Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets

Shifts in the microbial community and metabolome in rumen ecological niches during antler growth

Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.

Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

Effect of different genetic backgrounds on rumen microbiota and serum metabolic phenotypes in beef cattle

Species with different genetic backgrounds exhibit distinct metabolic traits. Nine beef cattle were selected for the experiment to study changes in serum metabolic phenotypes, rumen microbiota diversity, and composition in beef cattle from different genetic backgrounds. Three groups were Chinese Simmental (S group), Simmental×Chinese Holstein (SH group), and Simmental × Mongolian (SM group) cattle. We used ELISA to detect serum biochemical indicators. The Short-chain fatty acids (SCFAs) in the rumen were examined, and a significant difference was observed in the acetic acid content of the three experimental groups (p < 0.01). The propionic acid content in the rumen of the S group was significantly higher than that of the SH and SM groups (p < 0.05). The A/P ratios of both the S and SM groups were significantly higher than that of the SH group (p < 0.05). We analyzed rumen microbiota composition and diversity in each group of cattle using 16 S rRNA sequencing and found that their composition was generally similar in the three groups of crossbred fattening cattle; however, the f_Bacteroidales_RF16_group and g_norank_f_Bacteroidales_RF16_group were significantly enriched in the SH group, whereas Treponema and Spirochaetia were significantly enriched in the SM group. Spirochaetia was significantly enriched in the SM group. Differences in rumen bacterial enrichment indicated that starch, protein, and cellulolytic abilities differed among the S, SH, and SM groups. The results of Spearman correlation analysis confirmed the correlation between rumen genera and serum biochemical indices. Overall, differences in rumen microflora play an important role in influencing the serum metabolic phenotype.

Microbial Biogeography along the Gastrointestinal Tract of a Wild Chinese Muntjac (Muntiacus reevesi)

The gut microbiota plays an important role in host nutrient absorption, immune function, and behavioral patterns. Much research on the gut microbiota of wildlife has focused on feces samples, so the microbial composition along the gastrointestinal tract of wildlife is not well reported. To address this gap, we performed high-throughput sequencing of 16s rRNA genes and ITs rRNA genes in the gastrointestinal contents of a wild adult male Chinese muntjac (Muntiacus reevesi) to comparatively analyze the microbial diversity of different gastrointestinal regions. The results showed that the dominant bacterial phyla were Firmicutes (66.19%) and Bacteroidetes (22.7%), while the dominant fungal phyla were Ascomycetes (72.81%). The highest bacterial diversity was found in the stomach, and the highest fungal diversity was found in the cecum. The microbial communities of the large intestine and small intestine were of similar structures, which were distinct from that of the stomach. These results would facilitate the continued exploration of the microbial composition and functional diversity of the gastrointestinal tract of wild Chinese muntjacs and provide a scientific basis for microbial resource conservation of more wildlife.

The gut microbial differences between pre-released and wild red deer: Firmicutes abundance may affect wild adaptation after release

Insufficient density of red deer has affected the stability of forest ecosystems and the recovery of large carnivores (represented by Amur tiger). Conservation translocations from captivity to the wild has become an important way to restore the red deer populations. However, the difference in gut microbes between pre-release and wild red deer may affect the feeding adaptability of red deer after release. In this study, we clarified the differences in gut microbes between pre-released and wild red deer and screened the key gut microbes of the red deer involved in feeding by using metagenomic sequencing and feeding analysis. The results showed that the microbial difference between pre-released and wild red deer was mainly related to Firmicutes represented by Eubacteriales and Clostridia, and Firmicutes abundance in pre-released red deer (68.23%) was significantly lower than that of wild red deer (74.91%, p < 0.05). The expression of microbial metabolic pathways in pre-released red deer were significantly lower than those in wild red deer (p < 0.05), including carbohydrate metabolism, amino acid metabolism, glycan biosynthesis and metabolism, etc. The combinations of Firmicutes were significantly positively correlated with the intake of plant fiber and carbohydrate (p < 0.05), and were key microbes to help red deer deal with wild plant resources. Additionally, the combinations of Firmicutes represented by Eubacteriales and Clostridia lacking in pre-released red deer contributed the most to expression of microbial metabolic pathways (importance > 1), showing a significant positive correlation (p < 0.05). This study indicates that high abundance of Firmicutes is an important guarantee for red deer to adapt to the wild feeding environment, which provides critical implications for the recovery of red deer populations and the protection of endangered ungulates.

Co-production of lactate and volatile fatty acids through repeated-batch fermentation of fruit and vegetable waste: Effect of cycle time and replacement ratio

In this study, repeated-batch fermentation was used to convert fruit and vegetable waste to lactate and volatile fatty acids (VFAs), which are essential carbon sources for medium-chain fatty acids (MCFAs) production. The effect of cycle time and replacement ratio on acidification in long-term fermentation was investigated. The results showed that they had a significant impact on product yield, productivity, and type of products. Considering the yield, productivity, and lactate/VFAs ratio, a replacement ratio of 30% and a cycle time of 2 d may be more suitable for further production of MCFAs. Its productivity and lactate/VFAs ratio were 4.07 ± 0.24 g/(L·d) and 5 ± 0.6, respectively. The lactic acid bacteria, such as Enterococcus (63%) and Lactobacillus (33%), stabilized in the reactor, resulting in the generation of both lactate and VFAs by heterolactic fermentation. The present study demonstrated a new strategy with the potential to recover high-value products from organic waste streams.

