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In this study, rumen content was used to obtain three enrichments of anaerobic fungi and methanogens (F + M enrichment), bacteria and methanogens (B + M enrichment), and whole rumen content (WRC enrichment), to evaluate their respective ability to degrade lignocellulose and produce methane. Among the treatments, F + M enrichment elicited the strongest lignocellulose degradation and methane production ability with both rice straw and wheat straw as substrates. Quantitative real-time PCR analysis and diversity analyses of methanogens in the three enrichment treatments demonstrated that F + M had larger number of 16S rRNA gene copies of methanogens and higher relative abundance of Methanobrevibacter, the predominant methanogen found in all enrichments. Caecomyces was the main anaerobic fungal genus for co-culturing to provide substrates for methanogens in this enrichment. Importantly, the F + M enrichment was stable and could be maintained with transfers supplied every 3 days, confirming its potential utility in anaerobic digestion for lignocellulose degradation and methane production.

This study investigated the effects of low-protein diet supplemented with Lysine (Lys), Methionine (Met), Threonine (Thr), and Tryptophan (Trp) on small intestine morphology, enzyme activity, blood urea nitrogen, and gut microbiota and metabolites in weaned piglets. Eighteen weaned pigs weighing an average of 9.57 kg received one of three treatments: a normal protein diet with 20% crude protein (CP, diet [NP]), a moderately reduced protein diet with 17% CP (MP), or a low-protein diet with 14% CP (LP). All three diets were supplemented with Lys, Met, Thr and Trp to meet essential amino acid requirements for post-weaned piglets according to the NRC (2012). Following a 45 d study period, piglets on the LP and MP diets demonstrated atrophic small intestinal morphology, with decreased villus heights and lower ratios of villus height to crypt depth ( p < 0.05); pepsin activity in the stomach was also reduced in these two groups ( p < 0.05). Increased plasma cholesterol and decreased blood urea nitrogen presented in the MP and LP groups compared with the NP group ( p < 0.05). Overall, gastrointestinal hormones were not affected by dietary protein levels with the exception of reduced somatostatin levels in the MP and LP groups. Jejunum and colon microbiota were not affected at either the phyla or genera level in any of the diets. Colonic ammonia nitrogen concentration was reduced in MP and LP groups. Dietary protein level had no effect on short chain fatty acids or biogenic amines. Our data suggest that reducing dietary protein levels by 3% (MP) or 6% (LP) in weaned pigs has the potential to decrease nitrogen emissions and impaired digestive capacity. Therefore, dietary protein level cannot be reduced by more than 3% in consideration of maladaptive changes to small intestinal morphology and pepsin activity in weaned piglets.

Galacto-oligosaccharides (GOS), functional oligosaccharides with natural characteristics, are important active substances in milk that play an important role in the development of intestinal microbiota and the immune system of newborns. The intestinal maturation of piglets resembles that of human newborns and infants. Therefore, we used the newborn piglet model to study the effects of early-life GOS intervention. Six litters of neonatal piglets (10 piglets per litter) with the same average birth weight were divided into control (CON) and GOS (GOS) groups in each litter. Piglets in the GOS group were given 10 mL of GOS solution daily during the first week after birth, while piglets in the CON group were given the same dose of physiological saline orally. One pig per group from each litter was euthanized on day 8 and day 21. Results revealed that ileal microbiota composition was significantly enriched in Lactobacillus and unclassified Lactobacillaceae, and reduced in Clostridium sensu stricto on day 8 and day 21 after GOS intervention. Additionally, Escherichia significantly decreased on day 21 following the early-life GOS intervention. Moreover, the content of microbial metabolites, endocrine peptides, and the mRNA expression of anti-inflammatory cytokines and antimicrobial peptides increased in the GOS group. These findings provide guidelines for early prebiotic supplementation for lactating newborns.

