Influence of Sire Breed on the Interplay among Rumen Microbial Populations Inhabiting the Rumen Liquid of the Progeny in Beef Cattle

This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.     

基于16S rRNA高通量测序技术分析安格斯牛瘤胃微生物多样性和功能预测的研究

本研究旨在系统探索和分析安格斯牛瘤胃微生物多样性及其基因功能。选用体重550 kg左右的安格斯牛6头分成2组,利用基于16S rRNA高通量测序技术检测牛瘤胃液样本进行组学分析。结果表明,2组样本通过Illumina Miseq测序平台共获得86 298条高质量优质序列,聚类为346个操作分类单元(OUT),经分类学鉴定分属13个门,21个纲,24个目,40个科,123个属。拟杆菌门(Bacteroidetes)43.16%和厚壁菌门(Firmicutes)36.29%为优势菌群。基于属的组成,依次为普雷沃氏菌属_7 (Prevotella_7) 29.28%、琥珀酸弧菌科_UCG-001 (Succinivibrionaceae_UCG-001)11.30%、琥珀酸菌属(Succiniclasticum) 11.10%、普雷沃氏菌属_1 (Prevotella_1) 6.65%、瘤胃球菌属_1(Ruminococcus_1) 5.17%、琥珀酸弧菌属(Succinivibrio) 2.75%等。16S功能预测和COG、KEGG代谢通路数据库对比发现,功能集中在氨基酸运输和代谢、碳水化合物转运及代谢的相关基因上,可能含有丰富的蛋白分解、转运及代谢酶相关基因和大量的纤维素以及木质素降解酶基因。经碳水化合物活性酶(CAZymes)注释和KEGG代谢酶数据库比对显示,预测的功能基因糖苷水解酶和糖基转移酶所占比例较高;产乙酸和丁酸相关酶基因丰度较高。安格斯牛瘤胃内含有丰富的蛋白质分解、木质纤维素降解和挥发性脂肪酸生成菌群及酶系,为展示瘤胃微生物多样性,发现和筛选新的功能酶基因提供参考。     

Associations of rumen parameters with feed efficiency and sampling routine in beef cattle

Characterizing ruminal parameters in the context of sampling routine and feed efficiency is fundamental to understand the efficiency of feed utilization in the bovine. Therefore, we evaluated microbial and volatile fatty acid (VFA) profiles, rumen papillae epithelial and stratum corneum thickness and rumen pH (RpH) and temperature (RT) in feedlot cattle. In all, 48 cattle (32 steers plus 16 bulls), fed a high moisture corn and haylage-based ration, underwent a productive performance test to determine residual feed intake (RFI) using feed intake, growth, BW and composition traits. Rumen fluid was collected, then RpH and RT logger were inserted 5.5±1 days before slaughter. At slaughter, the logger was recovered and rumen fluid and rumen tissue were sampled. The relative daily time spent in specific RpH and RT ranges were determined. Polynomial regression analysis was used to characterize RpH and RT circadian patterns. Animals were divided into efficient and inefficient groups based on RFI to compare productive performance and ruminal parameters. Efficient animals consumed 1.8 kg/day less dry matter than inefficient cattle (P⩽0.05) while achieving the same productive performance (P⩾0.10). Ruminal bacteria population was higher (P⩽0.05) (7.6×10¹¹ v. 4.3×10¹¹ copy number of 16S rRNA gene/ml rumen fluid) and methanogen population was lower (P⩽0.05) (2.3×10⁹ v. 4.9×10⁹ copy number of 16S rRNA gene/ml rumen fluid) in efficient compared with inefficient cattle at slaughter with no differences (P⩾0.10) between samples collected on-farm. No differences (P⩾0.10) in rumen fluid VFA were also observed between feed efficiency groups either on-farm or at slaughter. However, increased (P⩽0.05) acetate, and decreased (P⩽0.05) propionate, butyrate, valerate and caproate concentrations were observed at slaughter compared with on-farm. Efficient had increased (P⩽0.05) rumen epithelium thickness (136 v. 126 µm) compared with inefficient cattle. Efficient animals also spent 318% and 93.2% more time (P⩽0.05) in acidotic (4.14% v. 1.30%) (pH⩽5.6) and optimal (5.6<pH<6.0) (8.53% v. 4.42%) RpH range compared with inefficient cattle. The circadian patterns revealed lower (P⩽0.05) RpH and no differences (P⩾0.10) in RT pre-, during, and post-prandial periods in efficient compared with inefficient cattle. In essence, superior feed efficiency in cattle seems linked to rumen features consistent with improved efficiency of feed utilization. Microbial abundance, rumen epithelial histomorphology, and RpH, may serve as indicators for feed efficiency in cattle. The divergences of assessments made on-farm and at slaughter should be considered in the development of proxies for feed efficiency.     

