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There are large number of complex and diverse microbiota in gastrointestinal tract, and the gut microbes play an important role in maintaining gut environment homeostasis, not only affecting nutrient absorption and energy metabolism, but also regulating host physiological functions. Intestinal microorganisms can use nutrients of the host and then produce microbial metabolites, finally form host-microbe metabolic axis between host and gut microbes. The axis plays an important role in animal nutrition metabolism and immune homeostasis, and eventually affects the overall metabolism of host. We reviewed the concept of host-microbe metabolic axis, gut-liver axis, gut-brain axis, the interaction between gut microbiota and the host intestinal metabolism axis, and its impact on host health, with the aim to deepen our understanding about the contribution of intestinal microbes to host metabolism.

Proteins are not only the main building blocks for the construction of tissue, but also crucial for metabolic activity in animals. The microbial community colonized in the gastrointestinal tract plays an important role in host nutrients metabolism, especially nitrogen nutrients. Bacteria in small intestine could metabolize parts of amino acids (AAs), which further affects the systemic AAs metabolism of host. Compared with that in small intestine, the density of bacteria is much higher and the retention time of chyme is much longer in large intestine. On the one hand, the metabolism and community structure of microflora could be affected by nitrogen nutrients entering the large intestine. Thus, the metabolism of nitrogen nutrients by large intestinal microflora can lead to the formation of several metabolites, which are generally presumed to be detrimental for the host health. This review summarized the effects of dietary protein on the community structure of large intestinal microflora, the microbial metabolites of AAs in large intestine and their impacts on intestinal physiology and host health.

Objective: This experiment was conducted to study different metabolic patterns of pig hindgut bacteria on aromatic amino acids by an in vitro fermentation method., Methods: Ileum, cecum and colon chyme in Duroc, Landrace and Yorkshire goods hybridization pigs were taken as inoculum. The single aromatic amino acid concentration was kept 10 mmol/L in fermentation flask. Then the fermentation flask was incubated at 37℃ for 24 h. Gas production was measured at 4, 8, 12, 16 and 24 h, and samples of fermentation collected at 0 h and 24 h were used to measure ammonia nitrogen NH3-N and microbial crude protein (MCP). Denaturing gradient gel electrophoresis (DGGE) and real-time PCR were used to monitor and quantify the development of bacteria community in zymotic fluid.[, Results: The concentrations of NH3-N and MCP were significantly affected by aromatic amino acids and intestinal segments (P<0.01). Intestinal segments also affected gas production (GP) significantly (P0.01). NH3-N, MCP and GP were affected by interaction of aromatic amino acids and intestinal segments. DGGE analysis showed bacteria of aromatic amino acids shared amount of bands together, especially similarity analysis of DGGE profile of Phe and Tyr in ileum, Tyr and Trp in colon were 87.9% and 80.5% separately. Shannon diversity indices analysis revealed that aromatic amino acids in cecum and colon varied significantly (P<0.05). Real-time PCR results showed that the quantity of total bacteria were affected by aromatic amino acids and intestinal segments significantly (P<0.05)., Conclusion: The potential as proportion of different aromatic amino acids are different. Compared with Trp and Phe, the diversity of bacteria utilizing Tyr in cecum or colon is low; compared with Tyr and Trp, a large number of Phe participated in synthesizing bacteria.The fermentation pattern of specific aromatic amino acids in different intestinal segment was unique. Compared with ileum and cecum, much more aromatic amino acids participated in the synthesis of bacteria in colon.

Objective: The objective of the study was to study the effects of Lactobacillus plantarum and Lactobacillus casei on the changes in composition and quantity of microbial populations and the concentrations of short chain fatty acids in the gut digesta of piglets before and after weaning, to explore the mechanisms of the tested two strains to relieve weaning stress., Methods: Fifteen litters of piglets (Duroc×Yorkshire×Landrace) at the age of 7 days were randomly allocated to 3 groups (5 each), including the control group with an oral administration of saline, LP group with L. plantarum and and LC group, with L. casei. On day 21, 24 and 35, the piglets were slaughtered, and the ileum and colon digesta were analyzed for microbial populations and short chain fatty acids., Results: In the ileum and colon, the test strains significantly increased the microbial diversity (P<0.05), promoted the growth of Lactobacilli spp. and Bifidobacteria spp. after 2 weeks of post-weaning. The two test strains increased the concentration of acetate, propionate, butyrate and total short chain fatty acids both in ileum and colon before weaning, and the concentration of acetate, total short chain fatty acids after weaning. Correlation analysis showed that the decreased diarrhea rate before weaning in the LP and LC groups was significant associated with the increased short chain fatty acids concentration and total bacteria of ileum and colon, the increased height of the ileum villi. The improved average daily gain presented a correlation with the increased concentration of acetate and total short chain fatty acids of colon., Conclusion: The findings imply that the tested strains are contribute to increase the microbial diversity, the quantities of beneficial bacteria and the production of short chain fatty acids in the gut intestinal tract of weaning piglets.