The objective of this study was to investigate the impact of a high-grain (HG) diet on the microbial fermentation, the composition of the mucosa-associated bacterial microbiota, and the gene expression of tight junction proteins in the small intestine of goats. In the present study, we randomly assigned 10 male goats to either a hay diet (n = 5) or a HG diet (56.5% grain; n = 5) and then examined changes in the bacterial community using Illumina MiSeq sequencing and the expression of tight junction proteins using qRT-PCR in the mucosa of the small intestine. The results showed that HG diet decreased the luminal pH (p = 0.005) and increased the lipopolysaccharide content (p < 0.001) in the digesta of the ileum, and it increased the concentration of total volatile fatty acids in the digesta of the jejunum (p = 0.015) and ileum (p = 0.007) compared with the hay diet. MiSeq sequencing results indicated that the HG diet increased (FDR = 0.007-0.028) the percentage of the genera Stenotrophomonas, Moraxella, Lactobacillus, and Prevotella in jejunal mucosa but decreased (FDR = 0.016) the abundance of Christensenellaceae R7 group in the ileal mucosa compared with the hay diet. Furthermore, the HG diet caused downregulation of the mRNA expression of claudin-4, occludin, and ZO-1 in jejunal and ileal mucosa (p < 0.05). Collectively, our data suggested that the HG diet induced changes in the relative abundance of some mucosa-associated bacteria, in addition to downregulation of the mRNA expression of tight junction proteins in the small intestine. These findings provide new insights into the adaptation response of the small intestine to HG feeding in ruminants., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

The cecum plays an important role in the feed fermentation of ruminants. However, information is very limited regarding the cecal microbiota and their methane production. In the present study, the cecal content from twelve local Chinese goats, fed with either a hay diet (0% grain) or a high-grain diet (71.5% grain), were used to investigate the bacterial and archaeal community and their methanogenic potential. Microbial community analysis was determined using high-throughput sequencing of 16S rRNA genes and real-time PCR, and the methanogenesis potential was assessed by in vitro fermentation with ground corn or hay as substrates. Compared with the hay group, the high-grain diet significantly increased the length and weight of the cecum, the proportions of starch and crude protein, the concentrations of volatile fatty acids and ammonia nitrogen, but decreased the pH values (P < 0.05). The high-grain diet significantly increased the abundances of bacteria and archaea (P < 0.05) and altered their community. For the bacterial community, the genera Bifidobacterium, Prevotella, and Treponema were significantly increased in the high-grain group (P < 0.05), while Akkermansia, Oscillospira, and Coprococcus were significantly decreased (P < 0.05). For the archaeal community, Methanosphaera stadtmanae was significantly increased in the high-grain group (P < 0.05), while Methanosphaera sp. ISO3-F5 was significantly decreased (P < 0.05). In the in vitro fermentation with grain as substrate, the cecal microorganisms from the high-grain group produced a significantly higher amount of methane and volatile fatty acids (P < 0.05), and produced significantly lower amount of lactate (P < 0.05). Conclusively, high-grain diet led to more fermentable substrates flowing into the hindgut of goats, resulting in an enhancement of microbial fermentation and methane production in the cecum.

This study evaluated the effects of nitrogen source composition and monensin on the populations of proteolytic and amino acid-fermenting bacteria using in vitro enrichment culture. The experiment was designed with a 2 × 2 factorial arrangement: two nitrogen sources, casein (Cas) and tryptone (Try), and two levels of monensin, 0 (C) and 5 µmol/L (M), resulting in four treatments: Cas-C, Cas-M, Try-C, and Try-M. Ruminal fluid collected from three cannulated Holstein dairy cows was used as the inoculum. Each treatment culture was consecutively transferred six times after 24 h of incubation. The results showed that ammonia concentration was lower in Cas than in Try, and it was reduced by monensin addition. In the 6th transfer enrichment cultures, the 16S rRNA gene copy numbers of total bacteria were reduced by monensin but was unaffected by nitrogen sources. Principal component analysis showed that the bacterial communities differed among the treatments. At the genus level, Peptostreptococcus accounted for as much as 41% of the total bacteria in Try-C, but it made up less than 0.02% in the other three treatments. A Pearson correlation analysis showed that the relative abundance of Peptostreptococcus was positively correlated with ammonia concentration. Overall, the results suggest that nitrogen source composition and monensin can affect ruminal ammonia production by modulating the ruminal proteolytic bacterial communities, and some hyper-ammonia-producing bacteria of the genus Peptostreptococcus may be among the main culprits contributing to the high ammonia concentration in the rumen.