Influence of Diet Composition on Cattle Rumen Methanogenesis: A Comparative Metagenomic Analysis in Indian and Exotic Cattle

Comparative metagenomics approach has been used in this study to discriminate colonization of methanogenic population in different breeds of cattle. We compared two Indian cattle breeds (Gir and Kankrej) and two exotic cattle (Holstein and Jersey) breeds. Using a defined dietary plan for selected Indian varieties, the diet dependent shifts in microbial community and abundance of the enzymes associated with methanogenesis were studied. This data has been compared with the available rumen metagenome data from Holstein and Jersey dairy cattle. The abundance of genes for methanogenesis in Holstein and Jersey cattle came from Methanobacteriales order whereas, majority of the enzymes for methanogenesis in Gir and Kankrej cattle came from Methanomicrobiales order. The study suggested that by using slow/less digestible feed, the propionate levels could be controlled in rumen; and in turn, this would also help in further reducing the hydrogenotrophic production of methane. The study proposes that with the designed diet plan the overall methanogenic microbial pool or the individual methanogens could be targeted for development of methane mitigation strategies.     

Effects of red cabbage extract rich in anthocyanins on rumen fermentation,rumen bacterial community,nutrient digestion,and plasma indices in beef bulls

Dietary anthocyanins (ATH) have probiotic and antioxidant functions in humans. They may also have beneficial impacts on rumen microorganisms and subsequently nutrient digestion in cattle. The experiment aimed to study the effects of dietary red cabbage extract (RCE) rich in ATH on rumen fermentation, rumen bacterial community, and nutrient digestibility in beef bulls. Eight Simmental beef bulls and two RCE levels (0 and 120 g/d) were allocated in a replicated 2 × 2 crossover design. Each experimental period included 15 days for adaptation and subsequent 5 days for sampling. The results showed that dietary addition of RCE increased the ruminal concentration of total volatile fatty acids and the molar proportion of propionate, decreased the acetate to propionate ratio, and tended to decrease the molar proportion of acetate, but it did not affect the ruminal pH and the concentrations of ammonia N, microbial CP, monophenols, polyphenols, and total phenolics. ATH was undetectable in the ruminal fluid of beef bulls in both groups. RCE did not affect the alpha diversity of rumen bacterial community, and the relative abundances of major rumen bacteria at the phylum level, but it increased the relative abundances of Ruminobacter and Anaerovibrio and tended to increase the relative abundances of Oribacterium and Monoglobus at the genus level. RCE tended to increase the plasma concentrations of globulin and total protein, but it did not affect the plasma albumin, urea, triglyceride, glucose, and antioxidant activities. Dietary addition of RCE did not affect the apparent nutrient digestibility. In conclusion, the ATH in RCE was highly hydrolysable in rumen fluid. Dietary addition of RCE increased the ruminal concentration of total volatile fatty acids, decreased the acetate to propionate ratio, and slightly modified the rumen bacterial community, but it did not affect the nutrient digestibility and the plasma antioxidants in beef bulls.     

The use of genetic relationships among cattle breeds in the formulation of rational breeding policies: an example with South Devon (South Africa) and Gelbvieh (Germany)*

At the instigation of the South Devon Cattle Breeders' Society of South Africa we studied the genetic relationships of South Devon cattle (South Africa) and Gelbvieh cattle (Germany) with eight other breeds including Red Angus and Black Angus (USA). On the basis of comparisons at ten immungenetic loci Gelbvieh and South Devon cattle are nearly as genetically similar as Red and Black Angus. The results indicate that Gelbvieh and South Devon had a common ancestry on the Continent and are distinct from other British breeds such as Hereford, Angus and Jersey. This study illustrates the application of studies of the genetic similarities of different breeds to the rational development of future breeding and preservation programs.     

Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance,rumen fermentation,and rumen microflora in sheep

Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.     

