This assembled genome spanned 709.77 Mb, with a contig N50 length of 4.98 Mb and a scaffold N50 length of 33.23 Mb. The assembly was anchored on 21 pseudo-chromosomes, covering 98.32% of the genome. A total of 18,665 protein-coding genes were identified, and BUSCO analysis revealed a completeness score of 97.1%. Additionally, non-coding RNAs (ncRNAs) were annotated, including miRNAs, rRNAs, tRNAs and snRNAs, providing a more complete functional understanding of the genome. The high-quality reference genome will enrich the current echinoderm genomic resources and provide a solid foundation for future studies on H. crassispina, including resource surveys, genomic breeding, and marine ranch management.

Large animal models enhance the study of crypt-mediated epithelial recovery from prolonged intestinal ischemia reperfusion injury.

Intestinal ischemia and reperfusion injury (IRI) is a deadly and common condition. Death is associated with sepsis due to insufficient epithelial repair, requiring stem cell-driven regeneration, typically beginning 48 h after injury. Animal models are critical to advancing this field. To effectively study epithelial healing, models must survive clinically relevant intestinal ischemic injury extending to the crypt. Although mouse models are indispensable to intestinal research, their application for studying epithelial repair following severe IRI may be limited. Ischemic injury was induced in mouse and porcine jejunum for up to 3 h, with up to 72 h of reperfusion. Histologic damage was scored by Chiu-Park grade, and animal survival was assessed. Findings were compared between species. A mouse IRI literature review was performed to evaluate the purported degree of injury, duration of recovery, and reported survival rates. In mice and pigs, 3 h of ischemia induced severe, reliable injury extending into the crypt. However, at 48 h, mouse survival was only 23.5% compared with 100% survival in pigs. In literature, ischemia was induced for >1 h in only 4 of 102 mouse studies and none to 3 h. Recovery was attempted for 48 h in only six reports. Forty-seven studies reported intestinal crypt injury. Of those that featured histologic intestinal crypt damage, survival rates at 48 h ranged from 10 to 50% (median 30%). Mouse models are not ideal for studying intestinal stem cell-mediated recovery from severe IRI. Alternative large animal models, like pigs, are recommended.NEW & NOTEWORTHY Additional research is needed to improve recovery from severe intestinal ischemia. The selection of the ideal animal model is critical to facilitating this work. Based on our experimentation and literature review, porcine models, with increased translatability and an improved ability to survive both prolonged ischemia and the recovery period, appear to be the most appropriate choice for future studies.

Preliminary exploration of the musk biosynthetic mechanism by transcriptomic sequencing in muskrats

Musk, secreted by adult male forest musk deer, is a kind of precious Chinese traditional medicine for treating cardiovascular, cerebrovascular and neurogenic diseases. However, a lack of knowledge on musk biosynthetic mechanism and limited musk deer population have seriously hindered the development of the musk industry. Fortunately, given that muskrat musk has similar constituents and pharmacological action with deer musk, muskrat is an ideal model animal for exploring musk biosynthetic mechanism. To explore the biosynthetic mechanism of muskrat musk, in the current study, transcriptomic analysis in the liver, kidney and musk glands of male muskrats between musk secreting and non-musk secreting stages was conducted. The findings indicated that the role of muskrat liver on musk biosynthesis was altering sugar, lipid and amino acid metabolism as well as producing basic resources to support musk glands. Moreover, Tigar, Slc11a2, Gpt, Hmgcr, Slc27a4, and Elovl1 were identified as candidate genes for musk biosynthesis via a remotely controlled process. Expression of the Tigar, Slc11a2, and Gpt genes in the liver are downregulated to support the production of musk in muskrat musk gland. And the Hmgcr, Slc27a4, and Elovl1 genes in the musk gland participate in muskrat musk synthesis by influencing lipid metabolism in the musk secreting period. This study provided novel insights into the musk biosynthetic pathway in muskrat by transcriptomic analysis and preliminarily suggested the remote control of metabolism from the liver to musk gland during musk biosynthesis, which was useful to further understanding the musk biosynthetic process and improve musk production in the future.

