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.

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.

Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM–receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.

The harmful effects of diarrhea on the growth performance of rabbits have been well documented, but the details of the potential mechanism of intestinal diarrhea when antibiotics are stopped are still unclear. Here, PacBio sequencing technology was used to sequence the full length 16S rRNA gene of the microbiota of intestinal content samples, in order to characterize the bacterial communities in the small intestine (duodenum and jejunum) and large intestine (colon and cecum) in normal Hyplus rabbits and those with diarrhea. The histopathological examination showed that intestinal necrosis occurred in different degrees in the diarrhea group, and that the mucosal epithelium was shed and necrotic, forming erosion, and the clinical manifestation was necrosis. However, the intestinal tissue structure of the normal group was normal. The results revealed that there were significant differences in bacterial communities and structure between the diarrhea and normal groups of four intestinal segments (p < 0.05). In general, 16 bacterial phyla, 144 bacterial genera and 22 metabolic pathways were identified in the two groups. Tax4Fun functional prediction analysis showed that KEGG related to amino acid metabolism and energy metabolism was enriched in the large intestines of rabbits with diarrhea, whereas lipid metabolism was more abundant in the small intestine of rabbits with diarrhea. In conclusion, the change in the relative abundance of the identified dominant microbiota, which could deplete key anti-inflammatory metabolites and lead to bacterial imbalance and diarrhea, resulted in diarrhea in Hyplus rabbits that stopped using antibiotics.

At present, it is common to feed calves with “Concentrate”, “Concentrate + hay” and TMR “Total Mixed Rations” feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the ‘GF’ feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.

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.