We previously reported that protein-restricted rats experienced compensatory growth when they were switched to a normal protein diet (NPD). This study aimed to investigate the changes in gene expression and microbiome in the jejunum of compensatory-growth rats. Weaned Sprague-Dawley rats were assigned to an N group, an LN group and an L group. The rats in the L and N groups were fed a low protein diet (LPD) and the NPD respectively. The rats in the LN group were fed with the LPD for 2 weeks, followed by the NPD. The experiment lasted 70 days, and the rats were sacrificed for sampling on days 14, 28 and 70 to determine the jejunal morphology, microbiome and gene expression related to digestive, absorptive and barrier function. The results showed that, although rats in the LN group had temporarily impaired morphology and gene expression in the jejunum on day 14 in response to the LPD, they had improved jejunal morphology and gene expression related to jejunal function on day 28 compared to rats in the N group. This improvement might promote compensatory growth of rats. However, lower expression of genes related to nutrient absorption and undifferentiated villous height (VH) were observed in the jejunum of rats in the LN group on day 70. In contrast, rats in the L group had lower VH on day 28 and day 70, while the expression of absorptive genes increased on day 28 compared to rats in the N group. Additionally, dramatic microbial changes in the jejunum of compensatory-growth rats were observed, principally for Lactobacillus, Streptococcus, Corynebacterium and Staphylococcus. Moreover, the abundance of Lactobacillus, Streptococcus, Corynebacterium and Staphylococcus significantly correlated with gene expression in the jejunum as revealed by the correlation analysis., (© 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)

This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The early development of gut microbiota plays a fundamental role in host health; so far, the main origins of the first colonization in newborn piglets are largely unclear. This study aimed to investigate the early development of gut microbiota in newborn piglets during lactation and their co-occurrence with microbes in the maternal and surrounding environments by Illumina MiSeq sequencing of 16S ribosomal RNA genes. The results showed that the microbial richness and diversity in piglets' feces (PF) significantly increased from birth to weaning (21 d). The composition and function of microbiota in the feces of piglets after birth tended to be similar to those from the slatted floor (FL), sow's milk (SM) and nipple surface (SN), and lacter, the fecal microbial communities of piglets later during lactation were more similar to their mother's. SourceTracker analysis showed that the microbiota from the FL, SM and SN were most likely the earliest passengers to the neonatal gastrointestinal tract, but did not have a long stay during lactation. The sow's fecal microbiota were easier to colonize in newborn piglet's guts via the co-occurrence effect with former settlers. This study suggests that microbes from the maternal and surrounding environments may play an important role in the microbial succession of newborn piglets after birth., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The effect of disodium fumarate (DF) on the ruminal fermentation profiles, the accumulation of lipopolysaccharide (LPS) and bioamines, and the composition of the ruminal bacterial community was investigated by in vitro rumen fermentation. The addition of DF increased the total gas production; the concentrations of propionate, valerate, total volatile fatty acids, and ammonia-nitrogen; and the rumen pH after a 24 h fermentation. By contrast, DF addition decreased the ratio of acetate to propionate and the concentrations of lactate, lipopolysaccharide, methylamine, tryptamine, putrescine, histamine, and tyramine (P < 0.05). Principal coordinates analysis and molecular variance analysis showed that DF altered the ruminal bacterial community (P < 0.05). At the phylum level, DF decreased the proportion of Proteobacteria, and increased the proportions of Spirochaetae and Elusimicrobia (P < 0.05). At the genus level, DF decreased the percentage of Ruminobacter, while increasing the percentage of Succinivibrio and Treponema (P < 0.05). Overall, the results indicate that DF modified rumen fermentation and mitigated the production of several toxic compounds. Thus, DF has great potential for preventing subacute rumen acidosis in dairy cows and for improving the health of ruminants.