Objective: This study was conducted to evaluate the effects of nisin on in vitro fermentation, methanogenesis and functional microbial populations of the rumen., Methods: The negative control did not contain any additives. Monensin (5 μmol/L) was added as positive control. Nisin was added at 3 doses:3 (NI-3), 9 (NI-9), and 27 mg/100 mL (NI-27). Each treatment contained 4 replicates. Gas and methane production was measured at 0, 3, 6, 9, 12, and 24 h after incubation. Samples of culture were collected at 24 h, and used to measure rumen fermentation parameters and functional microbial populations., Results: Compared with negative control, both nisin and monensin addition dramatically reduced gas and methane production (P<0.05). Nisin addition had no effect on pH, dry matter degradability, and organic matter degradability (P0.05). Ammonia concentration was reduced by NI-9 (P<0.05), but was not influenced by NI-3 and NI-27 (P0.05). In contrast, monensin addition significantly lowered dry matter degradability, organic matter degradability, and ammonia concentration (P<0.05), but had no influence on pH (P0.05). Compared with negative control, both nisin and monensin addition significantly reduced acetate concentration and acetate-propionate ratio (P<0.05), and increased propionate concentration (P<0.05). Quantitative real-time PCR results showed that both nisin and monensin addition had no effects on the populations of total bacteria and Bacteroides (P0.05). Compared with negative control, the populations of protozoa, methanogens, fungi and Firmicutes were not influenced by nisin (P0.05), but were significantly reduced by monensin addition (P<0.05). Both nisin and monensin addition significantly increased the populations of sulfur-reducing bacteria and Clostridium aminophilum (P<0.05), but had no influence on the population of Clostridium sticklandii (P0.05)., Conclusion: Appropriate nisin addition could reduce methanogenesis and ammoniagenesis, while had no adverse effect on feed digestion. These effects are probably associated with the variation of rumen functional microbial populations and communities.

Methane is produced exclusively through anaerobic fermentation of both endogenous and exogenous carbohydrates by methanogens. Methane production is detectable in about one third of healthy adult individuals. In recent years, many studies have found that methanogens played an important role in maintaining stability in the gut microbiota. Researches have paid much attention on the metabolism of the methane in the gut. The relationship between methane and intestinal dysfunction has also been investigated. The number of methanogens in irritable bowel syndrome patients is different when compared with the normal individuals. Besides, methanogens are potentially linked with obesity. This article reviewes the role of methanogens in gastrointestinal homeostasis and intestinal diseases (irritable bowel syndrome, colon cancer), as well as the relation between methanogens and obesity.

The human intestinal microbiota is essential in nutrients utilization, organ development, host metabolism, pathogen resistance, and regulation of immune responses. The establishment of early gut microflora in newborn infants experiences periods from less to more, simple to complex and unstable to stable and can be influenced by various factors. This article summarizes the effects of delivery mode, delivery period, rearing methods as well as antibiotics on the development of intestinal bacterial community.

Objective: We studied the microbial interaction between anaerobic fungi and methanogens in the rumen of Holstein Cow., Methods: Co-cultures of anaerobic fungi with indigenously associated methanogen were isolated by Hungate roll-tube technique. The anaerobic fungi were identified by morphology and 4', 6 diamidino-2-phylindole nucleus staining and the methanogens were identified by 16S rRNA gene sequencing., Results: A total of 28 co-cultures of anaerobic fungus with indigenously associated methanogen were obtained. The anaerobic fungi in the co-cultures were identified as monocentric genera Piromyces, Neocallimastix and Caeomyces. The indigenously associated methanogens were Methanobrevibacter olleyae like and Methanobrevibacter thaueri like strains. Four different phylotypes of fungus-methanogen co-cultures were obtained, which were Piromyces/Methanobrevibacter olleyae like strains, Neocallimastix/ Methanobrevibacter olleyae like strains, Neocallimastix/Methanobrevibacter thaueri like strains and Caecomyces/ Methanobrevibacter olleyae like strains., Conclusion: Our study isolated and identified 28 co-cultures of anaerobic fungus and associated methanogens, which provided new materials for further study the mechanism of methane emission in the rumen.

