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Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.

Chlorogenic acid (CGA) is a natural phenolic acid, which is an important component of biologically active dietary phenols isolated from various species. Two experiments were conducted to investigate the effects of CGA on growth performance, antioxidant capacity, nutrient digestibility, diarrhea incidence, intestinal digestion and absorption function, and the expression levels of intestinal digestion and absorption-related genes in weaned pigs. In Exp. 1, 200 weaned pigs were randomly allotted to four dietary treatments and fed with a basal diet or a basal diet supplemented with 250, 500, or 1,000 mg/kg CGA, respectively, in a 14-d trial. Pigs on the 1,000 mg/kg CGA-supplemented group had greater (P < 0.05) G:F compared with those on the control (CON) group. In Exp. 2, 24 weaned pigs were randomly allotted to two groups and fed with a basal diet (CON group) or a basal diet supplemented with 1,000 mg/kg CGA (the optimum does from Exp. 1; CGA group). After a 14-d trial, 8 pigs per treatment were randomly selected to collect serum and intestinal samples. Compared with the CON group, the ADG, G:F, as well as the apparent total tract digestibility of CP, crude fat, and ash were increased (P < 0.05), whereas the diarrhea incidence was decreased (P < 0.05) in the CGA group. Pigs on the CGA group had greater (P < 0.05) serum albumin and IGF-1, and lower (P < 0.05) serum urea nitrogen than pigs on the CON group. Furthermore, dietary CGA supplementation enhanced (P < 0.05) the activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT) in the serum, the activity of maltase in the jejunum and ileum, as well as the activities of sucrase and alkaline phosphatase (AKP) in the jejunum. The mRNA levels of sodium glucose transport protein-1 (SGLT1) and zinc transporter-1 (ZNT1) in the duodenum and the mRNA levels of SGLT1, glucose transporter-2 (GLUT2), and divalent metal transporter-1 (DMT1) in the jejunum were upregulated (P < 0.05) in pigs fed the CGA diet. These results suggested that dietary CGA supplementation has the potentials to improve the growth performance and decrease the diarrhea incidence of the weaned pigs, possibly through improving the antioxidant capacity and enhancing the intestinal digestion and absorption function.

Lactobacillus rhamnosus GG (LGG) has been regarded as a safe probiotic strain. The aim of this study was to investigate whether dietary LGG supplementation could alleviate diarrhea via improving jejunal mucosal barrier function in the weaned piglets challenged by RV, and further analyze the potential roles for apoptosis of jejunal mucosal cells and intestinal microbiota. A total of 24 crossbred barrows weaned at 21 d of age were assigned randomly to 1 of 2 diets: the basal diet and LGG supplementing diet. On day 11, all pigs were orally infused RV or the sterile essential medium. RV infusion increased the diarrhea rate, increased the RV-Ab, NSP4 and IL-2 concentrations and the Bax mRNA levels of jejunal mucosa (P<0.05), decreased the villus height, villus height: crypt depth, the sIgA, IL-4 and mucin 1 concentrations and the ZO-1, occludin and Bcl-2 mRNA levels of jejunal mucosa (P<0.05), and affected the microbiota of ileum and cecum (P<0.05) in the weaned pigs. Dietary LGG supplementation increased the villus height and villus height: crypt depth, the sIgA, IL-4, mucin 1 and mucin 2 concentrations, and the ZO-1, occludin and Bcl-2 mRNA levels of the jejunal mucosa (P<0.05) reduced the Bax mRNA levels of the jejunal mucosa (P<0.05) in weaned pigs. Furthermore, dietary LGG supplementation alleviated the increase of diarrhea rate in the weaned pigs challenged by RV (P<0.05), and relieve the effect of RV infection on the villus height, crypt depth and the villus height: crypt depth of the jejunal mucosa (P<0.05), the NSP4, sIgA, IL-2, IL-4, mucin 1 and mucin 2 concentrations of jejunal mucosa (P<0.05), the ZO-1, occludin, Bax and Bcl-2 mRNA levels of the jejunal mucosa (P<0.05), and the microbiota of ileum and cecum (P<0.05) in the weaned pigs challenged by RV. These results suggest that supplementing LGG in diets alleviated the diarrhea of weaned piglets challenged by RV via inhibiting the virus multiplication and improving the jejunal mucosal barrier function, which was possibly due to the decreasing apoptosis of jejunal mucosal cells and the improvement of intestinal microbiota.