Rumen Microbial Community Research Articles

Extending Burk Dehority's Perspectives on the Role of Ciliate Protozoa in the Rumen.

Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ciliated protozoa. We have summarized many of the advancements in knowledge from his work but also in his scientific way of thinking about interactions of ruminal ciliates with the entire rumen microbial community and animal host. As a dedication to his legacy, an electronic library of high-resolution images and video footage catalogs numerous species and techniques involved in taxonomy, isolation, culture, and ecological assessment of ruminal ciliate species and communities. Considerable promise remains to adapt these landmark approaches to harness eukaryotic cell signaling technology with genomics and transcriptomics to assess cellular mechanisms regulating growth and responsiveness to ruminal environmental conditions. These technologies can be adapted to study how protozoa interact (both antagonism and mutualism) within the entire ruminal microbiota. Thus, advancements and limitations in approaches used are highlighted such that future research questions can be posed to study rumen protozoal contribution to ruminant nutrition and productivity.

Characterization of variations within the rumen metaproteome of Holstein dairy cattle relative to morning feed offering

Few studies have utilized proteomic techniques to progress our knowledge of protein-mediated pathways within the rumen microbial community, and no previous research has used these techniques to investigate the patterns or variations of these proteins within this community. It was hypothesized that there would be fluctuations of rumen microbial protein abundances due to feed intake-mediated nutrient availability and that these could be identified using non gel-based proteomic techniques. This study investigated the fluctuations of bovine rumen metaproteome utilizing three mid to late-lactation Holsteins. Rumen fluid was collected at three timepoints on three days relative to their first morning feed offering (0 h, 4 h, and 6 h). Samples were pooled within timepoint within cow across day, analyzed using LC-MS/MS techniques, and analyzed for variations across hour of sampling using PROC MIXED of SAS with orthogonal contrasts to determine linear and quadratic effects. A total of 658 proteins were characterized across 19 microbial species, with 68 proteins identified from a variety of 15 species affected by time of collection. Translation-related proteins such as 50S and 30S ribosomal protein subunit variants and elongation factors were positively correlated with hour of sampling. Results suggest that as nutrients become more readily available, microbes shift from conversion-focused biosynthetic routes to more encompassing DNA-driven pathways.

Rumen bacterial community of young and adult of reindeer (Rangifer tarandus) from Yamalo-Nenets Autonomous District of Russia

Abstract The aim of the work was to compare the taxonomic composition of the rumen procariotic community in young and adult individuals of Nenets breed reindeer (Rangifer tarandus ) from the central part of the Yamal region by using the NGS method (next generation sequencing) and compare the microbiome composition of reindeer with the microbiome of their initial vegetation food material. The obtained data showed that the dominant position in microbial communities, like that of other ruminants, was occupied by representatives of phylum Firmicutes and Bacteroidetes, whose total share between observed groups did not differ significantly. The composition of the microbiome of the rumen of the investigated group of animals was completely different from the microbiome structure of the initial vegetation cover. Digestion of vegetation by reindeers resulted in complex transformation in the initial plant microbiome and an increase of biological diversity which was expressed in operational taxonomic unit (OTU) numbers increasing and changes in indexes of alpha-diversity parameters. According to the results of alpha- and beta- diversity of the rumen microbial communities, the greatest uniqueness was revealed for the microbiomes of the adults in comparison with calves and young. The presence of changes in the biodiversity indexes of the rumen microbiota in the reindeer, examined by us, confirm the opinion of the researchers that the microbial community may also reflect the physiological state of the animals. It has also been demonstrated that the presence of the phylum Verrucomicrobia, and the genera Stenotrophomonas, Pseudomonas, etc., may be specific to Nenets breed reindeer and have a pattern with their presence on various plants and lichens that are part of the reindeer diet. This is partially confirmed by data on plants microbiome taxonomy.

Metagenomic analysis exploring taxonomic diversity of rumen microbial communities in Vechur and crossbred cattle of Kerala state, India.