The large numbers of microorganisms that inhabit mammalian gastro-intestine have a highly coevolved relationship with the host's health in nutrition, immunity and other aspects. There is a complex relationship between microbiota and immune system. Although they can inhibit the pathogens invade epithelial tissue, many of these microbes have functions that are critical for stimulating host intestinal immune cells such as Tregs cells, Th17 cells differentiation. However, the disorder of the intestinal flora can cause bacterial translocation, intestinal barrier dysfunction. The mammalian immune system plays an essential role in maintaining homeostasis with resident microbial communities, though secreting a variety of immune effector cytokines such as MUC, sIgA, ITF, RegIIIgamma, and alpha-defensins. Here, we review the composition of intestinal flora on simple stomach animal and the interactions between resident microbes and the immune function.

Objective: The aim of the study was to investigate the influences of high-fat diet and methanogens inhibitor (bromochloromethane, BCM) on the gut microbiota and fat metabolism in mice., Methods: Thirty two female C57BL/6J mice were randomly divided into 4 groups: fed respectively by Low-fat diet, Low-fat diet + BCM, High-fat diet and High-fat diet + BCM. BCM was administrated through drinking water for six weeks. The body weight of mice was recorded every week. At the end of experiment, the blood was collected for serum biochemical analysis. Bacterial communities in cecal digesta were analyzed by denaturing gradient gel electrophoresis (DGGE) and real-time PCR. VFA (volatile fatty acid) concentrations in feces were determined by gas chromatography. Expressions of fat-related genes in liver were analyzed using real-time PCR., Results: DGGE analysis shows that samples from mice fed with high-fat diet gathered together, and separated with samples from low-fat diet group. However, both the fat level in diet and BCM treatment had no effect on the numbers of total bacteria, sulfate reducing bacteria and methanogens. The acetate proportion in feces was significantly decreased (P < 0.05) when fed high-fat diet to mice (P < 0.05). BCM treatment significantly increased the propionate proportion (P < 0.05). High-fat diet also significantly increased the levels of high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TG) in blood (P < 0.05). High-fat diet up-regulated the expression of TGH gene (P < 0.05)., Conclusion: High-fat diet affected cecal microbiota and fat metabolism of mice, whereas BCM treatment had little effect.

The intestinal environment is dependent on the host-microbiota interaction. Antigens of gut microbiota could affect the intestinal immunological homeostasis. Gut microbiota also participate in the metabolism of carbohydrate, lipid and protein. In return, the metabolites from these metabolic processes could regulate the bacterial metabolism, community composition and intestinal nutrient assimilation. MicroRNA serves as an important intracellular factor that regulates host gene expression. Gut microbiota could affect the host mRNA transcription and the post-transcription modification of certain genes by microRNA. Recent researches have revealed that gut microbiota could change the expression of microRNAs involved in gut inflammation and mucosal barrier via host-microbiota interaction. In this paper, we summarized recent advances in host-microbiota interaction and highlighted the research about microRNA regulation on gut homeostasis and host-microbiota interaction.

Objective: To compare volatile fatty acid (VFA) concentration and microbiota in faeces between healthy and diarrhoeal piglets., Methods: Fecal samples from healthy and diarrhoeal piglets were collected. VFA concentration was determined by GC analysis. Total bacterial DNA was extracted and used for molecular analysis of microbiota., Results: As compared to healthy piglets, the concentration of acetate in feces of diarrhoeal piglets tended to increase, while branched chain fatty acid (BCFA) decreased significantly (p < 0.05), total VFA (TVFA), propionate and butyrate tended to decrease. The ratio of acetate to TVFA in faeces of diarrhoeal piglets was significantly higher than that in healthy piglets (p < 0.05), while the ratio of propionate and BFVA to TVFA decreased significantly after diarrhoea (p < 0.05). DGGE analysis of total bacterial community and Clostridium cluster IV group showed no significant changes in both bacterial community were found in faeces of piglets after diarrhoea. Similarity analysis of DGGE profiles revealed that faecal samples of diarrhoeal piglets tended to gather in the same cluster. Real-time PCR results showed that as compared to healthy piglets, the 16S rRNA gene copies of total bacteria and Clostridium cluster IV decreased significantly in faeces of piglets after Diarrhea (p < 0.05), while there was no significant change in the numbers of E coli and Lactobacilli., Conclusion: VFA composition in faeces of diarrhoeal piglets changed accompanying with the shift of microbiota as compared to healthy piglets.

