Molecular characterization of gut microbiome in weaning pigs supplemented with multi-strain probiotics using metagenomic, culturomic, and metabolomic approaches

Abstract

Background Probiotics have been reported to exhibit positive effects on host health, including improved intestinal barrier function, preventing pathogenic infection, and promoting nutrient digestion efficiency. These internal changes are reflected to the fecal microbiota composition and, bacterial metabolites production. In accordance, the application of probiotics has been broadened to industrial animals, including swine, which makes people to pursue better knowledge of the correlation between changes in the fecal microbiota and metabolites. Therefore, this study evaluated the effect of multi-strain probiotics (MSP) supplementation to piglets utilizing multiomics analytical approaches including metagenomics, culturomics, and metabolomics. Results Six-week-old piglets were supplemented with MSP composed of Lactobacillus isolated from the feces of healthy piglets. To examine the effect of MSP supplement, piglets of the same age were selected and divided into two groups; one with MSP supplement (MSP group) and the other one without MSP supplement (Control group). MSP feeding altered the composition of the fecal microbiota, as demonstrated by metagenomics analysis. The abundance of commensal Lactobacillus was increased by 2.39%, while Clostridium was decreased, which revealed the similar pattern to the culturomic approach. Next, we investigated the microbial metabolite profiles, specifically SCFAs using HPLC–MS/MS and others using GC–MS, respectively. MSP supplement elevated the abundance of amino acids, including valine, isoleucine and proline as well as the concentration of acetic acid. According to the correlation analyses, these alterations were found out to be crucial in energy synthesizing metabolism, such as branched-chain amino acid (BCAA) metabolism and coenzyme A biosynthesis. Furthermore, we isolated commensal Lactobacillus strains enriched by MSP supplement, and analyzed the metabolites and evaluated the functional improvement, related to tight junction from intestinal porcine enterocyte cell line (IPEC-J2). Conclusions In conclusion, MSP administration to piglets altered their fecal microbiota, by enriching commensal Lactobacillus strains. This change contributed amino acid, acetic acid, and BCAA concentrations to be increased, and energy metabolism pathway was also increased at in vivo and in vitro. These changes produced by MSP supplement suggests the correlation between the various physiological energy metabolism functions induced by health-promoting Lactobacillus and the growth performance of piglets.

Allium tuberosum-derived nanovesicles with anti-inflammatory properties prevent DSS-induced colitis and modify the gut microbiome

“…Sample preparation was carried out as described previously, 39 and the HPLC-MS/MS analysis was carried out according to Song et al with modifications. 40 In brief, 250 mg of the mice cecal tissue were weighed, mixed with UltraPure™ water (Fisher Scientific, Hampton, NH, USA), and centrifuged at 16 000 g for 10 min at 4 °C.…”

“…Sample preparation was carried out as described previously, 39 and the HPLC-MS/MS analysis was carried out according to Song et al with modifications. 40 , and an autosampler temperature of 40 °C.…”

Culturomics: A critical approach in studying the roles of human and animal microbiota

“…The findings are crucial for understanding specific bacterial roles in swine production and health, aiding in the isolation of beneficial bacteria for potential use as probiotics. One of the more recent studies identified 267 bacterial colonies, with 42 species classified into 23 genera in culturomics study of weaning pig gut microbiome (Lee et al 2022). Lactobacillus species, particularly L. curvatus, L. sakei, and L. mucosae, were predominant among the cultured species.…”

Gut Microbiome Derived Lactic Acid Bacteria (GM-d-LAB) from Dwarf Goats (Capra aegagrus hircus) Inhibit the Resident Multiple Antibiotics Resistance Bacterial pathogens

“…LAB, when used as probiotics, can positively influence the microbial balance in the digestive tract of livestock. They contribute to a healthy gut microbiota, which is essential for proper digestion, and nutrient absorption, modulate the immune system of livestock, promote a balanced immune response, and prevent or mitigate the effects of bacterial infections [27,39,40]. The Nigerian dwarf goat, Capra aegagrus hircus, well adapted to varied environments, contributes substantially to smallholder farmers' livelihoods through the provision of meat, milk, and fiber.…”