Dietary fibres have been shown to affect early-life microbiota colonization in the large intestine of suckling piglets, however, much less is known as to whether they also modulate the composition and activity of butyrate-producing bacteria. Here, we investigated the effect of dietary fibres on the abundance, composition, and activity of butyrate-producing bacteria in suckling piglets. Piglets were fed a control diet or creep feeds containing alfalfa, wheat bran, or pure cellulose, respectively, from postnatal day 7 to 22. Large intestinal digesta and mucosa samples were collected for quantitative analysis of bacterial group-specific 16S ribosomal RNA- and butyrate production-related genes, and digesta samples for quantification of short-chain fatty acids. The alfalfa diet increased (P < 0.05) Clostridium cluster XIVa abundance, copies of genes encoding proteins involved in butyrate production (butyryl-CoA:acetate CoA-transferase, butyrate kinase), and butyrate concentration compared to the wheat bran diet in the digesta of the proximal colon. In the distal colonic digesta, animals fed the alfalfa diet had the highest number of butyryl-CoA:acetate CoA-transferase gene copies (P < 0.05) and numerically the highest butyrate concentration, albeit not significant (P > 0.05), compared to other groups. In the distal colonic mucosa, the cellulose diet increased (P < 0.05) the abundance of Clostridium cluster XIVa and copies of the butyryl-CoA:acetate CoA-transferase gene compared to the alfalfa diet. These results indicated that dietary fibres modulate the abundance and activity of butyrate-producing bacteria in the large intestine of suckling piglets, and that a moderate supplementation of alfalfa and cellulose may benefit early-life gut health through the delivery of butyrate to the mucosa.

Background: Diets containing high levels of carbohydrates provoke a rapid decrease of rumen pH and high levels of biogenic amines and lipopolysaccharides (LPS), which severely impair the health and performance of ruminants. The goal of this study was to evaluate the effects of sodium bicarbonate (BC) buffer on rumen fermentation, levels of LPS and biogenic amine, and composition of rumen microbiota using in vitro rumen cultures., Results: Sodium bicarbonate supplementation increased (P < 0.05) the final pH levels and concentrations of total volatile fatty acids and LPS, as well as the proportions of acetate, propionate, isobutyrate, isovalerate and valerate, and it decreased (P < 0.05) the proportion of butyrate and the levels of lactic acid, methylamine, tryptamine, tyramine, histamine and putrescine compared with the control. Pyrosequencing of the 16S rRNA gene showed that BC inclusion increased (P < 0.05) the bacterial diversity index compared with the control. Adding BC also decreased (P < 0.05) the relative abundance of Streptococcus and Butyrivibrio and increased (P < 0.05) the proportions of Ruminococcus, Succinivibrio and Prevotella., Conclusion: Sodium bicarbonate supplementation has beneficial effects in the reduction of bioamine levels and the increase in ruminal pH, and in modifying the microbial ecology of the rumen; however, it results in an accumulation of LPS under high-grain diet conditions. © 2016 Society of Chemical Industry., (© 2016 Society of Chemical Industry.)

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: 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.

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.

A reciprocal cross-fostering model with an obese typical Chinese piglet breed and a lean Western breed was used to identify genetic and maternal effects on the acquisition and development gut bacteria from birth until after weaning. Pyrosequencing of 16S rRNA genes results revealed an age- and diet-dependent bacterial succession process in piglets. During the first 3 days after birth, the bacterial community was relatively simple and dominated by Firmicutes with 79% and 65% relative abundance for Meishan and Yorkshire piglets, respectively. During the suckling period until day 14, the piglet breed and the nursing mother lead to increasing differentiation of the fecal bacterial community, with specific bacteria taxa associated with breed, and others with the nursing sow most likely due to its milk composition. Although the effect of nursing mother and the breed were evident through the suckling period, the introduction of solid feed and subsequent weaning were the major events occurring that dominated succession of the gut microbiota in the early life of piglets. This piglet cross-fostering model is a useful tool for studying the effects of diet, host genetics and the environment on the development and acquisition of the gut microbiota and over longer studies the subsequent impact on growth, health and performance of pigs., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