Rumen, one of the most productive diverse microbial habitats plays a vital role in the breakdown of feed to produce energy for maintenance and milk production in cattle. Culture-based procedures could identify only 10% of microbial species present in the rumen. Kerala, one of the southern states of India, owns only one native cattle breed, the Vechur cattle, which is noted for its short stature, disease resistance and adaptability to hot humid climate. Lower population density and decreased milk production potential of Vechur cattle led to the development of crossbred cattle of Kerala, with higher milk yield. A study was conducted to assess the rumen microbial profile of low productive Vechur cattle and high productive crossbred cattle for a better understanding of the relationship between the host and microbial community. DNA isolated from rumen liquor of five cattle each from both genetic groups maintained on standard ration (forage, concentrate ratio of 50:50) was subjected to whole metagenome sequencing. Bioinformatics and statistical analysis revealed that bacteria followed by archaea and eukaryota dominated in the Vechur cattle as well as the crossbred cattle rumen. Bacterial community was dominated by Bacteroidetes and Firmicutes phyla in both genetic groups with a higher Firmicutes to Bacteroidetes ratio of 0.45 in Vechur cattle. Among archaea, Euryarchaeota was more abundant, which constitute methanogens, contributing 98% of total archaeal reads. Prevalent protozoal genus found in the Vechur cattle rumen was Entodinium and in crossbred cattle rumen was Entamoeba. In Vechur and crossbred cattle rumen, 1086 and 1262 microbial species were observed exclusively and 4731 species were shared between habitats. There was a significant difference in total microbial species abundance between the two genetic groups and Vechur cattle displayed significantly higher microbial diversity compared to crossbred. As per literature, this is presumably the first report of rumen metagenome profile of Vechur cattle, a unique short breed of India.

Ruminal Microbiota and Fermentation in Response to Dietary Protein and Energy Levels in Weaned Lambs.

Simple SummaryRuminants, such as sheep, are economically important because they contribute to digesting and converting plant materials into edible meat and milk for humans to consume. An adequate plane of nutrients, such as energy and protein, is essential for rumen development and growth. However, sheep production is mostly affected by inadequate nutrition in rural areas of China. As one of the most prolific and perennial estrus breeds in China, Hu sheep has huge potential for catering to the growing meat demands of the market and consumers. In this study, the effects of dietary energy and protein levels on growth performance, microbial diversity, and physiological properties of the rumen in weaned lambs were evaluated. The results showed that a low dietary energy level restrained growth performance and changed the microbiota and associated ruminal fermentation phenotypes of lambs. However, protein had a minor effect. The findings are of great significance for promoting rumen development and establishing the optimal nutrient supply strategy for lambs.Supplying sufficient nutrients, such as dietary energy and protein, has a great effect on the growth and rumen development of ruminants. This study was conducted to evaluate the effects of dietary energy and protein levels on growth performance, microbial diversity, and structural and physiological properties of the rumen in weaned lambs. A total of 64 two-month-old Hu lambs were randomly allotted to 2 × 2 factorial arrangements with four replicates and with four lambs (half male and half female) in each replicate. The first factor was two levels of dietary metabolizable energy (ME) density (ME = 10.9 MJ/Kg or 8.6 MJ/Kg), and the second factor was two levels of dietary crude protein (CP) content (CP = 15.7% or 11.8%). The trial lasted for 60 days. A low dietary energy level restrained the growth performance of lambs (p < 0.05). The ruminal concentration of acetate and the ratio of acetate to propionate increased but the propionate concentration decreased significantly with the low energy diet. However, the rumen morphology was not affected by the diet energy and protein levels. Moreover, a low energy diet increased ruminal bacterial diversity but reduced the abundance of the phylum Proteobacteria (p < 0.05) and genus Succinivibrionaceae_uncultured (p < 0.05), which was associated with the change in ruminal fermentation phenotypes. By indicator species analysis, we found three indicator OTUs in the high energy group (Succinivibrionaceae_uncultured, Veillonellaceae_unclassified and Veillonellaceae_uncultured (p < 0.01)) and two indicator OTUs in the low energy group (Bacteroidales_norank and Lachnospiraceae_uncultured (p < 0.01)). In conclusion, these findings added new dimensions to our understanding of the diet effect on rumen microbial community and fermentation response, and are of great significance for establishing the optimal nutrient supply strategy for lambs.