Methionine Supplementation Affects Fecal Bacterial Community and Production Performance in Sika Deer (Cervus nippon)

Amino acid balance is central to improving the efficiency of feed protein utilization and for reducing environmental pollution caused by intensive farming. In previous studies, supplementation with limiting amino acids has been shown to be an effective means of improving animal nutrient utilization and performance. In this experiment, the effects of methionine on the apparent digestibility of nutrients, antler nutrient composition, rumen fluid amino acid composition, fecal volatile fatty acids and intestinal bacteria in antler-growing sika deer were investigated by randomly adding different levels of methionine to the diets of three groups of four deer at 0 g/day (CON), 4 g/day (LMet) and 6 g/day (HMet). Methionine supplementation significantly increased the apparent digestibility of organic matter, neutral detergent fiber (NDF) and acid detergent fiber (ADF) in the LMet group (p < 0.05). The crude protein and collagen protein of antlers were significantly higher in the LMet and HMet groups compared to the CON group and also significantly higher in the HMet group compared to the LMet group, while the calcium content of antlers was significantly lower in the HMet group (p < 0.05). Ruminal fluid free amino acid composition was altered in the three groups of sika deer, with significant changes in aspartic acid, citrulline, valine, cysteine, methionine, histidine and proline. At the phylum level, Firmicutes and Bacteroidetes were highest in the rectal microflora. Unidentified bacterial abundance was significantly decreased in the HMet group compared to the CON group. Based on the results of principal coordinate analysis (PCoA) and Adonis analysis, there was a significant difference in the composition of the intestinal flora between the CON and HMet groups (p < 0.05). At the genus level, compared with the CON group, the abundance of Rikenellaceae_RC9_gut_group and Lachnospiraceae_UCG-010 in the LMet group increased significantly (p < 0.05), the abundance of dgA-11_gut_group in the HMet group decreased significantly (p < 0.05) and the abundance of Lachnospiraceae_UCG-010, Saccharofermentans and Lachnospiraceae_NK3A20_group increased significantly. Taken together, the results showed that methionine supplementation was beneficial in increasing the feed utilization efficiency and improving antler quality in sika deer, while affecting the composition of fecal bacteria.

Integrated Transcriptome and Microbiota Reveal the Regulatory Effect of 25-Hydroxyvitamin D Supplementation in Antler Growth of Sika Deer

The level of plasma 25-hydroxyvitamin D (25(OH)D) is associated with the growth of the antler, a fast-growing bone organ of Cervidae. However, the benefits of 25(OH)D supplementation on antler growth and the underlying mechanisms remain unclear. Here, the antler growth profile and transcriptome, plasma parameters, rumen bacteria, and metabolites (volatile fatty acids and amino acids) were determined in sika deer in a 25(OH)D supplementation group (25(OH)D, n = 8) and a control group (Ctrl, n = 8). 25(OH)D supplementation significantly increased the antler weight and growth rate. The levels of IGF-1,25(OH)D and 1,25-dihydroxyvitamin D were significantly higher in the 25(OH)D group than in the Ctrl group, while the levels of LDL-C were lower. The levels of valerate and branched-chain amino acids in the rumen fluid were significantly different between the 25(OH)D and Ctrl groups. The bacterial diversity indices were not significantly different between the two groups. However, the relative abundances of the butyrate-producing bacteria (families Lachnospiraceae and Succinivibrionaceae) and the pyruvate metabolism pathway were higher in the 25(OH)D group. The transcriptomic profile of the antler was significantly different between the 25(OH)D and Ctrl groups, with 356 up- and 668 down-regulated differentially expressed genes (DEGs) in the 25(OH)D group. The up-regulated DEGs were enriched in the proteinaceous extracellular matrix and collagen, while the down-regulated DEGs were enriched in the immune system and lipid metabolism pathways. Overall, these results provide novel insights into the effects of 25(OH)D supplementation on the host metabolism, rumen microbiota, and antler transcriptome of sika deer.

Diversity of growth performance and rumen microbiota vary with feed types

Diet is a major factor in influencing the growth performance and the microbial community of lambs. This study aimed to investigate how diverse diets influence their growth performance and rumen microbiota. Ninety male lambs were randomly allocated into three groups in a completely randomized design with equal lambs: non-pelleted native grass hay (HA) as the control diet and pelleted native grass hay (GP) and pelleted native grass hay with concentrate (GPC) as experimental diets. The rumen fluid samples of the lambs in the HA, GP, and GPC groups were used to study rumen microbiota diversity through 16S rDNA high-throughput sequencing. In the present study, the final body weight, dry matter intake, and average daily gain differed significantly (p &lt; 0.05) among the HA, GP, and GPC groups. Compared to the HA group, higher final body weight, dry matter intake, and average daily gain were found in the GP group. Similarly, better animal performance was observed in the GPC group than in the GP group. The principal coordinates analysis displayed that the composition of the rumen microbiota in the three groups was distinctly separated from each other. Bacteroidetes and Firmicutes were the dominant members of the community in the HA and GP groups, while Bacteroidetes, Firmicutes, and Proteobacteria became the predominant members in the GPC group. The comparison among these groups showed significant (p &lt; 0.05) differences in Rikenellaceae_RC9_gut_group, Prevotella_1, Ruminococcaceae_NK4A214_group, and Succiniclasticum. These results suggest that the GP and GPC diets are more beneficial for growth performance than the HA diet and also indicate that the rumen microbiota varied in response to different feed types. In conclusion, these results could provide strategies to influence rumen microbiota for better growth and a healthier ecosystem on the Mongolian Plateau and lay the theoretical groundwork for feeding the pelleted native grass diet.