Objective: We investigated the correlation between the methanogen diversity in the piglet colon and the environmental factor (weaning stress, diet type and age)., Methods: The colonic contents of piglets at 7, 14, 21, 28 and 35 days old were collected for the determination of volatile fatty acids and total DNA extraction. DNA was subject to PCR-DGGE (Denaturing gradient gel electrophoresis) analysis and interesting bands were excised and sequenced. Redundancy analysis (RDA) was performed for the correlation between methanogen diversity and environmental factors., Results: As the piglets grew, acetate, propionate and the total volatile fatty acid production increased significantly (P < 0.05), but butyrate concentration remained stable (P > 0.05). The similarity indices of DGGE profiles was higher during the period of the 7 day to 24 day after birth, with grouped in one cluster, and the samples from the 35 days were dropped into another cluster. DGGE analysis showed three dominant bands appeared in samples of 35 d old, with their 16S rRNA gene sequences closely related to Methanobacteria and a novel group of uncultivated Achaean. Redundancy analysis (RDA) showed that age has the largest relevance to the community structure of bacteria in colonic samples, followed by the diet type., Conclusion: The results indicated that the methanogen community in the piglet colon was stable during the first 24 days after birth, and became more diverse at 35 days of age. The methanogens community was mainly affected by age and the diet type.

Objective: To investigate the change of Clostridium cluster IV community in the colon of piglets from 7 to 35 days of age, and its correlation with butyrate concentration., Methods: Three litters of neonatal piglets were used. One piglet from each litter was sacrificed randomly at the age of 7, 14, 21 (weaning day), 24 and 35 days, digestive samples in the colon were collected. The concentration of volatile fatty acid (VFA) was determined by gas chromatography. 16S rRNA gene-based denaturing gradient gel electrophoresis (DGGE) and real-time PCR were used for qualitative and quantitative analysis of Clostridium cluster IV community., Results: Similarity analysis of DGGE profile revealed that samples from piglets at the age of 7 days formed a coherent cluster with indices above 90%, no significant changes in Clostridium cluster IV community were found around weaning period. Real-time PCR analysis showed that 16S rRNA gene copies of total bacteria in the colon of piglets decreased significantly 3 days after weaning, this tendency was in accordance with the changes in concentration of total VFA and butyrate in colon, while there was no significant difference in copies of Clostridium cluster IV group. Sequencing analysis indicated that Clostridium cluster IV group in the colon of piglets were dominated by Faecalibacterium prausnitzii, Subdoligranulum variabile and other uncultured bacteria., Conclusion: Changes in Clostridium cluster IV community in the colon of piglets were found from the age of 7 days to 14 days, while there was no significant difference during the weaning transition.

Objective: A molecular-based approach for anaerobic fungal community analysis was developed. The diversity of anaerobic fungi in the co-cultures with or without methanogens was analyzed by amplified ribosomal intergenic spacer analysis., Methods: Co-cultures of anaerobic fungi and methanogens were obtained from rumen digesta using anaerobic fungal medium and the addition of penicillin and streptomycin and ampicillin alternatively and then subcultured 15 times by transferring cultures every 3 d separately for each replicate. At the end of the third subcultures, the co-cultures were inoculated to another bottles adding with chloramphenicol to obtain fungal cultures without methanogens. Total DNA from the original rumen digesta and subcultured co-cultures and fungal cultures was used for amplified ribosomal intergenic spacer analysis., Results: The diversity of anaerobic fungi decreased corresponding with the subculture of the co-cultures. The anaerobic fungi represented by 354-375 and 425-438 bp in the amplified ribosomal intergenic spacer analysis profiles were not deteched in the co-cultures after the second subcultures and the anaerobic fungi represented by 383, 389-391 and 413-418 bp were dominant along with the subcultures. The community of anaerobic fungi was different in the co-cultures with or without methanogens. The anaerobic fungi represented by 383.51, 391.44 and 413.55 bp in the amplified ribosomal intergenic spacer analysis profiles were dominant in the co-cultures with methanogens, while the anaerobic fungi represented by 415.80, 425.66, 437.46 and 438.47 bp were dominant in the co-cultures without methangens., Conclusion: The molecular-based approach amplified ribosomal intergenic spacer analysis was suitable for analysis of anaerobic fungi in the environmental samples. The diversity of anaerobic fungi decreased along with the subculture of the co-cultures and the anaerobic fungal community became stable after the 4th subculture of the co-cultures. The anaerobic fungal community was different in the co-cultures with or without methanogens.