Staring into a crystall ball: understanding evolution and development of in vivo aquatic organismal transparency

Organismal transparency is an ecologically important trait that can provide camouflage advantages to diverse organisms. Transparent organisms are quite common—especially in oceans. Organismal transparency requires low absorption and scattering of light in the body across multi-scale levels. However, it is still not fully understood how such organisms achieve these requirements. Understanding this process requires multiple approaches from various fields and methods. Here, we offer recent insights on this topic from the viewpoints of evolution, developmental biology, and evaluation methodologies of organismal transparency. We also propose “organismal transparency biology” as a new interdisciplinary field of study. Furthermore, we suggest that tunicates are an ideal model animal for studying in vivo organismal transparency.

The Development of Animal Models for Respiratory Syncytial Virus (RSV) Infection and Enhanced RSV Disease.

The development of immunoprophylactic products against respiratory syncytial virus (RSV) has resulted in notable advancements, leading to an increased demand for preclinical experiments and placing greater demands on animal models. Nevertheless, the field of RSV research continues to face the challenge of a lack of ideal animal models. Despite the demonstration of efficacy in animal studies, numerous RSV vaccine candidates have been unsuccessful in clinical trials, primarily due to the lack of suitable animal models. The most commonly utilized animal models for RSV research are cotton rats, mice, lambs, and non-human primates. These animals have been extensively employed in mechanistic studies and in the development and evaluation of vaccines and therapeutics. However, each model only exemplifies some, but not all, aspects of human RSV disease. The aim of this study was to provide a comprehensive summary of the disease symptoms, viral replication, pathological damage, and enhanced RSV disease (ERD) conditions across different RSV animal models. Furthermore, the advantages and disadvantages of each model are discussed, with the intention of providing a valuable reference for related RSV research.

Establishing a Mandibular Osteosarcoma Model in SD Rats Using Tissue Block Transplantation.

To investigate the feasibility of establishing a mandibular osteosarcoma model in Sprague-Dawley (SD) rats using tissue block transplantation, providing a foundational model for osteosarcoma research. Fourteen male SD rats, 3 weeks old and SPF grade, were randomly divided into a control group (n=4) and a mandibular osteosarcoma group (n=10). Using tissue block transplantation, UMR106 cell-induced tumor tissues were transplanted subcutaneously into the left mandibular marrow cavity of the SD rats. Observations included behavioral changes, weight variations, tumor growth, and tumor formation rate. Bone changes were monitored via micro-CT scanning, and histological analysis was conducted using HE staining. Two weeks post-transplantation, the mandibular osteosarcoma group exhibited significant left facial swelling, malocclusion, eating difficulties, and weight loss compared to the control group. The tumor formation rate was 80% (8/10). Micro-CT scans indicated significant bone destruction in the osteosarcoma group. HE staining revealed high cellular atypia and pathological mitoses in both subcutaneous and mandibular osteosarcoma cells, with no notable abnormalities in lung tissues. Tissue block transplantation is a viable method to establish a mandibular osteosarcoma model in SD rats. This method is simple, with a high tumor formation rate, providing an ideal animal model for mandibular osteosarcoma research.

Omics in IgG4-related disease.

Research on IgG4-related disease (IgG4-RD), an autoimmune condition recognized to be a unique disease entity only two decades ago, has processed from describing patients' symptoms and signs to summarizing its critical pathological features, and further to investigating key pathogenic mechanisms. Challenges in gaining a better understanding of the disease, however, stem from its relative rarity-potentially attributed to underrecognition - and the absence of ideal experimental animal models. Recently, with the development of various high-throughput techniques, "omics" studies at different levels (particularly the single-cell omics) have shown promise in providing detailed molecular features of IgG4-RD. While, the application of omics approaches in IgG4-RD is still at an early stage. In this paper, we review the current progress of omics research in IgG4-RD and discuss the value of machine learning methods in analyzing the data with high dimensionality.

Mouse Model of Glucocorticoid-Induced Glaucoma.

Extended glucocorticoid (GC) treatment can lead to ocular hypertension and induce iatrogenic open-angle glaucoma. GC-induced glaucoma mimics many clinical and pathological features of primary open-angle glaucoma (POAG), and therefore mouse models of GC-induced glaucoma are utilized to study pathophysiology of glaucoma. We have recently demonstrated that weekly periocular injections of dexamethasone-21-acetate (Dex-Ac) lead to robust and significant intraocular pressure (IOP) elevation, retinal ganglion cell (RGC) loss, and optic nerve degeneration in mice. Our mouse model exhibits signature features of POAG including significant IOP elevation due to reduced outflow facility, progressive optic nerve degeneration, and structural and functional loss of RGCs. Dex-induced IOP elevation is associated with increased aqueous outflow resistance due to trabecular meshwork (TM) dysfunction including excessive extracellular matrix deposition and induction of endoplasmic reticulum stress. Mouse model of Dex-induced glaucoma represents an ideal animal model to investigate both glaucomatous damage to the TM and RGC axons and to develop novel therapies. Here, we present a detailed protocol for developing this model in laboratory settings.