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon)

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

Effect of Methionine Supplementation on Serum Metabolism and the Rumen Bacterial Community of Sika Deer (Cervus nippon)

Methionine is the first or second limiting amino acid for ruminants, such as sika deer, and has a variety of biological functions such as antioxidant activity, immune response, and protein synthesis. This study aimed to investigate the effects of methionine supplementation on antler growth, serum biochemistry, rumen fermentation, and the bacterial community of sika deer during the antler-growing period. Twelve 4-year-old male sika deer were randomly assigned to three dietary groups supplemented with 0 g/day (n = 4, CON), 4.0 g/day (n = 4, LMet), and 6.0 g/day (n = 4, HMet) methionine. No significant difference (p > 0.05) was found in the production performance between the three groups, but antler weight was higher in both the LMet and HMet groups than in the CON group. Methionine supplementation significantly increased the serum glutathione peroxidase activity (p < 0.05). The serum immunoglobulin G level was significantly higher in the HMet group than in the other two groups (p < 0.05). No significant effect was found on the apparent amino acid digestibility of the three groups, but cysteine and methionine digestibility were higher in the LMet group. The serum hydroxylysine level was significantly lower in the LMet and HMet groups, whereas the serum lysine level was significantly lower in the HMet group compared with the CON group (p < 0.05). The LMet group had the highest but a nonsignificant total volatile fatty acid content and significantly higher microbial protein content in the rumen than the CON group (p < 0.05). The phyla Bacteroidetes, Firmicutes, and Proteobacteria were dominant in the rumen of the sika deer. The principal coordinate analysis (PCoA) and analysis of similarities (ANOSIM) results showed a significant change in the bacterial composition of the three groups (p < 0.05). The relative abundance of Prevotella and Rikenellaceae-RC9 was significantly higher in the LMet group compared with the CON group and CON and HMet groups, respectively. These results revealed that methionine supplementation improved the antioxidant activity and immune status, affecting amino acid metabolism and rumen microbial composition of the sika deer.

Effects of Different Roughage Diets on Fattening Performance, Meat Quality, Fatty Acid Composition, and Rumen Microbe in Steers

This study aimed to evaluate different roughages on fatting performance, muscle fatty acids, rumen fermentation and rumen microbes of steers. Seventy-five Simmental crossbred steers were randomly divided into wheat straw group (WG), peanut vine group (PG) and alfalfa hay group (AG), with 5 replicates of 5 steers each. The results showed a highest average daily gain and lowest feed/gain ratio in AG group (P = 0.001). Steers fed alfalfa hay had the highest muscle marbling score and n-3 polyunsaturated fatty acid (PUFA), and also the rumen NH3-N and microbial protein (MCP) concentration among the three groups (P < 0.05). Correlation analysis showed that ruminal NH3-N and MCP were negatively correlated with muscle saturated fatty acid (SFA), while ruminal MCP was positively correlated with muscle PUFA and n-3 PUFA (P < 0.05). 16S rRNA analysis indicated that fed alfalfa hay decreased the abundance of Ruminococcaceae_UCG-001(P = 0.005). More importantly, muscle SFA deposition were positively correlated to the abundance of Ruminococcaceae_UCG-001 (P < 0.05), while the muscle PUFA and n-3 PUFA deposition were negatively correlated to it (P < 0.01). Therefore, alfalfa hay provides a better fattening effect on steers. Alfalfa rich in n-3 PUFA would reduce the abundance of Ruminococcaceae_UCG-001 involved in hydrogenation, increase the rumen protective effect of C18:3 n-3, which is beneficial to the deposition of muscle n-3 PUFA and PUFA.

Whole-plant corn silage improves rumen fermentation and growth performance of beef cattle by altering rumen microbiota

In recent years, whole-plant corn silage has been widely used in China. Roughage is an important source of nutrition for ruminants and has an important effect on rumen microbiota, which plays an important role in animal growth performance and feed digestion. To better understand the effects of different silages on rumen microbiota, the effects of whole-plant corn silage or corn straw silage on growth performance, rumen fermentation products, and rumen microbiota of Simmental hybrid cattle were studied. Sixty healthy Simmental hybrid cattle were randomly divided into 2 groups with 6 replicates in each group and 5 cattle in each replicate. They were fed with whole-plant corn silage (WS) diet and corn straw silage (CS) diet respectively. Compared with corn straw silage, whole-plant corn silage significantly increased daily gain and decreased the feed intake-to-weight gain ratio (F/G) of beef cattle. Whole-plant corn silage also decreased the acetic acid in the rumen and the acetate-to-propionate ratio (A/P) compared with corn straw silage. On the genus level, the relative abundance of Prevotella_1 was significantly increased while the relative abundance of Succinivibrionaceae_UCG-002 was decreased in cattle fed whole-plant corn silage compared with those fed corn straw silage. Prevotella_1 was positively correlated with acetic acid and A/P. Succinivibrionaceae_UCG-002 was positively correlated with propionic acid and butyric acid, and negatively correlated with pH. Feeding whole-plant corn silage improved amino acid metabolism, nucleotide metabolism, and carbohydrate metabolism. Correlation analysis between rumen microbiota and metabolic pathways showed that Succinivibrionaceae_UCG-002 was negatively correlated with glycan biosynthesis and metabolism, metabolism of co-factors and vitamins, nucleotide metabolism, and translation while Prevotellaceae_UCG-003 was positively correlated with amino acid metabolism, carbohydrate metabolism, energy metabolism, genetic information processing, lipid metabolism, membrane transport, metabolism of cofactors and vitamins, nucleotide metabolism, replication and repair, and translation. Ruminococcus_2 was positively correlated with amino acid metabolism and carbohydrate metabolism. Feeding whole-plant corn silage can improve the growth performance and rumen fermentation of beef cattle by altering rumen microbiota and regulating the metabolism of amino acids, carbohydrates, and nucleotides. KEY POINTS: • Feeding whole-plant corn silage could decrease the F/G of beef cattle • Feeding whole-plant corn silage improves rumen fermentation in beef cattle • Growth performance of beef cattle is related to rumen microbiota and metabolism.

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing

The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François’ langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François’ langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.

Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan

To understand the nutritional status of culled wild sika deer (Cervus nippon), we compared the ruminal microbes of deer living in habitats differing in food composition (Nagano winter, Nagano spring, and Hokkaido winter) using next-generation sequencing. Twenty-nine sika deer were sampled. Alpha and beta diversity metrics determined via 16S and 18S rRNA amplicon-seq analysis showed compositional differences. Prevotella, Entodinium, and Piromyces were the dominant genera of bacteria, fungi and protozoa, respectively. Moreover, 66 bacterial taxa, 44 eukaryotic taxa, and 46 chloroplastic taxa were shown to differ significantly among the groups by the linear discriminant analysis effect size (LEfSe) technique. Total RNA-seq analysis yielded 397 significantly differentially expressed transcripts (q < 0.05), of which 48 (q < 0.01) were correlated with the bacterial amplicon-seq results (Pearson correlation coefficient > 0.7). The ruminal microbial composition corresponded with the presence of different plants because the amplicon-seq results indicated that chloroplast from broadleaf trees and Stramenopiles-Alveolates-Rhizaria (SAR) were enriched in Nagano, whereas chloroplast from graminoids, Firmicutes and the dominant phylum of fungi were enriched in Hokkaido. These results could be related to the severe snow conditions in Hokkaido in winter and the richness of plants with leaves and acorns in Nagano in winter and spring. The findings are useful for understanding the nutritional status of wild sika deer.

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer.

IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep

In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.

Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China

Simple Summary

The Qinghai–Tibetan plateau is considered as the third Pole of the world and is characterized by low oxygen, high altitude, extreme cold weather and strong ultraviolet radiation. Yak, as the main domestic animals raised on the plateau, play various roles in local herdsmen’s lives by supplying necessities such as meat, milk and fuel. Yak are adapted to the harsh environment on the plateau; microbiota in gut equip the hosts with special abilities including adaptability, as illustrated by numerous research projects. Accordingly, the microbes in the gastrointestinal tract of yak must be characteristically profiled as a strategy to adapt to the environment. However, little is known about the microbial community in whole tract of yak; almost all of reported researches focused on rumen. Therefore, in the current study the bacterial community in the gastrointestinal tract of yak was explored using 16S rDNA amplicon sequencing technology, and the community profiling characteristic in each section was clearly elucidated.

Abstract

In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples—the most abundant phyla were Firmicutes (34.58%), Bacteroidetes (33.96%) and Verrucomicrobia (11.70%). At the genus level, a total of 66 genera were obtained—Rikenellaceae_RC9_gut_group (7.24%), Akkermansia (6.32%) and Ruminococcaceae_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (p < 0.05). Bacteroidete were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals.

Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

Background

The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability.

Results

The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups.

Conclusion

The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor (Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference (P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

Dynamic modulation of gut microbiota improves post-myocardial infarct tissue repair in rats via butyric acid-mediated histone deacetylase inhibition

The complex and dynamic population of gut microbiota exerts a marked influence on the host during homeostasis and disease. Imbalance of gut microbiota metabolites may lead to cardiac dysfunction in patients with heart failure, which is related to myocardial infarction(MI) severity. However, the role of gut microbiota in the repair process after MI has rarely been reported. To explore the role of gut microbiota in MI repair and its underlying mechanism, we mixed antibiotics in drinking water to interfere with gut microbiota in rats. Hematoxylin and eosin staining, Sirius red staining, western blotting, and immunohistochemistry were used to detect tissue repair and fibrosis. We found that the expressions of alpha-smooth muscle actin, collagen, and histone deacetylase (HDAC) activities were significantly increased. We detected gut microbiota at different time points after MI using 16S ribosomal RNA sequencing and detected that Prevotellaceae, Clostridiaceae, and Lachnospiraceae were significantly altered among the butyric acid producers. We administered sodium butyrate via drinking water and discovered that sodium butyrate reduced HDAC activities and adverse repair. Therefore, we speculated that gut microbiota influences the acetylation level and tissue repair process after MI by affecting butyric acid production.

Effects of Arginine Supplementation on Serum Metabolites and the Rumen Bacterial Community of Sika Deer (Cervus nippon)

Velvet antler is a regeneration organ of sika deer (Cervus nippon) and an important Chinese medicine, and nutrient metabolism affects its growth. Here, we investigated the effects of arginine supplementation on antler growth, serum biochemical indices, and the rumen bacterial community of sika deer during the antler growth period. Fifteen male sika deer (6 years old) were randomly assigned to three dietary groups, which were supplemented with 0 (n = 5, CON), 2.5 (n = 5, LArg), or 5.0 g/d (n = 5, HArg) L-arginine. The IGF-1, ALT and AST concentrations in the serum of LArg sika deer were significantly higher than those in the serum of CON (P < 0.05) and HArg deer (P < 0.05). The phyla Bacteroidetes, Firmicutes, and Proteobacteria were dominant in the rumen of sika deer among the three groups. Comparison of alpha diversities showed that the ACE and Chao1 indices significantly increased in the LArg and HArg groups compared with those in the CON group. PCoA and ANOSIM results showed that the bacterial community was significantly changed between the CON and LArg groups. Moreover, the relative abundances of Fibrobacter spp. and Prevotellaceae UCG-003 increased, but those of Clostridium sensu stricto 1 and Corynebacterium 1 decreased in the LArg and HArg groups compared with those in the CON group. Additionally, the relative abundances of 19 OTUs were significantly different between the LArg and HArg groups. These results revealed that arginine supplementation affected the sika deer rumen bacterial community and serum biochemical indices.

Effects of king grass and sugarcane top in the absence or presence of exogenous enzymes on the growth performance and rumen microbiota diversity of goats

In the present study, the feasibility of sugarcane top (ST) application in the goat's diet was evaluated. A total of 20 goats were randomly divided into four groups. The dietary treatments were set as follows: animals were fed with king grass (KG), KG with exogenous enzymes (KGE), ST, and ST with exogenous enzymes (STE). The animals were given free access to feed and water. After 15 days of adaptation and 60 days of the experiment, the growth performance, plasma parameters, and rumen microbiota of goats were assessed. The results showed that the KG, ST, and exogenous enzyme supplement had no significant effects on the growth performance and plasma parameters. The diet affected the rumen microbiota diversity and structure, and the alpha and beta diversity in the animals fed with ST were dramatically greater compared with the animals fed with KG. The abundances of Proteobacteria, Cyanobacteria, and Elusimicrobia were significantly decreased in the animals fed with KG or KGE, while the abundances of Firmicutes and Euryarchaeota were significantly higher in the animals fed with KG or KGE. Furthermore, the microbial communities were also different at the genus level. Moreover, the exogenous enzymes had a slight effect on rumen microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the greatest differences were found in bacterial taxa, and these specific taxa could be used as biomarkers to distinguish rumen microbiota. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional profile prediction indicated that the dietary treatments of ST and KG could also alter the gene expression pattern in nutrient and energy metabolism, as well as replication and repair of genetic information pathways. Collectively, the dietary treatments of KG and ST in the absence or presence of exogenous enzymes had similar effects on the growth performance and plasma parameters of goats. Besides, the KG and ST diets could affect the rumen microbiota community and function of goats. Therefore, ST could be used as a promising alternative feed resource for ruminants without the addition of exogenous enzymes in tropical regions.