Use of different carbohydrate sources associated with urea and implications for in vitro fermentation and rumen microbial populations

Context Alternative feed sources have been investigated as replacements for green forages and cereal grains traditionally used in ruminant feed. We hypothesised that, when replacing sources of true protein with non-protein nitrogen (NPN) in the ruminant diet, the efficiency of utilisation of the NPN may be affected by the source of energy and that different energy resources used as alternatives to maize may improve efficiency and maximise ruminal fermentation characteristics. Aims The objective of this study was to evaluate the effects of diets containing different carbohydrate sources associated with urea on in vitro ruminal fermentation and rumen microbial profile. Methods Four diets based on Tifton 85 Bermuda grass hay (584 g/kg dry matter) were tested as substrates: cornmeal + soybean meal (C + SM, typical diet), cornmeal + urea (C + U), cassava scraping + urea (CS + U), and spineless cactus + urea (SC + U). The experimental design consisted of randomised blocks with four treatments and five blocks. Five adult Nellore cattle with permanent fistula in the rumen were used as inoculum donors. The semi-automatic in vitro gas production technique was used in two experiments. Quantitative real-time PCR was used to monitor the changes in the rumen microbial community. Key results The diets containing C + U and CS + U decreased (P &amp;lt; 0.05) concentrations of isobutyrate, isovalerate, and valerate after 24 h of incubation, and all diets containing urea decreased (P &amp;lt; 0.05) concentrations of isobutyrate, isovalerate and valerate after 96 h and increased (P &amp;lt; 0.05) acetate:propionate ratio. After 96 h of incubation, the diets containing CS + U and SC + U resulted in a lower (P &amp;lt; 0.05) population of Ruminococcus flavefaciens than the C + U diet, and a lower (P &amp;lt; 0.05) population of Streptococcus bovis than the C + SM diet. Conclusions From our results, a diet containing cassava scraping produces more methane per unit of degraded organic matter, which reduces fermentation efficiency. Diets that contain corn with either soybean meal or urea result in greater degradability with lower gas production rates than diets that contain either cassava scrapings or spineless cactus with urea. Diets containing urea as a total substitution for soybean meal alter the production of short-chain fatty acids and reduce the populations of S. bovis and R. flavefaciens. Implications Use of urea to replace soybean meal in the ruminant diet alters ruminal fermentation and rumen microbial population.

Effect of pineapple stem starch feeding on rumen microbial fermentation, blood lipid profile, and growth performance of fattening cattle.

Pineapple stem starch (PS) was evaluated for its suitability as a new starch source in concentrate for fattening cattle, based on the growth performance, blood profile, and rumen parameters of 36 steers in a 206-day feeding study. PS was formulated as a 40% concentrate and fed with forage in comparison with ground corn (GC) and ground cassava (CA) formulated at the same level. PS feeding improved weight gain and feed conversion ratio without affecting feed intake. PS did not obviously influence blood lipid profiles throughout the experiment. Ruminal concentration of total short-chain fatty acids (SCFA) increased with PS without affecting SCFA composition throughout the feeding study. Rumen amylolytic group, especially Ruminococcus bromii, was dominant in the rumen microbial community, and showed increased abundance by PS feeding throughout the experiment. These results clearly indicate the potential of PS as a useful starch source for fattening cattle in terms of rumen fermentation and growth performance.