Mining of potentially stem cell-related miRNAs in planarians.

Stem cells and regenerative medicine have recently become important research topics. However, the complex stem cell regulatory networks involved in various microRNA (miRNA)-mediated mechanisms have not yet been fully elucidated. Planarians are ideal animal models for studying stem cells owing to their rich stem cell populations (neoblasts) and extremely strong regeneration capacity. The roles of planarian miRNAs in stem cells and regeneration have long attracted attention. However, previous studies have generally provided simple datasets lacking integrative analysis. Here, we have summarized the miRNA family reported in planarians and highlighted conservation in both sequence and function. Furthermore, we summarized miRNA data related to planarian stem cells and regeneration and screened potential involved candidates. Nevertheless, the roles of these miRNAs in planarian regeneration and stem cells remain unclear. The identification of potential stem cell-related miRNAs offers more precise suggestions and references for future investigations of miRNAs in planarians. Furthermore, it provides potential research avenues for understanding the mechanisms of stem cell regulatory networks. Finally, we compiled a summary of the experimental methods employed for studying planarian miRNAs, with the aim of highlighting special considerations in certain procedures and providing more convenient technical support for future research endeavors.

Investigation of a Camera-Based Contactless Pulse Oximeter with Time-Division Multiplex Illumination Applied on Piglets for Neonatological Applications.

(1) Objective: This study aims to lay a foundation for noncontact intensive care monitoring of premature babies. (2) Methods: Arterial oxygen saturation and heart rate were measured using a monochrome camera and time-division multiplex controlled lighting at three different wavelengths (660 nm, 810 nm and 940 nm) on a piglet model. (3) Results: Using this camera system and our newly designed algorithm for further analysis, the detection of a heartbeat and the calculation of oxygen saturation were evaluated. In motionless individuals, heartbeat and respiration were separated clearly during light breathing and with only minor intervention. In this case, the mean difference between noncontact and contact saturation measurements was 0.7% (RMSE = 3.8%, MAE = 2.93%). (4) Conclusions: The new sensor was proven effective under ideal animal experimental conditions. The results allow a systematic improvement for the further development of contactless vital sign monitoring systems. The results presented here are a major step towards the development of an incubator with noncontact sensor systems for use in the neonatal intensive care unit.

Simulating the clinical manifestations and disease progression of human sepsis: A monobacterial injection approach for animal modeling

ABSTRACT Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection, with great clinical heterogeneity, high morbidity, and high mortality. At the same time, there are many kinds of infection sources, the pathophysiology is very complex, and the pathogenesis has not been fully elucidated. An ideal animal model of sepsis can accurately simulate clinical sepsis and promote the development of sepsis-related pathogenesis, treatment methods, and prognosis. The existing sepsis model still uses the previous Sepsis 2.0 modelling standard, which has some problems, such as many kinds of infection sources, poor repeatability, inability to take into account single-factor studies, and large differences from clinical sepsis patients. To solve these problems, this study established a new animal model of sepsis. The model uses intravenous tail injection of a single bacterial strain, simplifying the complexity of multibacterial infection, and effectively solving the above problems.

Human neural stem cells transplanted during the sequelae phase alleviate motor deficits in a rat model of cerebral palsy