Objective: A lactate-utilizing, propionate-producing bacterium, strain L9, was isolated from rumen of goat fed with high concentrate by utilizing modified Hungate technique and anaerobic culture technique. The effect of the strain L9 culture on the rumen fermentation was further studied., Methods: According to the characteristics of morphology, physiology, biochemistry tests and sequence comparison of 16S rRNA gene, strain L9 was identified as selenomonas ruminantium. The influence of strain L9 culture on in vitro rumen fermentation was studied using mixed rumen micro-organisms of goats as inoculums., Results: The results of the metabolism experiment showed that it was capable of using lactate as the sole carbon source, and 90 mmol/L lactate in LH medium could be completely utilized after 24 h incubation. As compared with the control, strain L9 culture addition significantly increased the total volatile fatty acids (TVFA), the percentage of propionate and pH value, while reduced the ratio of acetate to propionate and lactate production (P < 0.05)., Conclusion: The results suggested that strain L9 can reduce lactic acid production and enhance the TVFA and propionate production in in vitro fermentation, and thus could be beneficial for the fermentation of rumen microorganisms.

Objective: To identify Lactobacillus sp. strain S1 from the intestine of piglet, and compare the genomic difference between this strain and Lactobacillus sobrius 001T., Methods: Analysis of 16S rRNA gene sequence and species-specific polymerase chain reaction assay were used to identify Lactobacillus sp. strain S1. Representational difference analysis (RDA) was used to compare these two strains., Results: The 16S rRNA gene sequence analysis of strain S1 showed that its closest known species in the GenBank database was L. sobrius. Denaturing gradient gel electrophoresis analysis showed that the predominant bands in profiles from bacteria in the jejunum and ileum of piglets had the identical migrating position with strain S1. Cloning and sequencing of 16S rRNA gene analysis revealed that this band matched clone (Clone S) was also related closely to L. sobrius. Phylogenetic analysis of 16S rRNA gene showed that homology between strain S1 and Clone S was 99.8%, and that between strain S1 and L. sobrius was 99.6%. Both strains could be detected in 1.2% agarose gel by L. sobrius-specific PCR assay. Recently, RDA has been adapted to study the genomic diversity of bacterial strains. This analysis showed that there was no genomic difference between the two strains., Conclusion: Piglet-derived strain S1 belonged to L. sobrius. Piglet-derived L. sobrius 001T and L. sobrius S1 were the similar strain.

Molecular diversities of rumen archaea of Jinnan (South Shanxi Province, China) cattle was analyzed and compared by 16S rRNA gene sequencing from three clone libraries generated using three different archaea-specific primer sets, respectively. DNA from rumen of 4 Jinnan cattle was extracted, and methanogen 16S rRNA gene was amplified using archaea-specific primer sets. Three clone libraries were generated by using vector pGEM-T and cloning into E.coli JM109. One hundred clones were randomly picked up for each library and RFLP was analyzed for each clone to obtain OTUs. Sequences from each OTU were analyzed and compared with available sequences in GenBank. The first library, generated with primers Arch f364/1386, produced four groups of sequences, affiliated with 4 Methanobrevibacter strains, 1Y (61% of clones), SM9 (23% of clones), NT7 (14% of clones), and AK-87(2% of clones). The second library, generated with primers 1 Af/1100Ar, two groups of sequences, one affiliated with Methanobacterium aarhusense (72% of clones) and the other with Methanosphaera stadtmanae DSM 3091 (28% of clones). The third library, generated with primers Met86F/Met1340R, produced a high degree of diversity. It included the sequence groups found in the first and the second libraries, as well as sequences affiliated with the Methanomicrobium mobile (2% of clones) and uncultured euryarchaeote sequences (7% of clones). The phylogenetic analysis indicated that archaea found in the three libraries were clustered in Methanobrevibacter, Methanobacterium, Methanosphaera, Methanomicrobium, and unidentified euryarchaeote of the Euryarcharota. There were 25 unidentified sequences belonged to Euryarchaeota. This suggests the existence of novel methanogens in the rumen of Jinnan cattle.

PCR and denaturing gradient gel electrophoresis (DGGE) were used to monitor the development of bacterial community in faeces of 12 weaning piglets. The regions V6 to V8 of the 16S rDNA of faecal bacteria were amplified. DGGE profiles of the PCR amplicons were compared by similarity analysis. Results revealed simple DGGE profiles for faecal samples from piglets on the first day of weaning and piglets from the same sow showed similar DGGE profiles. After weaning as the piglets grew DGGE profiles became complicated and diverse. Each individual piglet had its unique DGGE profile, with low similarity between piglets. The source of sow and the diet showed no apparent effect on the DGGE profiles. For the piglets fed a diet containing oliogofructose, DGGE similarity analysis showed bacterial community in the faeces developed fast during the first week and relatively slow later after weaning.