Rumen Microbiome from Steers Differing in Feed Efficiency

The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.     

Correlation of Particular Bacterial PCR-Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits

The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.A fundamental understanding of microbial ecology and relationships to ruminant physiology is essential for successful manipulation of ruminal microflora and subsequent improvement in animal production since rumen microflora play important roles in the nutrient and energy uptake of the host (25). Hence, principles such as niche occupancy, selective pressure, adaptation, and interactions among populations (42) as well as the kinetics of substrate utilization (18) have to be taken into account when evaluating the ruminal microflora and host interactions. Bacterial density in the rumen is high, with direct counts as high as 10 billion cells per gram of ruminal contents (19, 33). Due to the limited understanding of the complex nature of the microbial component and activities in the rumen, the mechanisms of host-microbe and microbe-microbe interactions and whether such interactions impact host biology have not been well established.Many recent studies have employed molecularly based culture-independent techniques to investigate bacterial profiles (11, 22, 24, 39). PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis has been applied to assess ruminal microbial diversity based upon PCR-amplified 16S rRNA fragments to study community interactions (34), monitor populations shifts (23), and screen clone libraries (10). The PCR-DGGE banding patterns are considered to be representative of the dominant bacterial groups (26) and can be applied to screen changes of dominant species in the microflora for large numbers of environmental samples. A new terminology of “microbiome” has been applied to the study of the rumen microbial community, and such studies have further confirmed the complexity of this environment (7). However, many questions remain unanswered. For example, how does the microbiome change in large numbers of animals in response to host, diet, environment, health, and other factors? Which is more important to the host, the whole microbiome or the core microbiome? What is the function of a particular microbiome? Therefore, defining the ruminal microbiome to study its functions and interactions with the host has been an immense challenge. The selection of the rumen microbiome with particular functions after screening by culture-independent methods such as PCR-DGGE, therefore, is essential for high-throughput sequence analysis.Feed efficiency is one of the most critical factors that impact feed utilization by cattle. We hypothesized that particular bacterial populations in the rumen are associated with fermentation metabolites, which can also influence host feed efficiency. A recent study suggested that the bacterial structure may be associated with cattle''s residual feed intake (14); however, the small number of animals used in this study did not provide a direct linkage between a particular microbial population and host feed efficiency traits. The rumen microbial community changes in response to the feeding time (20). Since previous studies have shown that the concentration of volatile fatty acids (VFA) at prefeeding had less variation by diet (31) or by feeding cycles (43) and because of limited access to rumen fluid sampling from the examined commercial population in this study, we centered on the characterization of prefeeding dynamics in the ruminal bacteria and in the fermentation metabolites in 58 steers to test our hypothesis. Therefore, we focused on investigating the associations between rumen bacteria and host feed efficiency traits using PCR-DGGE analysis, aiming to identify the functional rumen microflora. The traits evaluated were daily dry matter intake (DMI), average daily gain (ADG), feed conversion ratio (FCR) (feed/gain), and residual feed intake (RFI) to measure the feed efficiency of cattle (1, 2, 28). Furthermore, we developed a multivariate statistical analysis to correlate bacterial PCR-DGGE profiles with fermentation measurements such as VFA and ammonia-nitrogen (NH₃-N) in the rumen and with feed efficiency traits, including, DMI, FCR, ADG, and RFI.     

Effects of guanidinoacetic acid supplementation on growth performance,nutrient digestion,rumen fermentation and blood metabolites in Angus bulls