Ruminal Degradation of Rumen-Protected Glucose Influences the Ruminal Microbiota and Metabolites in Early-Lactation Dairy Cows

Rumen-protected glucose (RPG) plays an important role in alleviating the negative energy balance of dairy cows. This study used a combination of rumen microbes 16S and metabolomics to elucidate the changes of rumen microbial composition and rumen metabolites of different doses of RPG's rumen degradation part in early-lactation dairy cows. Twenty-four multiparous Holstein cows in early lactation were randomly allocated to control (CON), low-RPG (LRPG), medium-RPG (MRPG), or high-RPG (HRPG) groups in a randomized block design. The cows were fed a basal total mixed ration diet with 0, 200, 350, and 500 g of RPG per cow per day, respectively. Rumen fluid samples were analyzed using Illumina MiSeq sequencing and ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. MRPG supplementation increased bacterial richness and diversity, including increasing the relative abundance of cellulolytic bacteria, such as Ruminococcus, Lachnospiraceae_NK3A20_group, Ruminiclostridium, and Lachnospiraceae_UCG-008 MRPG significantly increased the concentrations of acetate, propionate, butyrate, and total volatile fatty acid in the rumen. Ruminal fluid metabolomics analysis showed that RPG supplementation could significantly regulate the synthesis of amino acids digested by protozoa in the rumen. Correlation analysis of the ruminal microbiome and metabolome revealed some potential relationships between major bacterial abundance and metabolite concentrations. Our analysis found that RPG supplementation of different doses can change the diversity of microorganisms in the rumen and affect the rumen fermentation pattern and microbial metabolism and that a daily supplement of 350 g of RPG might be the ideal dose.IMPORTANCE Dairy cows in early lactation are prone to a negative energy balance because their dry matter intake cannot meet the energy requirements of lactation. Rumen-protected glucose is used as an effective feed additive to alleviate the negative energy balance of dairy cows in early lactation. However, one thing that is overlooked is that people often think that rumen-protected glucose is not degraded in the rumen, thus ignoring its impact on the microorganisms in the rumen environment. Our investigation and previous experiments have found that rumen-protected glucose is partially degraded in the rumen. However, there are few reports on this subject. Therefore, we conducted research on this problem and found that rumen-protected glucose supplementation at 350 g/day can promote the development and metabolism of rumen flora. This provides a theoretical basis for the extensive application of rumen bypass glucose at a later stage.

Evaluation of Changes in the Levels of Firmicutes and Bacteroidetes Phyla of Sheep Feces Depending on the Breed

Simple Summary

The microbiome plays an important role in the digestive system of ruminants. It affects the health status of animals and their development and production rates. However, its composition may be influenced by factors such as diet, age, gender, and health condition. The study was conducted on three breeds of sheep that were kept in one environment and fed with the same feed. The microbiological analysis showed that the animal microbiome is also influenced by breed.

Abstract

Studies carried out so far have indicated the effect of the microbiome on the composition of ruminant products. Recent studies have shown that not only diet, but also genetic factors can affect the microbiological composition of the digestive system. The aim of the study was to determine the differences in the levels of selected bacterial phyla in terms of breed differences. Three sheep breeds, i.e., Olkuska, Romanov, and old-type Polish Merino, differing in their use (meat–wool, meat, prolificacy) and country of breed origin were included in the study. Sheep at the same age and of the same sex were kept for a period of 3 months in the same environmental conditions and fed the same feed in the same proportions. The study included real-time PCR (polymerase chain reaction) analysis of feces collected before the slaughter and measurements of body weight and chilled carcasses. The obtained results showed significant differences between the breeds in the levels of bacterial populations tested. There were also differences in body weight between the breeds during the first weight measurements, however, the final results did not show any differences—after three months of maintenance all of them reached similar body weights, despite differences in fecal microbiological composition. The study suggests that in addition to diet and environmental conditions, the microbiology can also be influenced by breed.

Combined signature of rumen microbiome and metabolome in dairy cows with different feed intake levels

Feed intake is a major factor in maintaining the balance between ruminal fermentation and the microbial community of dairy cows. To explore the relationship among feed intake, microbial metabolism, and ruminal fermentation, we examined the combined signatures of the microbiome and metabolome in dairy cows with different feed intake levels. Eighteen dairy cows were allocated to high feed intake (HFI), medium feed intake (MFI), and low feed intake (LFI) groups according to their average daily feed intake. 16S rDNA sequencing results revealed that the relative abundance of Firmicutes in the HFI group was significantly higher than that in the MFI and LFI groups (P < 0.05). The ratio of Bacteroidetes to Firmicutes was significantly lower in the HFI group than in the MFI and LFI groups (P < 0.05). The relative abundance of Lachnospiraceae_unclassified, Veillonellaceae_unclassified, and Saccharofermentants was significantly higher in the HFI group than in the LFI and MFI groups (P < 0.05). The relative abundance of Erysipelotrichaceae_unclassified and Butyrivibrio was significantly higher in the HFI group than in the MFI and LFI groups (P < 0.05). Ultra high performance liquid chromatography-mass spectrometry revealed five key pathways, including the linoleic acid metabolism pathway, alpha-linolenic acid metabolism, arginine and proline metabolism, glutathione metabolism, and valine, leucine, and isoleucine biosynthesis, which are closely related to energy and amino acid metabolism. Linoleic acid, glutamate, alpha-linolenic acid, l-methionine, and l-valine levels were significantly lower in the HFI group than in the MFI and LFI groups (q < 0.05), while the relative content of glutamate was significantly lower in the MFI group than in the LFI group (q < 0.05). Stearic acid content was significantly higher in the HFI group than in the LFI group (q < 0.05). Our findings provide insight into the rumen microbiome of dairy cows with different feed intake and the metabolic pathways closely associated with feed intake in early-lactating cows. The candidates involved in these metabolic pathways may be useful for identifying variations in feed intake. The signatures of the rumen microbiome and metabolome in dairy cows may help make decisions regarding feeding.

