The prohibition of the use of growth-promoting drug additives in feeds was implemented in China in 2020. However, rabbits can experience symptoms of intestinal disease, such as diarrhea and flatulence, when switching from standard normal diets with antibiotics to antibiotic-free diets. The molecular mechanisms related to the occurrence of these diseases as well as associated physiological and metabolic changes in the intestine are unclear. Thus, the objectives of this study were to study the pathogenesis of intestinal inflammation using untargeted metabolomics. This was done to identify differential metabolites between a group of antibiotic-free feed Hyplus rabbits (Dia) whose diet was abruptly changed from a standard normal diet with antibiotics to an antibiotic-free diet, and an antibiotic diet group Hyplus rabbits (Con) that was fed a standard normal diet with antibiotics. Morphological damage to the three intestinal tissues was determined through visual microscopic examination of intestinal Dia and Con tissue samples stained with hematoxylin and eosin (HE). A total of 1969 different metabolites were identified in the three intestinal tissues from Dia and Con rabbits. The level of 1280 metabolites was significantly higher and the level of 761 metabolites was significantly lower in the Dia than in the Con group. These differential metabolites were involved in five metabolic pathways associated with intestinal inflammation (tryptophan metabolism, pyrimidine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, lysine degradation, and bile secretion). Rabbits in the Dia group developed metabolic disorders that affected the intestinal microbiota and changed the permeability of the intestinal tract, thereby triggering intestinal inflammation, affecting feed utilization, reducing production performance, and activating the intestinal tract self-repair mechanism. Thus, the abrupt transition from a diet with antibiotics to an antibiotic-free diet affected the structure and metabolism of the intestinal tract in Hyplus rabbits. Consequently, to avoid these problems, the antibiotic content in a rabbit diet should be changed gradually or alternative antibiotics should be found.

Heat stress can impair the rabbit immune system, induce oxidative stress, and cause many complications. These diseases are characterized by metabolic disorders, but the underlying mechanism is unknown. As a result, the current research determines the effects of HS on intestinal microorganisms in rabbits and the metabolic pathway disorders caused by HS. Twelve rabbits were randomly assigned to one of two groups: CON (22–24°C) and HS (30°C–32°C). Both the groups were treated for 15 days. Blood and fecal samples were collected on day 15. Serum immune oxidation indices were determined using a commercial ELISA kit, and the microbiome of rabbit feces was studied using 16S rRNA gene sequencing. Non-targeted metabolomics was analyzed using ultra-high-performance liquid chromatography-mass spectrometry (UHPC MS/MS). The findings revealed that HS significantly increased IgG and T-AOC levels in serum, whereas it decreased TNF-α and IL-10. NMDS analysis revealed a substantial difference in bacterial community composition between HS and CON groups. At the phylum level, the abundance of Firmicutes, Protobacteria, and Verrucomicrobiota was significantly higher in the HS group, whereas the abundance of Bacteriodota was reduced in the CON group. V9D2013 group, Haloplasma, Comamonas, Clostridium sensu stricto 1, Ruminiclostridium, Syntrophus Lutispora, at the genus level Syntrophorhabdus, Paeniclostridium, Clostridium sensu stricto 6, Candidatus Caldatribacterium, Spirochaeta Synergistaceae, Syner-01, [Eubacterium] xylanophilum group, Cellulosilyticum, ADurb.Bin120, and Devosia were significantly upregulated in the HS group. The metabolism of the HS group was considerably upregulated compared with the metabolism of the CON group, according to principal component analysis (PCA) and least-squares discriminant analysis (PLS-DA). HS increased the concentrations of 4-pyridoxic acid, kynurenine, 20-OH-leukotriene B4, and dopamine and decreased the concentration of pyridoxal. In the rabbit gut, these compounds primarily impact the metabolic pathways of vitamin B6, tryptophan, neutrophil activation, and prolactin. 4-Pyridoxic acid, pyridoxal, kynurenine, 20-OH-leukotriene B4, and dopamine are essential inflammatory response markers and oxidative stress.

With the comprehensive prohibition of antibiotics in the feed industry in China, the incidence of diarrhea in rabbits increased, such as loss of appetite, vomiting, and excretion of atheromatous feces. In order to explore the pathological and the molecular mechanisms of the diarrhea in the rabbitry fed with antibiotic-free diet, we used microbial metagenomics, transcriptome, and non-targeted metabolomics sequencing. The results showed that the Firmicutes level was significantly decreased (p < 0.001) and the Proteobacteria level was significantly increased (p < 0.05). The functional enrichment of cecum revealed that most differentially expressed genes (DEGs) were expressed in immune, inflammatory, and metabolic processes. The enrichment of the cecal fecal metabolites focused on the bile secretion, antifolate resistance, and tryptophan metabolism pathways, which are mainly associated with inflammation. The results of correlation analysis showed that Fournierella was positively correlated with myricetin, ursolic acid, and furtherly might cause bile secretion and tryptophan metabolism disorder, aggravate intestinal inflammation, change intestinal permeability, and reduce host immunity, leading to diarrhea in rabbits. This study provides a theoretical basis for illustrating the reason for diarrhea and developing new feeds for the health of rabbits.

China officially promulgated the announcement of banning the use of antibiotics in the animal industry in 2020. However, the prohibition of antibiotics in the animal industry would reduce the feed conversion rate and increase the mortality of animals. In order to obtain information about the pathogenesis and host immune response of rabbits with diarrhea after being fed an antibiotic-free diet, we first analyzed the intestinal tissue sections of rabbits. Secondly, the gene expression differences of rabbit intestinal segments were analyzed by high-throughput sequencing. Our analysis identified 168, 593, 2069, 334, 321, and 1423 DEGs in the comparison groups S_Z (the duodenum of healthy rabbits) vs. S_B (diarrhea in the duodenum of rabbits), K_Z (healthy rabbit jejunum) vs. K_B (rabbits with diarrhea in the jejunum), H_Z (healthy rabbit ileum) vs. H_B (rabbits with diarrhea in the ileum), M_Z (healthy cecum of rabbits) vs. M_B (rabbits with diarrhea in the cecum), J_Z (healthy rabbit colon) vs. J_B (colon of rabbits with diarrhea), and Z_Z (healthy rabbit rectum) vs. Z_B (rectum of rabbits with diarrhea), respectively. The reproducibility and repeatability of the results were validated by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed the host DEGs that are potentially related to acute inflammation, stress response, tissue dehydration, adaptive immune response, protein binding, activation of related enzymes, migration of immune cells, and so on. In this descriptive study, our findings revealed the changes in the host transcriptome expression profile after feeding an antibiotic-free diet and suggested that feeding an antibiotic-free diet alters the host’s metabolic network and the expression of antiviral proteins, which provides a theoretical basis for further study on the immune response of animals fed an antibiotic-free diet.

Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.