AimsCerebral palsy (CP) is the most common physical disability in children, yet lacks an ideal animal model or effective treatment. This study aimed to develop a reliable CP model in neonatal rats and explore the effectiveness and underlying mechanisms of human neural stem cells (hNSCs) transplantation during the sequelae phase of CP. MethodsVasoconstrictor endothelin-1 (ET-1) was administered intracranially to the motor cortex and striatum of rats on postnatal day 5 to establish a CP model. hNSCs (5 × 105/5 μL) pretreated with hypoxia (5% O2 for 24 h) were transplanted near the infarct 3 weeks after ET-1 injury (the sequelae phase). The distribution and differentiation of hNSCs were observed after transplantation. Changes in neurotrophic factors, neurogenesis, angiogenesis, axonal plasticity, and motor function were analyzed. ResultsNeurobehavioral tests showed poor muscle strength and postural control in young ET-1 rats. Motor deficits of the left forelimb and gait abnormalities persisted into adulthood. Histopathological findings and MRI indicated the atrophy of the cortex, striatum, and adjacent corpus callosum in ET-1 rats. At 56 days after transplantation, hNSCs were widely distributed in the ipsilateral hemisphere, and differentiated into neurons, oligodendrocytes and astrocytes. Transplantation of hNSCs increased BDNF and VEGF expression, EdU+ cell number in the SVZ area, RECA-1+ vessel density and GAP-43 intensity around the lesion in ET-1 rats. The cylinder test revealed a significant increase in the left forelimb motor function from 28 days after transplantation, and the staircase and CatWalk tests showed improvements in fine motor function and gait parameters. ConclusionsIntracerebral injection of ET-1 modelled key functional and histopathological features of CP. hNSCs transplanted during the sequelae phase of CP resulted in long-term improvement in motor performance, possibly attributed to its capacity to stimulate neurotrophic factors, facilitate neurogenesis, angiogenesis, and promote axonal plasticity.

P-707 Discovery of novel serum biomarkers for premature ovarian insufficiency through machine-learning bioinformatic analysis

Abstract Study question Can we develop predictive, practical biomarkers for premature ovarian insufficiency (POI) from normal ovaries and human blood, tested and validated by machine-learning (ML) algorithm? Summary answer Applying random forest and XGBoost algorithms, we pinpointed 60 significant genes from ovarian tissues; transcriptome analysis identified RPM1 as the most significant biomarker. What is known already Accelerated ovarian aging has been suggested as one of the possible underlying mechanisms of POI; previous literature has focused on identifying its cause in genetic realm, commonly adopting first-generation sequencing (Sanger) and next-generation sequencing (NGS). However, such powerful tools are still limited in accurately depicting the complete transcript information of ovarian tissue. Moreover, theoretical value of such disease-predictive gene candidates needs to be validated using human tissues and blood, and finally, underlying mechanisms should be confirmed with ideal animal model and cell line. Study design, size, duration To overcome the existing limitations and maximize clinical relevance of disease-predictive gene analysis and theoretical biomarker exploration, the current study incorporated the transcriptome expression data from both young and old ovaries obtained from the Genotype-Tissue Expression (GTEx) database. Using supervised machine learning techniques, potential marker genes were identified, and a meaningful predictive index was subsequently developed using human plasma samples of control and POI women with and without pregnancy history. Participants/materials, setting, methods The performance evaluation of two ML models were achieved using the area under receiver operating characteristic curve (AUROC), accuracy, kappa, and F1 score, among various age groups. The expression profiles of final candidate marker genes were analyzed within the GTEx datasets, in relation to their correlation pattern with age. Finally, the potential transcriptome biomarkers were quantitatively evaluated using human blood samples from 92 controls and 108 POI women visiting a tertiary center in 2023. Main results and the role of chance We found 41 significant genes using the random forest algorithm and 19 significant genes using the XGboost algorithm. We then tested the ML-characterized 7 final candidate biomarkers in human blood samples (all p < 0.05). The AUROC and interventional predictive index results demonstrated the potential of RPM1 as a predictive marker with AUROC of 0.784, comparable to the AUROC of anti-mullerian hormone (AMH) as 0.659 and inhibin B (INHB) as 0.646. Limitations, reasons for caution To avoid potential biases, RPMs should be tested in a larger, multinational cohort with different genetic and geographic backgrounds, possibly incorporating Mendelian randomization method to estimate the causal effect of RPMs on POI. Finally, to ultimately confirm their therapeutic potential, preclinical studies should be considered using RPM recombinant proteins. Wider implications of the findings Our results proposed that predictive biomarkers for POI could be associated with premature, accelerated ovarian aging of the disease mechanism, and these biomarkers can be developed as evaluation metrics for the efficacy, progress, and prognosis of interventions and treatment modalities assigned to POI women seeking fertility. Trial registration number 202302240001

Sheep litter size heredity basis using genome-wide selective analysis.

Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-β (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.

Application of modified no-touch technique in rabbit arteriovenous fistula model and its effect on venous neointimal hyperplasia.