69 The ability of an artificial sweetener (Sucram®) to influence microbial community structure in the rumen papillae and content through the production of microbial-based neurochemicals

Abstract The study of microorganisms to produce and utilize neurochemical signaling molecules that interact with the host is the emerging field known as microbial endocrinology. Production of these molecules can be regulated by several different environmental factors, including diet. The effect of artificial sweeteners on ruminant gastrointestinal tract microbiota and the ability of individual members to produce neurochemicals that may determine community composition and affect host physiology are unknown. To analyze whether an artificial sweetener (Sucram®, Pancosma, Switzerland) affects rumen content (RC) and rumen papillae (RP) microbiota, six fistulated, lactating Holstein cows were sampled before (baseline) and after exposure to Sucram®. 16S rRNA gene sequencing was conducted to identify Sucram®-induced microbial community changes. Additionally, ex vivo microbial cultures were used to identify neurochemical production in RP bacteria. Exposure to Sucram significantly increased the abundance of Operational Taxonomic Units (OTUs) belonging to Ruminobacter, Prevotella, Sharpea, Ruminococcus and Rikenella on the RP. These organisms have been reported to aid in digestion of feedstuffs and methane reduction, suggesting that Sucram® may induce beneficial shifts in rumen microbial communities. To gain preliminary insight into neurochemical production of RP microorganisms, we tested four different Lactobacillus isolates from RP for neurochemical production. We observed that the neurochemicals DOPAC (3,4-Dihydroxyphenylacetic acid) and L-DOPA (L-3,4-dihydroxyphenylalanine) were produced by three and four isolates, respectively. Ongoing experiments are evaluating the effects of Sucram® on neurochemical production in a larger number of rumen microbes. Overall, we observed significant differences in OTU abundance in response to the addition of Sucram®. Additionally, we confirmed that RP bacteria can produce neurochemicals. Both of these results are key to understanding how Sucram® modifies microbial communities within the rumen and possibly influences host physiology. Research into microbial endocrinology-based neurochemical signaling between rumen microbiota and their animal hosts may lead to advancement of livestock feed efficiency and welfare.

Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis

The common management practices of dairy calves leads to increased starch concentration in feed, which subsequently may cause rumen acidosis while on milk and during weaning. Until recently, few attempts were undertaken to understand the health risks of prolonged ruminal acidosis in post weaning calves. Resultantly, the molecular changes in the digestive tracts in post-weaning calves with ruminal acidosis remain largely unexplored. In this study, we investigated the liver transcriptome changes along with its correlation with the rumen microbial rRNA expression changes in young calves using our model of feed induced ruminal acidosis. In this model, new born calves were fed a highly processed, starch-rich diet starting from one week of age through 16 weeks. A total of eight calves were involved in this study. Four of them were fed the acidosis-inducing diet (Treated) and the rest of the four were fed a standard starter diet (Control). Liver and rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses were carried out in the liver tissues and rRNA meta-transcriptome analysis were done using the rumen epithelial tissues. The correlation analysis was performed by comparing the liver mRNA expression with the rumen epithelial rRNA abundance at genus level. Calves with induced ruminal acidosis had significantly lower ruminal pH in comparison to the control group, in addition to significantly less weight-gain over the course of the experiment. In liver tissues, a total of 428 differentially expressed genes (DEGs) (fold-change, FC ≥ 1.5; adjusted P ≤ 0.1) were identified in treated group in comparison to control. Biological pathways enriched by these DEGs included cellular component organization, indicating the impact of ruminal acidosis on liver development in young calves. Specifically, the up-regulated genes were enriched in acute phase response (P < 0.01), pyruvate metabolic process (P < 0.01) and proton-acceptors (P ≪ 0.001), indicating the liver’s response to feed induced acidosis at the transcriptome level. Twelve transferase activity related genes had significant correlation with rumen microbial rRNA expression changes. Among these genes, two up-regulated genes were reported with involvement in lipid metabolism in the liver, implying the direct effect of feed-induced acidosis on both the rumen microbial community and liver metabolism. Our study provides insight into the physiological remodeling in the liver resultant from the prolonged acidosis in post weaning calves, which may facilitate future RNA-seq based diagnosis and precision management of rumen acidosis in dairy calves.

Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep

The productivity of ruminants depends largely on rumen microbiota. However, there are few studies on the age-related succession of rumen microbial communities in grazing lambs. Here, we conducted 16 s rRNA gene sequencing for bacterial identification on rumen fluid samples from 27 Tibetan lambs at nine developmental stages (days (D) 0, 2, 7, 14, 28, 42, 56, 70, and 360, n = 3). We observed that Bacteroidetes and Proteobacteria populations were significantly changed during the growing lambs’ first year of life. Bacteroidetes abundance increased from 18.9% on D0 to 53.9% on D360. On the other hand, Proteobacteria abundance decreased significantly from 40.8% on D0 to 5.9% on D360. Prevotella_1 established an absolute advantage in the rumen after 7 days of age. The co-occurrence network showed that the different microbial of the rumen presented a complex synergistic and cumbersome relationship. A phylogenetic tree was constructed, indicating that during the colonization process, may occur a phenomenon in which bacteria with close kinship are preferentially colonized. Overall, this study provides new insights into the colonization of bacterial communities in lambs that will benefit the development of management strategies to promote colonization of target communities to improve functional development.

Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements

BackgroundDietary intake is known to be a driver of microbial community dynamics in ruminants. Beef cattle go through a finishing phase that typically includes very high concentrate ratios in their feed, with consequent effects on rumen metabolism including methane production. This longitudinal study was designed to measure dynamics of the rumen microbial community in response to the introduction of high concentrate diets fed to beef cattle during the finishing period.A cohort of 50 beef steers were fed either of two basal diet formulations consisting of approximately 10:90 or 50:50 forage:concentrate ratios respectively. Nitrate and oil rich supplements were also added either individually or in combination. Digesta samples were taken at time points over ~ 200 days during the finishing period of the cattle to measure the adaptation to the basal diet and long-term stability of the rumen microbiota.Results16S rRNA gene amplicon libraries were prepared from 313 rumen digesta samples and analysed at a depth of 20,000 sequences per library. Bray Curtis dissimilarity with analysis of molecular variance (AMOVA) revealed highly significant (p < 0.001) differences in microbiota composition between cattle fed different basal diets, largely driven by reduction of fibre degrading microbial groups and increased relative abundance of an unclassified Gammaproteobacteria OTU in the high concentrate fed animals. Conversely, the forage-based diet was significantly associated with methanogenic archaea. Within basal diet groups, addition of the nitrate and combined supplements had lesser, although still significant, impacts on microbiota dissimilarity compared to pre-treatment time points and controls. Measurements of the response and stability of the microbial community over the time course of the experiment showed continuing adaptation up to 25 days in the high concentrate groups. After this time point, however, no significant variability was detected.ConclusionsHigh concentrate diets that are typically fed to finishing beef cattle can have a significant effect on the microbial community in the rumen. Inferred metabolic activity of the different microbial communities associated with each of the respective basal diets explained differences in methane and short chain fatty acid production between cattle. Longitudinal sampling revealed that once adapted to a change in diet, the rumen microbial community remains in a relatively stable alternate state.

Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities.

MotivationWe present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of ‘Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux’, a family of methods designed to integrate information from heterogeneous data. Here, we extend the classical approach to deal with broader datasets (e.g. compositional data), methods for variable selection and taxon-set enrichment analysis.ResultsThe methodology is demonstrated by integrating rumen microbial communities from cows for which methane yield () was individually measured. Our approach reproduces the significant link between rumen microbiota structure and CH4 emission. When analyzing the TARA’s ocean data, Link-HD replicates published results, highlighting the relevance of temperature with members of phyla Proteobacteria on the structure and functionality of this ecosystem.Availability and implementationThe source code, examples and a complete manual are freely available in GitHub https://github.com/lauzingaretti/LinkHD and in Bioconductor https://bioconductor.org/packages/release/bioc/html/LinkHD.html.

Effects of Nutritional Deprivation and Re-Alimentation on the Feed Efficiency, Blood Biochemistry, and Rumen Microflora in Yaks (Bos grunniens).