The bacterial community composition and function in the gastrointestinal tracts (GITs) of dairy cattle is very important, since it can influence milk production and host health. However, our understanding of bacterial communities in the GITs of dairy cattle is still very limited. This study analysed bacterial communities in ten distinct GIT sites (the digesta and mucosa of the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon and rectum) in six dairy cattle. The study observed 542 genera belonging to 23 phyla distributed throughout the cattle GITs, with the Firmicutes, Bacteroidetes and Proteobacteria predominating. In addition, data revealed significant spatial heterogeneity in composition, diversity and species abundance distributions of GIT microbiota. Furthermore, the study inferred significant differences in the predicted metagenomic profiles among GIT regions. In particular, the relative abundances of the genes involved in carbohydrate metabolism were overrepresented in the digesta samples of forestomaches, and the genes related to amino acid metabolism were mainly enriched in the mucosal samples. In general, this study provides the first deep insights into the composition of GIT microbiota in dairy cattle, and it may serve as a foundation for future studies in this area.

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.

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.

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.

Clone library of bacterial 16S rRNA gene was constructed to evaluate the bacterial diversity and community structure of uterus samples obtained from three postpartum healthy cows and three metritic cows on days 10 and 40. Sequences were assigned to five major groups (Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, and Tenericutes) and to an uncultured group. On day 10, Bacteroidetes, Firmicutes, and Fusobacteria were the dominant group both in healthy and metritic cows. On day 40, the major sequences were affiliated with Bacteroidetes, Firmicutes, Tenericutes, and Proteobacteria. Tenericutes (Ureaplasma diversum) were revealed only from healthy cows, while Proteobacteria (Histophilus somni) were found only from metritic cows. Quantitative PCR revealed that metritic cows on day 10 showed higher value of total bacteria, Bacteroidetes, Peptostreptococcus, and Fusobacterium compared with healthy cows, while only a higher value of Fusobacterium spp. was observed from the metritic cows on day 40 compared with that from healthy cows (P < 0.05). Our data indicates that great difference in the uterine bacterial community in both phyla level and species level exists between healthy and metritic postpartum cows, and dynamic changes in bacterial community occur over time.

As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.

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.

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.

The study aimed to evaluate the effects of early antibiotic intervention (EAI) on bacterial fermentation patterns and mucosal immune markers in the colon of pigs with different protein level diets. Eighteen litters of piglets at day (d) 7 were fed creep feed without or with growth promoting antibiotics until d 42. At d 42, pigs within each group were further randomly assigned to a normal- or low-crude protein (CP) diet. At d 77 and d 120, five pigs per group were slaughtered for analyzing colonic bacteria, metabolites, and mucosal gene expressions. Results showed that low-CP diet increased propionate and butyrate concentrations at d 77 but reduced ammonia and phenol concentrations ( P < 0.05). EAI increased p-cresol and indole concentrations under normal-CP diet at d 77 ( P < 0.05). Low-CP diet significantly affected ( P < 0.05) some bacteria groups ( Firmicutes, Clostridium cluster IV, Clostridium cluster XIVa, Escherichia coli, and Lactobacillus), but EAI showed limited effects. Low-CP diet down-regulated gene expressions of pro-inflammatory cytokines, toll-like receptor (TLR4), myeloid differentiating factor 88 (MyD88), and nuclear factor-κB p65 (NF-κB p65) ( P < 0.05). EAI up-regulated mRNA expressions of interleukin-8 (IL-8) and interferon-γ (IFN-γ) under normal-CP diet at d 77 ( P < 0.05). Furthermore, reductions of E. coli and ammonia under low-CP diet were positively correlated with down-regulated gene expressions of pro-inflammatory cytokines, which were positively correlated with the down-regulated TLR4-MyD88-NF-κB signaling pathway. In conclusion, EAI had short-term effects under normal-CP diet with increased aromatic amino acid fermentation and gene expressions of pro-inflammatory cytokines. Low-CP diet markedly reduced protein fermentation, modified microbial communities, and down-regulated gene expressions of pro-inflammatory cytokines possibly via down-regulating TLR4-MyD88-NF-κB signaling pathway. [ABSTRACT FROM AUTHOR]