Guanidinoacetic acid (GAA) can improve the growth performance of bulls. This study investigated the influences of GAA addition on growth, nutrient digestion, ruminal fermentation and serum metabolites in bulls. Forty-eight Angus bulls were randomly allocated to experimental treatments, that is, control, low-GAA (LGAA), medium-GAA (MGAA) and high-GAA (HGAA), with GAA supplementation at 0, 0.3, 0.6 and 0.9 g/kg DM, respectively. Bulls were fed a basal diet containing 500 g/kg DM concentrate and 500 g/kg DM roughage. The experimental period was 104 days, with 14 days for adaptation and 90 days for data collection. Bulls in the MGAA and HGAA groups had higher DM intake and average daily gain than bulls in the LGAA and control groups. The feed conversion ratio was lowest in MGAA and highest in the control. Bulls receiving 0.9 g/kg DM GAA addition had higher digestibility of DM, organic matter, NDF and ADF than bulls in other groups. The digestibility of CP was higher for HGAA than for LGAA and control. The ruminal pH was lower for MGAA, and the total volatile fatty acid concentration was greater for MGAA and HGAA than for the control. The acetate proportion and acetate-to-propionate ratio were lower for MGAA than for LGAA and control. The propionate proportion was higher for MGAA than for control. Bulls receiving GAA addition showed decreased ruminal ammonia N. Bulls in MGAA and HGAA had higher cellobiase, pectinase and protease activities and Butyrivibrio fibrisolvens, Prevotella ruminicola and Ruminobacter amylophilus populations than bulls in LGAA and control. However, the total protozoan population was lower for MGAA and HGAA than for LGAA and control. The total bacterial and Ruminococcus flavefaciens populations increased with GAA addition. The blood level of creatine was higher for HGAA, and the activity of l-arginine glycine amidine transferase was lower for MGAA and HGAA, than for control. The blood activity of guanidine acetate N-methyltransferase and the level of folate decreased in the GAA addition groups. The results indicated that dietary addition of 0.6 or 0.9 g/kg DM GAA improved growth performance, nutrient digestion and ruminal fermentation in bulls.     

A gastrointestinal nematode in pregnant and lactating mice alters maternal and neonatal microbiomes

The maternal microbiome is understood to be the principal source of the neonatal microbiome but the consequences of intestinal nematodes on pregnant and lactating mothers and implications for the neonatal microbiome are unknown. Using pregnant CD1 mice infected with Heligmosomoides bakeri, we investigated the microbiomes in maternal tissues (intestine, vagina, and milk) and in the neonatal stomach using MiSeq sequencing of bacterial 16S rRNA genes. Our first hypothesis was that maternal nematode infection altered the maternal intestinal, vaginal, and milk microbiomes and associated metabolic pathways. Maternal nematode infection was associated with increased beta-diversity and abundance of fermenting bacteria as well as Lactobacillus in the maternal caecum 2 days after parturition, together with down-regulated carbohydrate, amino acid and vitamin biosynthesis pathways. Maternal nematode infection did not alter the vaginal or milk microbiomes. Our second hypothesis was that maternal infection would shape colonization of the neonatal microbiome. Although the pup stomach microbiome was similar to that of the maternal vaginal microbiome, pups of infected dams had higher beta-diversity at day 2, and a dramatic expansion in the abundance of Lactobacillus between days 2 and 7 compared with pups nursing uninfected dams. Our third hypothesis that maternal nematode infection altered the composition of neonatal microbiomes was confirmed as we observed up-regulation of several putatively beneficial microbial pathways associated with synthesis of essential and branched-chain amino acids, vitamins, and short-chain fatty acids. We believe this is the first study to show that a nematode living in the maternal intestine is associated with altered composition and function of the neonatal microbiome.     

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana,USA

We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.     

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows

Microbes present in the rumen of dairy cows are essential for degradation of cellulosic and nonstructural carbohydrates of plant origin. The prepartum and postpartum diets of high-producing dairy cows are substantially different, but in what ways the rumen microbiome changes in response and how those changes may influence production traits are not well elucidated. Here, we sequenced the 16S and 18S rRNA genes using the MiSeq platform to characterize the prepartum and postpartum rumen fluid microbiomes in 115 high-producing dairy cows, including both primiparous and multiparous animals. Discriminant analysis identified differences between the microbiomes of prepartum and postpartum samples and between primiparous and multiparous cows. 18S rRNA sequencing revealed an overwhelming dominance of the protozoan class Litostomatea, with over 90% of the eukaryotic microbial population belonging to that group. Additionally, fungi were relatively more prevalent and Litostomatea relatively less prevalent in prepartum samples than in postpartum ones. The core rumen microbiome (common to all samples) consisted of 64 bacterial taxa, of which members of the genus Prevotella were the most prevalent. The Chao1 richness index was greater for prepartum multiparous cows than for postpartum multiparous cows. Multivariable models identified bacterial taxa associated with increased or reduced milk production, and general linear models revealed that a metagenomically based prediction of productivity is highly associated with production of actual milk and milk components. In conclusion, the structure of the rumen fluid microbiome shifts between the prepartum and first-week postpartum periods, and its profile within the context of this study could be used to accurately predict production traits.     

