Gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. The correlation among gut microbiota, glycolipid metabolism, and metabolic diseases has been well reviewed in humans. However, the interplay between gut microbiota and host metabolism in swine remains incompletely understood. Given the limitation in conducting human experiments and the high similarity between swine and humans in terms of anatomy, physiology, polyphagy, habits, and metabolism and in terms of the composition of gut microbiota, there is a pressing need to summarize the knowledge gained regarding swine gut microbiota, its interplay with host metabolism, and the underlying mechanisms. This review aimed to outline the bidirectional regulation between gut microbiota and nutrient metabolism in swine and to emphasize the action mechanisms underlying the complex microbiome–host crosstalk via the gut microbiota–gut–brain axis. Moreover, it highlights the new advances in knowledge of the diurnal rhythmicity of gut microbiota. A better understanding of these aspects can not only shed light on healthy and efficient pork production but also promote our knowledge on the associations between gut microbiota and the microbiome–host crosstalk mechanism. More importantly, knowledge on microbiota, host health and metabolism facilitates the development of a precise intervention therapy targeting the gut microbiota.

Unlike the strictly hierarchical organization in the circadian clock system, the gut microbiota rhythmicity has a more complex multilayer network of all taxonomic levels of microbial taxa and their metabolites. However, it is worth noting that the functionality of the gut microbiota rhythmicity is highly dependent on the host circadian clock and host physiological status. Here, we discussed the diurnal rhythmicity of the gut microbiota; its crucial role in host physiology, health, and metabolism; and the crosstalk between the gut microbial rhythmicity and host circadian rhythm. This knowledge lays the foundation for the development of chronotherapies targeting the gut microbiota. However, the formation mechanism, its beneficial effects on the host of gut microbial rhythmicity, and the dynamic microbial–host crosstalk are not yet clear and warrant further research.

Studies on rodents indicate the daily oscillations of the gut microbiota have biological implications for host. However, the responses of fluctuating gut microbes to the dynamic nutrient substrates are not fully clear. In the study, we found that the feed intake, nutrient substrates, microbiota and metabolites in the colon underwent asynchronous oscillation within a day. Short-chain fatty acids (SCFAs) including acetate, propionate, butyrate and valerate peaked during T24 ~ T27 (Timepoint 24, 12:00 pm, T27, 03:00 am) whereas branched SCFAs isobutyrate and isovalerate peaked during T09 ~ T12. Further extended local similarity analysis (eLSA) revealed that the fluctuation of feed intake dynamically correlated with the colonic carbon substrates which further influenced the oscillation of sugar metabolites and acetate, propionate, butyrate and valerate with a certain time shift. The relative abundance of primary degrader Ruminococcaceae taxa was highly related to the dynamics of the carbon substrates whereas the fluctuations of secondary degraders Lactobacillaceae and Streptococcaceae taxa were highly correlated with the sugar metabolites. Meanwhile, colonic nitrogen substrates were correlated with branched amino acids and the branched SCFAs. Furthermore, we validated the evolution of gut microbes under different carbohydrate and protein combinations by using an in vitro fermentation experiment. The study pictured the dynamics of the micro-ecological environment within a day which highlights the implications of the temporal dimension in studies related to the gut microbiota. Feed intake, more precisely substrate intake, is highly correlated with microbial evolution, which makes it possible to develop chronotherapies targeting the gut microbiota through nutrition intervention.

Time-restricted feeding (TRF) mode is a potential strategy in improving the health and production of farm animals. However, the effect of TRF on microbiota and their metabolism in the large intestine of the host remains unclear. Therefore, the present study aimed to investigate the responses of microbiome and metabolome induced by TRF based on a growing-pig model. Twelve crossbred growing barrows were randomly allotted into two groups with six replicates (1 pig/pen), namely, the free-access feeding group (FA) and TRF group. Pigs in the FA group were fed free access while the TRF group were fed free access within a regular time three times per day at 07:00–08:00, 12:00–13:00, and 18:00–19:00, respectively. Results showed that the concentrations of NH4-N, putrescine, cadaverine, spermidine, spermine, total biogenic amines, isobutyrate, butyrate, isovalerate, total SCFA, and lactate were increased while the pH value in the colonic digesta and the concentration of acetate was decreased in the TRF group. The Shannon index was significantly increased in the TRF group; however, no significant effects were found in the Fisher index, Simpson index, ACE index, Chao1 index, and observed species between the two groups. In the TRF group, the relative abundances of Prevotella 1 and Eubacterium ruminantium group were significantly increased while the relative abundances of Clostridium sensu sticto 1, Lactobacillus, and Eubacterium coprostanoligenes group were decreased compared with the FA group. PLS-DA analysis revealed an obvious and regular variation between the FA and TRF groups, further pathway enrichment analysis showed that these differential features were mainly enriched in pyrimidine metabolism, nicotinate and nicotinamide metabolism, glycerolipid metabolism, and fructose and mannose metabolism. In addition, Pearson's correlation analysis indicated that the changes in the microbial genera were correlated with the colonic metabolites. In conclusion, these results together indicated that although the overall microbial composition in the colon was not changed, TRF induced the gradient changes of the nutrients and metabolites which were correlated with certain microbial genera including Lactobacillus, Eubacterium_ruminantium group, Eubacterium coprostanoligenes group, Prevotella 1, and Clostridium sensu sticto 1. However, more studies are needed to understand the impacts of TRF on the health and metabolism of growing pigs.

Background: Lactic acid bacteria (LAB) participating in milk fermentation naturally release and enrich the fermented dairy product with a broad range of bioactive metabolites, which has numerous roles in the intestinal health-promoting of the consumer. However, information is lacking regarding the application prospect of LAB fermented milk in the animal industry. This study investigated the effects of lactic acid bacteria-fermented formula milk (LFM) on the growth performance, intestinal immunity, microbiota composition, and transcriptomic responses in weaned piglets. A total of 24 male weaned piglets were randomly divided into the control (CON) and LFM groups. Each group consisted of 6 replicates (cages) with 2 piglets per cage. Each piglet in the LFM group were supplemented with 80 mL LFM three times a day, while the CON group was treated with the same amount of drinking water. Results: LFM significantly increased the average daily gain of piglets over the entire 14 d (P < 0.01) and the average daily feed intake from 7 to 14 d (P < 0.05). Compared to the CON group, ileal goblet cell count, villus-crypt ratio, sIgA, and lactate concentrations in the LFM group were significantly increased (P < 0.05). Transcriptomic analysis of ileal mucosa identified 487 differentially expressed genes (DEGs) between two groups. Especially, DEGs involved in the intestinal immune network for IgA production pathways, such as polymeric immunoglobulin receptor (PIGR), were significantly up-regulated (P < 0.01) by LFM supplementation. Moreover, trefoil factor 2 (TFF2) in the LFM group, one of the DEGs involved in the secretory function of goblet cells, was also significantly up-regulated (P < 0.01). Sequencing of the 16S rRNA gene of microbiota demonstrated that LFM led to selective enrichment of lactate-producing and short-chain fatty acid (SCFA)-producing bacteria in the ileum, such as an increase in the relative abundance of Enterococcus (P = 0.09) and Acetitomaculum (P < 0.05). Conclusions: LFM can improve intestinal health and immune tolerance, thus enhancing the growth performance of weaned piglets. The changes in microbiota and metabolites induced by LFM might mediate the regulation of the secretory function of goblet cells.