Simple SummaryYak, the predominant and semi-domesticated livestock on the Qinghai–Tibet Plateau, suffers severe starvation and body weight reduction in the cold season and recovers relatively rapid growth in the warm season every year, because of the harsh highland environment. Rumen microorganisms have critical nutritional and physiological functions for the growth of ruminant, but the strategy of rumen microorganism of yaks to cope with the starvation and re-alimentation challenges and the contributions of rumen microflora to compensatory growth remain unclear. Herein, we investigated the effects of starvation and refeeding on the growth, feed efficiency, blood biochemistry and rumen microbial community as well as functions of yaks. Our results indicated that the rumen microorganism, in part, contributed to yak adaption to starvation and compensatory growth during re-alimentation. Our study is helpful in the understanding and utilization of this natural character of yaks to explore and improve their growth potential.Yak suffers severe starvation and body weight reduction in the cold season and recovers relatively rapid growth in the warm season every year. Herein, we investigated the effects of starvation and refeeding on the growth, feed efficiency, blood biochemistry and rumen microbial community as well as functions of yaks. The results showed that starvation significantly reduced the body weight of yaks. Serum glucose and triglyceride concentrations significantly decreased, and β-hydroxybutyric acid and non-esterified fatty acid levels were significantly increased during the starvation period. Starvation also dramatically inhibited rumen microbial fermentations. Whereas, refeeding with the same diet significantly increased the feed efficiency, nutrient digestibility together with rumen acetate, propionate and microbial protein productions compared with those before starvation. The 16S rDNA sequencing results showed that starvation mainly decreased the ruminal protein-degrading bacteria Prevotella and propionate-producing bacteria Succiniclasticum populations and dramatically increased the denitrifying bacteria Thauera populations. Refeeding reduced the Euryarchaeota population and increased propionate-producing bacteria Succinivibrionaceae UCG-002 and starch-degrading bacteria Ruminobacter populations when compared with those before starvation. The predicted microbial metabolic pathways, related to amino acid and starch metabolisms, were also significantly altered during the starvation and refeeding. The results indicated that the rumen microorganisms and their metabolism pathways changed with feed supply, and these alterations in part contributed to yak adaption to starvation and re-alimentation. This study is helpful for enhancing the understanding and utilization of this natural character of yaks to explore and improve their growth potential.

Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications.

SummaryIncreasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.

Provision of beta-glucan prebiotics (cellooligosaccharides and kraft pulp) to calves from pre- to post-weaning period on pasture.

We conducted two feeding experiments to evaluate the effects of supplementation with either cellooligosaccharide or kraft pulp on growth performance in grazing beef calves (Japanese Black) from 4weeks pre-weaning to 12 to 16weeks post-weaning. In Experiment 1 (20-week duration), nine calves (2.9-month-old females) were assigned to either a control group (CON) or an experimental group (CEL) fed cellooligosaccharide at a rate of 10g/day mixed with concentrate. Average daily weight gain tended to be greater in CEL than in CON, especially after 1month of weaning. In Experiment 2 (16-week duration), 10 calves (2.0-month-old females) were assigned to either a control group or an experimental group (KRA) fed kraft pulp at a rate of 10% replacement of total digestible nutrients with concentrate. The proportion of fibrolytic bacteria increased and that of methanogenic Archaea decreased in the rumen microbial community composition of KRA calves in Experiment 2, whereas the decrease in Fibrobacter and Archaea was observed in CEL calves at first 4weeks in Experiment 1. We conclude that beta-glucan prebiotic supplementation to grazing calves at pre-weaning would affect rumen microbial composition and modified rumen fermentation characteristics, leading to a better rumen environment via different means.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation

Supplementation of appropriate probiotics can improve the health and productivity of ruminants while mitigating environmental methane production. Hence, this study was conducted to determine the effects of Enterococcus faecium SROD on in vitro rumen fermentation, methane concentration, and microbial population structure. Ruminal samples were collected from ruminally cannulated Holstein–Friesian cattle, and 40:60 rice straw to concentrate ratio was used as substrate. Fresh culture of E. faecium SROD at different inclusion rates (0, 0.1%, 0.5%, and 1.0%) were investigated using in vitro rumen fermentation system. Addition of E. faecium SROD had a significant effect on total gas production with the greatest effect observed with 0.1% supplementation; however, there was no significant influence on pH. Supplementation of 0.1% E. faecium SROD resulted in the highest propionate (P = 0.005) but the lowest methane concentration (P = 0.001). In addition, acetate, butyrate, and total VFA concentrations in treatments were comparatively higher than control. Bioinformatics analysis revealed the predominance of the bacterial phyla Bacteroidetes and Firmicutes and the archaeal phylum Euryarchaeota. At the genus level, Prevotella (15–17%) and Methanobrevibacter (96%) dominated the bacterial and archaeal communities of the in vitro rumen fermenta, respectively. Supplementation of 0.1% E. faecium SROD resulted in the highest quantities of total bacteria and Ruminococcus flavefaciens, whereas 1.0% E. faecium SROD resulted in the highest contents of total fungi and Fibrobacter succinogenes. Overall, supplementation of 0.1% E. faecium SROD significantly increased the propionate and total volatile fatty acids concentrations but decreased the methane concentration while changing the microbial community abundance and composition.

Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake.

Identifying factors that influence the composition of the microbial population in the digestive system of dairy cattle will be key in regulating these populations to reduce greenhouse gas emissions. In this study, we analyzed rumen and fecal samples from five high residual feed intake (RFI) Holstein cows, five low RFI Holstein cows, five high RFI Jersey cows and five low RFI Jersey cows, fed either a high-concentrate diet (expected to reduce methane emission) or a high-forage diet. Bacterial communities from both the rumen and feces were profiled using Illumina sequencing on the 16S rRNA gene. Rumen archaeal communities were profiled using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) targeting the mcrA gene. The rumen methanogen community was influenced by breed but not by diet or RFI. The rumen bacterial community was influenced by breed and diet but not by RFI. The fecal bacterial community was influenced by individual animal variation and, to a lesser extent, by breed and diet but not by RFI. Only the bacterial community correlated with methane production. Community differences seen in the rumen were reduced or absent in feces, except in the case of animal-to-animal variation, where differences were more pronounced. The two cattle breeds had different levels of response to the dietary intervention; therefore, it may be appropriate to individually tailor methane reduction strategies to each cattle breed.

Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach.

Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.

Effect of cashew nut shell liquid feeding on fermentation and microbiota in the rumen of Thai native cattle and swamp buffaloes

Effects of cashew nut shell liquid (CNSL) feeding on rumen fermentation and microbial profiles were investigated using Thai native cattle (n = 4) and swamp buffaloes (n = 4). Rumen fistulated animals were assigned to an experiment in one factor design: they were fed a concentrate (1 kg) and rice straw (90% of ad libitum intake) diet supplemented with control pellets followed by CNSL-containing pellets for 4 wk each (control and CNSL periods, respectively). Rumen content was sampled at the end of the control period (d 27 and 28) and at 2 wk (d 13 and 14) and 4 wk (d 27 and 28) of the CNSL period to monitor rumen characteristics. Feed intake, ruminal DM disappearance, ruminal pH and ammonia concentration were not obviously affected by CNSL feeding. Methane production potential, monitored by a batch culture system supplemented with the same diet formula, was decreased by 53% and 73%, after 4-wk CNSL feeding to Thai native cattle and swamp buffaloes, respectively. Although volatile fatty acid level in the rumen was not changed by CNSL feeding, propionate proportion was greatly elevated by 23% and 31% in native cattle and buffaloes, respectively, after 4-wk CNSL feeding. Enhanced propionate was observed even in the 2-wk samples. Results of quantitative PCR analysis showed that although numbers of methanogenic archaea in the rumen did not change, protozoa were decreased and some bacterial groups including genus Prevotella were increased by CNSL feeding in both native cattle and buffaloes. This is in agreement with the results of Miseq analysis of 16S rRNA genes of rumen microbes, which showed increases of Prevotella with CNSL feeding. Increase of Succiniclasticum and decrease of unclassified Bacteroidales by CNSL were also observed for both native cattle and buffaloes. Changes in archaeal community were also similar between these two genera of ruminants. These ruminal responses indicate that CNSL feeding is useful for modulating rumen fermentation in Thai local ruminants, major contributors to methane emission in this area. This is the first report describing the effect of CNSL feeding on rumen fermentation in relation to detailed analysis of rumen microbial community.