Altered Microbiomes in Bovine Digital Dermatitis Lesions,and the Gut as a Pathogen Reservoir

Bovine digital dermatitis (DD) is the most important infectious disease associated with lameness in cattle worldwide. Since the disease was first described in 1974, a series of Treponema species concurrent with other microbes have been identified in DD lesions, suggesting a polymicrobial etiology. However, the pathogenesis of DD and the source of the causative microbes remain unclear. Here we characterized the microbiomes of healthy skin and skin lesions in dairy cows affected with different stages of DD and investigated the gut microbiome as a potential reservoir for microbes associated with this disease. Discriminant analysis revealed that the microbiomes of healthy skin, active DD lesions (ulcerative and chronic ulcerative) and inactive DD lesions (healing and chronic proliferative) are completely distinct. Treponema denticola, Treponema maltophilum, Treponema medium, Treponema putidum, Treponema phagedenis and Treponema paraluiscuniculi were all found to be present in greater relative abundance in active DD lesions when compared with healthy skin and inactive DD lesions, and these same Treponema species were nearly ubiquitously present in rumen and fecal microbiomes. The relative abundance of Candidatus Amoebophilus asiaticus, a bacterium not previously reported in DD lesions, was increased in both active and inactive lesions when compared with healthy skin. In conclusion, our data support the concept that DD is a polymicrobial disease, with active DD lesions having a markedly distinct microbiome dominated by T. denticola, T. maltophilum, T. medium, T. putidum, T. phagedenis and T. paraluiscuniculi. Furthermore, these Treponema species are nearly ubiquitously found in rumen and fecal microbiomes, suggesting that the gut is an important reservoir of microbes involved in DD pathogenesis. Additionally, the bacterium Candidatus Amoebophilus asiaticus was highly abundant in active and inactive DD lesions.     

Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen

The effects of cashew nut shell liquid (CNSL) feeding on the methane (CH₄) emission and the ruminal microbiome of Lai Sind beef cattle were investigated. Changes in the methane production and rumen microbiome by CNSL feeding were monitored by a respiration chamber and 16S rRNA gene amplicon sequencing respectively. The results demonstrated that CNSL feeding mitigated 20.2%–23.4% of the CH₄ emission in vivo without apparent adverse effects on feed intake and feed digestibility. The rumen fluid analysis revealed a significant increase in the proportion of propionate in the total short-chain fatty acids. The relative abundance of methanogen (order Methanobacteriales) decreased significantly, indicating the direct inhibitory effect of CNSL on methanogens. The predicted function of the rumen microbiome indicated that carbohydrate and lipid metabolisms including propionate production were upregulated by CNSL feeding, whereas CH₄ metabolism was downregulated. A network analysis revealed that methanogen changed its partner bacteria after CNSL feeding. The δ¹³C of CH₄ ranged from −74.2‰ to −66.6‰ with significant fluctuation by CNSL feeding, in agreement with the shift of the rumen microbiome. Our findings demonstrate that CNSL feeding can mitigate the CH₄ emission from local cattle production systems in South-East Asia by modifying the rumen microbiome and its function.     

Dietary fat sources affect feed intake,digestibility, rumen microbial populations,energy partition and methane emissions in different beef cattle genotypes