Metagenomics Reveals Diet-Specific Specialization of Bacterial Communities in Fungus Gardens of Grass- and Dicot-Cutter Ants

Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Differences between community composition and functional capacity of the bacteria in the two types of fungus gardens reflect differences in the substrates that the ants incorporated. These results show that different substrate inputs matter for fungus garden bacteria and shed light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

The gut bacterial diversity of sheep associated with different breeds in Qinghai province

Background

Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique.

Results

The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7 N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05).

Conclusions

In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.

The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle

Improvement of the food value of rice straw is urgently required in rice crop growing areas to mitigate pollution caused by rice straw burning and enhance the supply of high-quality forages for ruminants. The aims of the present study were to compare the effects of fresh corn Stover and rice straw co-fermented with probiotics and enzymes on rumen fermentation and establish the feasibility of increasing the rice straw content in ruminant diets and, by extension, reducing air pollution caused by burning rice straw. Twenty Simmental hybrid beef cattle were randomly allotted to two groups with ten cattle per group. They were fed diets based either on rice straw co-fermented with probiotics and enzymes or fresh corn Stover for 90 days. Rumen fluid was sampled with an esophageal tube vacuum pump device from each animal on the mornings of days 30, 60, and 90. Bacterial diversity was evaluated by sequencing the V4–V5 region of the 16S rRNA gene. Metabolomes were analyzed by gas chromatography/time-of-flight mass spectrometry (GC–TOF/MS). Compared to cattle fed fresh corn Stover, those fed rice straw co-fermented with probiotics and enzymes had higher (P < 0.05) levels of acetic acid and propionate in rumen liquid at d 60 and d 90 respectively, higher (P < 0.05) abundances of the phyla Bacteroidetes and Fibrobacteres and the genera Ruminococcus, Saccharofermentans, Pseudobutyrivibrio, Treponema, Lachnoclostridium, and Ruminobacter, and higher (P < 0.05) concentrations of metabolites involved in metabolisms of amino acid, carbohydrate, and cofactors and vitamins. Relative to fresh corn Stover, rice straw co-fermented with probiotics and enzymes resulted in higher VFA concentrations, numbers of complex carbohydrate-decomposing and H₂-utilizing bacteria, and feed energy conversion efficiency in the rumen.

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs

Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes correlated negatively with propionate and TVFA (P < 0.05); and Elusimicrobia correlated negatively with propionate and butyrate (P < 0.05). Actinobacteria and Verrucomicrobia correlated positively correlated with NH₃-N. In conclusion, supplementary feeding of lambs before weaning promoted the development of rumen tissue morphology and rumen microorganisms.

Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs

The aim of the study was to evaluate the ruminal function and microbial community of lamb under different nutrient levels. Sixty-four lambs with similarity body weight were randomly assigned to four groups after weaning off ewe’s milk on the 17th day (6.2 ± 0.2 kg). The lambs of the control group (CON) were fed a basal diet, and the other three groups were subjected to a diet of decreased protein (PR), digestible energy (ER) or both of them at 20% (BR) of basal diet. The decrease of dietary protein or energy level decreased the average daily gain, ruminal weight and mucosal thickness of lambs (P < 0.05). The total volatile fatty acid (TVFA), acetate and propionate concentration of the CON group were significantly higher than that of the other three groups. The dietary protein and energy level affected the microbial diversity, and low energy level increased the relative abundance of phyla of Fibrobacteres, whereas at the genus level, increased the relative abundance of Butyrivibrio and Prevotellaceae. Under different dietary energy and protein levels, 14 genera exhibited significant correlation with ruminal fermentation. These findings supplied new perspective for the understanding of the dietary effect on ruminal microbial community interactions and are of great significance for establishing the optimal nutrient supply strategy for lambs.

Bacterial community and metabolome shifts in the cecum and colon of captive sika deer (Cervus nippon) from birth to post weaning

Ruminant productivity is associated with the gastrointestinal tract bacterial community, which matures progressively with animal growth. However, knowledge of the bacteriome and metabolome dynamics in cecum and colon during the early lives of neonatal ruminants is limited. Thus, we examined the bacteriome and metabolomes of the cecum and colon in neonatal sika deer at days 1, 42 and 70. The bacterial diversity and richness in the cecum and colon increased with age, and the bacterial community significantly changed across three time points. For cecum and colon, the proportions of Bacteroides spp., Escherichia-Shigella, Clostridium sensu stricto 1, Lachnoclostridium spp. and Lactobacillus spp. were predominated at day 1 and decreased with age, while the proportions of Ruminococcaceae UCG 005, Ruminococcaceae UCG 010, Rikenellaceae RC9 and Prevotellaceae UCG 003 were predominated at days 42 and 70 and increased with age. The concentrations of creatine and serine were significantly decreased, whereas the concentrations of total short-chain volatile fatty acids, pelargonic acid and leucine were increased in both the cecum and colon during development. These data document the development of the bacterial community and the metabolites in the cecum and colon of sika deer, and suggest a possible importance of ecology niche on gut development.

Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau

Diet is the great determinant of bacterial composition in the rumen. However, little is known about the rumen bacterial community of Tibetan sheep living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. In the present study, we used high-throughput sequencing to investigate the rumen bacterial community of Tibetan sheep associated with two primary diets: alpine pasture diet (a continuation of the sheep's natural grazing diet) and oat (Avena sativa) hay diet on the QTP. The results showed that bacterial community richness and species diversity of the oat hay diet group were significantly greater than that of the native pasture diet group (p < 0.05). Principal co-ordinate analysis and analysis of similarities revealed that the bacterial community of the oat hay diet group was distinctly different from that of the native pasture diet group (p < 0.05). Bacteroidetes and Firmicutes were the predominant microbial phyla in the rumen. The rumen of oat-hay-fed sheep had higher proportions of Proteobacteria and novel bacteria species than the rumen of native-pasture-fed sheep. Actinobacteria, an uncommon bacterial phylum, occurred only in the oat-hay-fed group. At the genus level, Komagataeibacter, Ruminococcaceae_UCG-014, and Ruminococcaceae_NK4A214 showed significantly higher relative abundance in the oat-hay-fed sheep than in the native-pasture-fed sheep (p < 0.05). This study is the first of the QTP to employ high-throughput sequencing to examine the influence of diet on the rumen microbiome of Tibetan sheep.

Characterisation of the bacterial community in the gastrointestinal tracts of elk (Cervus canadensis)

The resident bacteria of the gastrointestinal tract (GIT) and the behaviour of these microbes have been poorly characterised in elk as compared to other ruminant animal species such as sheep and cattle. In addition, most microbial community studies of deer gut have focused on rumen or faeces, while other parts of the GIT such as the small and large intestine have received little attention. To address this issue, the present study investigated the diversity of the GIT bacterial community in elk (Cervus canadensis) by 16S rRNA pyrosequencing analysis. Eight distinct GIT segments including the stomach (rumen, omasum, and abomasum), small intestine (duodenum and jejunum), and large intestine (cecum, colon, and rectum) obtained from four elks were examined. We found that bacterial richness and diversity were higher in the stomach and large intestine than in the small intestine (P < 0.05). A total of 733 genera belonging to 26 phyla were distributed throughout elk GITs, with Firmicutes, Bacteroidetes, and Proteobacteria identified as the predominant phyla. In addition, there was spatial heterogeneity in the composition, diversity, and species abundance of microbiota in the GIT (P < 0.0001). To the best of our knowledge, this is the first study to characterise bacterial communities from eight GIT regions of elk by 16S rRNA pyrosequencing.

Different Sex-Based Responses of Gut Microbiota During the Development of Hepatocellular Carcinoma in Liver-Specific Tsc1-Knockout Mice

Gut microbial dysbiosis is correlated with the development of hepatocellular carcinoma (HCC). Therefore, analyzing the changing patterns in gut microbiota during HCC development, especially before HCC occurrence, is essential for the diagnosis and prevention of HCC based on gut microbial composition. However, these changing patterns in HCC are poorly understood, especially considering the sex differences in HCC incidence and mortality. Here, with an aim to determine the relationship between gut microbiota and HCC development in both sexes, and to screen potential microbial biomarkers for HCC diagnosis, we studied the changing patterns in the gut microbiota from mice of both sexes with liver-specific knockout of Tsc1 (LTsc1KO) that spontaneously developed HCC by 9–10 months of age and compared them to the patterns observed in their wide-type Tsc1^fl/fl cohorts using high-throughput sequencing. Using the LTsc1KO model, we were able to successfully exclude the continuing influence of diet on the gut microbiota. Based on gut microbial composition, the female LTsc1KO mice exhibited gut microbial disorder earlier than male LTsc1KO mice during the development of HCC. Our findings also indicated that the decrease in the relative abundance of anaerobic bacteria and the increase in the relative abundance of facultative anaerobic bacteria can be used as risk indexes of female HCC, but would be invalid for male HCC. Most of the changes in the gut bacteria were different between female and male LTsc1KO mice. In particular, the increased abundances of Allobaculum, Erysipelotrichaceae, Neisseriaceae, Sutterella, Burkholderiales, and Prevotella species have potential for use as risk indicators of female HCC, and the increased abundances of Paraprevotella, Paraprevotellaceae, and Prevotella can probably be applied as risk indicators of male HCC. These relationships between the gut microbiota and HCC discovered in the present study may serve as a platform for the identification of potential targets for the diagnosis and prevention of HCC in the future.

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis

The ruminal microbiota plays major roles in feed digestion. The composition and fermentation of the bacterial communities in 3 important ruminant species have been studied previously. Here, we extended this research to the effect of concentrate-to-forage ratios on ruminal bacterial communities in Tarim red deer (Cervus elaphus yarkandensis). Different concentrate-to-forage ratios (2:8, 3:7, 4:6, and 5:5) were fed to Tarim red deer for 20 days. Ruminal bacterial communities were elucidated by 16S ribosomal RNA gene sequencing on an Illumina HiSeq 2500 platform. The microbial composition and biodiversity at the different concentrate-to-forage ratio levels were analyzed using clustering of operational taxonomic units based on 97% sequence identity, taxonomic classification at the phylum and genus levels, α diversity, and β diversity. Rumen microorganisms of deer fed a diet with a concentrate-to-forage ratio of 2:8 had the highest species diversity, followed by ratios of 3:7, 4:6, and 5:5. The community structure of the A1 and A2 samples and the A3 and A4 samples was similar. The bacterial composition appeared to be affected by diet, with a lower dietary concentrate level tending to increase the richness and diversity of ruminal bacteria in the rumen of Tarim red deer.