To investigate the technical advantages of a modified no-touch technique (MNTT) in constructing arteriovenous fistulas (AVF) compared to the conventional technique (CT) and assess its potential to reduce neointimal hyperplasia in the outflow vein. Forty-seven New Zealand rabbits were randomly divided into three groups: control, CT, and MNTT. Rabbits in control group were observed using ultrasound and then euthanized to obtain external jugular vein (EJV) for Hematoxylin-eosin (H-E). We established common carotid artery (CCA)-EJV AVF using MNTT in the MNTT group and the CT in the CT group. AVF patency and complications were compared between the CT and MNTT groups. Rabbits with patent AVF in both groups were observed using ultrasound 2 weeks after surgery to evaluate changes in the vessel diameter and blood flow spectrum of the AVFs. H-E staining measured the intima thickness of EJV adjacent to the anastomosis and histologic characteristics of the AVF at 2 and 4 weeks after surgery. Five rabbits died after surgery with common symptoms of sneezing, coughing, runny nose, anorexia, and diarrhea; two in the MNTT group and three in the CT group. There were significant differences in the diameter (p = 0.010) and peak systolic velocities (PSV) (p = 0.001) of EJV between the CT and MNTT groups 2 weeks after surgery. Spiral laminar flow (SLF) was observed in CCA and EJV adjacent to anastomosis in the MNTT group. Additionally, histological observations showed less venous neointimal hyperplasia in the MNTT group than in the CT group 4 weeks after surgery. The rabbit model of CCA-EJV AVF established using MNTT demonstrated fewer complications, larger vein diameters, and reduced venous neointimal hyperplasia, indicating that this maybe an ideal animal model to further investigate the application of MNTT in AVF surgery.

Chromosome-level genome assembly of ridgetail white shrimp Exopalaemon carinicauda

Exopalaemon carinicauda, a eurythermal and euryhaline shrimp, contributes one third of the total biomass production of polyculture ponds in eastern China and is considered as a potential ideal experimental animal for research on crustaceans. We conducted a high-quality chromosome-level genome assembly of E. carinicauda combining PacBio HiFi and Hi-C sequencing data. The total assembly size was 5.86 Gb, with a contig N50 of 235.52 kb and a scaffold N50 of 138.24 Mb. Approximately 95.29% of the assembled sequences were anchored onto 45 pseudochromosomes. BUSCO analysis revealed that 92.89% of 1,013 single-copy genes were highly conserved orthologs. A total of 44, 288 protein-coding genes were predicted, of which 70.53% were functionally annotated. Given its high heterozygosity (2.62%) and large proportion of repeat sequences (71.49%), it is one of the most complex genome assemblies. This chromosome-scale genome will be a valuable resource for future molecular breeding and functional genomics research on E. carinicauda.

Infrequent spontaneous fundus lesions in a Macaca fascicularis cohort from southern China: A case-series study

Introduction: Non-Human Primates (NHPs) are suitable for studying human visual biology and ocular diseases since they share almost identical anatomic structure and biological function. From this eye study of a NHP cohort, some infrequent fundus lesions were shown and ideal animal models were provided for further exploration on pathogenesis and potential treatments of these diseases.

Neurotoxicity of Some Environmental Pollutants to Zebrafish

The aquatic environment encompasses a wide variety of pollutants, from plastics to drug residues, pesticides, food compounds, and other food by-products, and improper disposal of waste is the main cause of the accumulation of toxic substances in water. Monitoring, assessing, and attempting to control the effects of contaminants in the aquatic environment are necessary and essential to protect the environment and thus human and animal health, and the study of aquatic ecotoxicology has become topical. In this respect, zebrafish are used as model organisms to study the bioaccumulation, toxicity, and influence of environmental pollutants due to their structural, functional, and material advantages. There are many similarities between the metabolism and physiological structures of zebrafish and humans, and the nervous system structure, blood–brain barrier function, and social behavior of zebrafish are characteristics that make them an ideal animal model for studying neurotoxicity. The aim of the study was to highlight the neurotoxicity of nanoplastics, microplastics, fipronil, deltamethrin, and rotenone and to highlight the main behavioral, histological, and oxidative status changes produced in zebrafish exposed to them.

Diversity and host interaction of the gut microbiota in specific pathogen-free pigs.

Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the TCN1 gene and Prevotella dentalis, possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the BDH1 gene and Roseburia hominis, possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.