The mitigation of enteric methane emission in beef cattle production is important for reducing feed energy loss and increasing environmental sustainability. The main objective of this study was to evaluate the effect of different oilseeds included in fermented total mixed rations (whole soyabean seed (SBS, control), whole kapok seed (KPS) and cracked oil palm fruit (OPF)) on feed intake, digestibility, rumen microbial populations, energy partition and methane emissions in different cattle genotypes (Charolais crossbred v. Japanese Black crossbred). Three Charolais crossbred and three Japanese Black crossbred bulls were studied in a replicated 3×3 Latin square experimental design; genotypes were analysed in separate squares including three periods of 21 days each and three dietary oilseed treatments fed ad libitum. The cattle were placed in a metabolic cage equipped with a ventilated head box respiration system for evaluating digestibility and energy balance. As compared with Charolais crossbred individuals, Japanese Black crossbred bulls showed consistently lower dry matter intake (15.5%, P<0.01), metabolisable energy (ME) intake (13.8%, P<0.05), ME requirement for maintenance (10.3%; 386 v. 430 kJ/kg metabolic BW, respectively), faeces energy loss (19.2%, P<0.001) and enteric methane emissions (18.5%, P<0.001). However, these two genotypes did not differ in energy retention (ER) (P=0.80). Among the three dietary oilseed treatments, OPF exhibited higher NDF intake (P<0.01) and digestibility (P<0.01), which was associated with a larger (P<0.05) total number of bacteria in the rumen. In addition, the OPF diet contributed to higher ME intake and ER than that of the KPS diet, whereas the SBS diet presented intermediate values (P<0.05). The methane conversion factor of these crossbreds was not significantly affected by genotype (P>0.05) or diet (P>0.05) under the experimental conditions and ranged from 5.8% to 6.0% of gross energy intake. This value is lower than that reported by the Intergovernmental Panel on Climate Change (6.5%) for cattle fed with low-quality crop residues or by-products. Thus, our results imply that the Japanese Black crossbred cattle consume less feed and emits less enteric methane than the Charolais crossbred does, mainly owing to its lower ME requirement for maintenance. The OPF diet could be used to replace SBS for high beef production, although further studies are required to evaluate their application across a wide range of beef production systems.     

Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza

The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor “species” levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor “species” level, the upper respiratory tract microbiomes were composed of 13-20 “species” and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.     

The effect of regular or reduced‐fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community

Aims

The effect of feeding dried distillers grains with solubles (DDGS) or reduced‐fat DDGS (RFDG) on ruminal methanogenesis and the rumen bacterial community of dairy cattle was evaluated.

Methods and Results

Treatments were CONT, a diet with no distillers grains; DG, inclusion of 20% DDGS; rfDG, inclusion of 20% RFDG; and MIX, inclusion of 10% DDGS and 10% RFDG. Methane emission was measured; rumen bacterial community was evaluated by sequencing the V4 region of the 16S rRNA gene. Total methane production remained unaffected. However, feeding distillers grains tended to reduce methanogenesis per unit of feed intake, decreased the abundance of the phylum Bacteroidetes and tended to increase Firmicutes. The abundance of Prevotellaceae positively correlated with feed intake; methane emission was positively correlated with the abundance of Prevotellaceae and was negatively correlated with the abundance of Succinivibrionaceae.

Conclusions

DDGS or RFDG may reduce methanogenesis per unit of feed intake; shifts in the abundance of predominant ruminal bacterial families may influence methane formation, likely because of their role on hydrogen liberation and utilization pathways.

Significance and Impact of the Study

Replacing corn and soybean meal with DDGS or RFDG in dairy rations may reduce the proportion of dietary energy wasted as methane, without detrimental effects on the overall bacterial population.     

肉牛剩余采食量相关瘤胃及粪便微生物特征比较分析

本试验旨在研究不同剩余采食量（residual feed intake, RFI）相关肉牛胃肠道微生物物种组成及相对丰度、微生物基因功能注释与富集特征。选取30头牛进行81 d饲喂试验,试验结束后选取极端RFI个体各5头屠宰并采集瘤胃液及肠道末端粪便样用于宏基因组测序。结果表明：共获得259 045.47 Mb有效数据,组装得到 4 318 393条Scaftigs,基因预测得到7 008 053个开放阅读框（ORFs）。进行物种注释后发现粪便样中Top10物种相对丰度在高剩余采食量（high residual feed intake, HRFI）、低剩余采食量（low residual feed intake, LRFI）组间无差异（P>0.05）,瘤胃液中的Top10微生物在LRFI组的相对丰度均低于HRFI组;粪便中、瘤胃液中优势菌门均为拟杆菌门和厚壁菌门;粪便中的优势属为拟杆菌属,瘤胃液中的优势属为普雷沃菌属。LefSe分析显示,在粪便中LRFI组的丹毒丝菌纲（Erysipelotrichia）显著富集（P<0.05）,瘤胃液中差异最显著的是甲烷杆菌纲（Methanobacteria）,且该菌在HRFI组的相对丰度显著高于LRFI组（P<0.05）。使用KEGG、eggNOG和CAZy数据库进行功能注释分析表明,在胃肠道中微生物的一些功能基因的丰度与RFI的分组有关。不同RFI肉牛瘤胃液、粪便中的微生物结构存在显著差异,丹毒丝菌纲、甲烷杆菌纲可能是区分肉牛饲料效率的潜在生物标志物之一。