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning

The dense and diverse community of microorganisms inhabiting the gastrointestinal tract of ruminant animals plays critical roles in the metabolism and absorption of nutrients, and gut associated immune function. Understanding microbial colonization in the small intestine of new born ruminants is a vital first step toward manipulating gut function through interventions during early life to produce long-term positive effects on host productivity and health. Yet the knowledge of microbiota colonization and its induced metabolites of small intestine during early life is still limited. In the present study, we examined the microbiota and metabolome in the jejunum and ileum of neonatal sika deer (Cervus nippon) from birth to weaning at days 1, 42, and 70. The microbial data showed that diversity and richness were increased with age, but a highly individual variation was observed at day 1. Principal coordinate analysis revealed significant differences in microbial community composition across three time points in the jejunum and ileum. The abundance of Halomonas spp., Lactobacillus spp., Escherichia–Shigella, and Bacteroides spp. tended to be decreased, while the proportion of Intestinibacter spp., Cellulosilyticum spp., Turicibacter spp., Clostridium sensu stricto 1 and Romboutsia spp. was significantly increased with age. For metabolome, metabolites separated from each other across the three time points in both jejunum and ileum. Moreover, the amounts of methionine, threonine, and putrescine were increased, while the amounts of myristic acid and pentadecanoic acid were decreased with age, respectively. The present study demonstrated that microbiota colonization and the metabolome becomes more developed in the small intestine with age. This may shed new light on the microbiota-metabolome-immune interaction during development.

The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing

Cervus albirostris (white-lipped deer) is an endemic species in China. As the name implies, C. albirostris has a characteristic pure white marking around their mouth and on the underside of the throat. The animal is a typical alpine species normally living at the height of 3500-4300 m. In this study, by pyrosequencing the 16S rRNA gene sequences, we for the first time analyzed the gut bacterial community composition in eight feces samples of wild C. albirostris. From a total of 243,634 high-quality sequences, we identified 186 genera, included in 17 prokaryotic phyla in the feces. The relative proportions of Firmicutes and Bacteroidetes were highly consistent in each individual sample. The most frequently detected genus was Ruminococcaceae UCG-005, ranging from 6.70 to 21.00%, displaying positively connections with the Rikenellaceae RC9 gut group. The bacterial communities associated with C. albirostris provide the basic knowledge for further microbiological studies and facilitates the conservation efforts of this vulnerable deer species.

Bacterial community in the rumen of Tibetan sheep and Gansu alpine fine-wool sheep grazing on the Qinghai-Tibetan Plateau, China

The rumen microbiome plays a vital role in ruminant nutrition and health, and its community is affected by environmental factors. However, little is known about the rumen bacterial community of ruminants living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. The objectives of this study were to investigate the rumen bacterial community of the typical plateau sheep (Tibetan sheep, TS, and Gansu alpine fine-wool sheep, GS) grazing on the QTP, using 16S rRNA gene sequence analysis, and to evaluate the relationship between the rumen bacterial community and the QTP environment. A total of 116 sequences (201 clones) were examined and divided into 53 operational taxonomic units (OTUs) in the TS library and 46 OTUs in the GS library. Phylogenetic analysis showed that the sequences that belonged to the Firmicutes were the most predominant bacteria in both TS and GS libraries, representing 79.4% and 62.8% of the total clones, respectively. The remaining sequences belonged to Bacteroidetes, Proteobacteria, Actinobacteria, or were unclassified bacteria. Sequence analysis revealed that the TS and GS rumens harbored many novel sequences associated with uncultured bacteria that accounted for 63.6% and 46.8% of the total clones, respectively. Comparison of the composition and diversity of the TS and GS rumen bacteria revealed few overlapping known bacteria between the two breeds, and a higher diversity in TS. The rumen bacteria of the plateau sheep showed higher percentages of bacteria that belonged to Firmicutes and novel species compared with the low-elevation sheep. The unique bacterial community in the plateau sheep rumens is perhaps one of the major reasons that they can adapt to the harsh plateau environment. These results can help identify the rumen bacterial community of the ruminants in the QTP, and provide bacteria resources and basic data to improve ruminant productivity.

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)

The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.

Diversity of formyltetrahydrofolate synthetase genes in the rumens of roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed different diets

Reductive acetogenesis by homoacetogens represents an alternative pathway to methanogenesis to remove metabolic hydrogen during rumen fermentation. In this study, we investigated the occurrence of homoacetogen in the rumens of pasture-fed roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed either oak-leaf-based (tannin-rich, 100 mg/kg dried matter), corn-stover-based, or corn-silage-based diets, by using formyltetrahydrofolate synthetase (FTHFS) gene sequences as a marker. The diversity and richness of FTHFS sequences was lowest in animals fed oak leaf, indicating that tannin-containing plants may affect rumen homoacetogen diversity. FTHFS amino acid sequences in the rumen of roe deer significantly differed from those of sika deer. The phylogenetic analyses showed that 44.8% of sequences in pasture-fed roe deer, and 72.1%, 81.1%, and 37.5% of sequences in sika deer fed oak-leaf-, corn-stover-, and corn-silage-based diets, respectively, may represent novel bacteria that have not yet been cultured. These results demonstrate that the rumens of roe deer and sika deer harbor potentially novel homoacetogens and that diet may influence homoacetogen community structure.

Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants

High throughput sequencing was used to examine the rumen microbiota of sika deer fed high (OLH) and low concentration (OLL) of tannin rich oak leaves. The results showed that Prevotella spp. were the most dominant bacteria. The most predominant methanogens were the members of the order Methanoplasmatales. The dominant rumen protozoa were Entodinium longinucleatum, Eudiplodinium maggii, and Epidinium caudatum, and the fungal communities were mostly represented by Piromyces spp. Moreover, the relative abundance of Pseudobutyrivibrio spp. (P=0.026), unidentified bacteria (P=0.028), and Prevotella spp. (P=0.022) was lower in the OLH group than in the OLL group. The concentration of propionate in the OLH group was greater than in the OLL group (P=0.006). Patterns of relationships showed that methanogens belonging to the order Methanoplasmatales were negatively correlated with Treponema spp., Ent. Longinucleatum, and acetate. Methanosphaera stadtmanae was positively correlated to propionate, while Methanobrevibacter ruminantium was negatively associated with Methanobrevibacter thaueri and Methanobrevibacter millerae. Tannins altered the rumen microbes and fermentation patterns. However, the response of the entire rumen microbiota and the relationship between rumen microorganisms and the fermentation parameters were not fully understood.