Rumen Microbial Diversity Research Articles

Comparison of microbial diversity in rumen and small intestine of Xinong Saanen dairy goats using 16S rRNA gene high-throughput sequencing

Context Gastrointestinal microorganisms play an important role in ruminant digestion and metabolism, immune regulation and disease prevention and control. Different parts of the digestive tract have different functions and microbial community structures. Aims This study aims to explore the microbial diversity in the rumen and the small intestine of Xinong Saanen dairy goats. Methods Rumen fluid and jejunum fluid from three Xinong Saanen dairy bucks with the average slaughter weight of 33.93 ± 0.68 kg were collected and analysed for microbial diversity, by using 16S rRNA gene high-throughput sequencing. Key results In total, 1118 operational taxonomic units (OTUs) were identified, with 1020 OTUs and 649 OTUs being clustered to rumen and jejunum samples respectively. Alpha-diversity indices were significantly (P < 0.05) different between rumen and jejunum, as indicated by the fact that the rumen microbial community diversity, richness and uniformity/evenness were higher than those of jejunum. At the phylum level, the dominant phyla in the rumen were Bacteroidetes (66.7%) and Firmicutes (25.1%), accounting for 91.8% of the rumen microorganisms. The dominant phylum in the jejunum was Firmicutes, accounting for 73.0% of the jejunum microorganisms. At the genus level, the dominant bacteria in the rumen were Prevotella_1, norank_f_Bacteroidales_BS11_gut_group, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group and Family_XIII_AD3011_group, whereas the dominant bacteria in the jejunum were Omboutsia, Aeriscardovia, Intestinibacter, unclassified_f_Peptostreptococcaceae and unclassified_f_Bifidobacteriaceae. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the major functions of microorganisms in the rumen and jejunum were carbohydrate metabolism, amino acid metabolism, nucleotide metabolism, membrane transport and translation. Interestingly, fructose and mannose metabolism and peptidoglycan biosynthesis were abundant in the rumen, while homologous recombination and nucleotide excision repair were abundant in the jejunum. Conclusions Our study clarified the differences in microbial diversity and community structure between the rumen and the jejunum in Xinong Saanen dairy goats. Prevotella was the most predominant genus in the rumen, compared with Romboutsia, Bifidobacterium as well as Peptostreptococcaceae genera, which were the predominant genera in the jejunum. Implications In combination with the functional prediction of microorganisms and the metabolic characteristics of different parts of the digestive tract in ruminants, our findings provided information for further exploring the relationship among genes, species and functions of microorganisms and their hosts’ nutritional and physiological functions.

Effect of DNA isolation method and host species on the metagenomic DNA recovery and microbial community coverage

The introduction of next generation sequencing to characterize rumen microbial diversity has expanded the scope of animal nutrition to understand ruminal fermentation in greater details. Although diis technique is highly accurate, it suffers from biases introduced at different stages of sample processing, sequencing and bioinformatics analysis. It is well established that the outcome of metagenomics (using DNA) is affected by the source and method of DNA isolation. The present study aimed to evaluate two popular rumen metagenomic DNA isolation methods, Repeated Bead Beating plus Column (RBBC) and ZR Fecal DNA Microprep Kit, for their effect on the DNA quality and quantity, and microbial community assessment in four ruminant species, namely cattle, buffalo, goat and sheep. Metagenomic DNA was isolated from total rumen contents using these methods, and the quality and quantity of the purified DNA were determined. The coverage of microbial diversity was assessed by the Terminal Restriction Fragment Length Polymorphism (TRFLP) technique using two restriction enzymes (Mspl and BsuRI). The number and peak area of terminal restriction fragments (TRFs) were used to compare the efficiency of the DNA isolation methods across the species. The study established that although the metagenomic DNA recovery was greater using the RBBC method, the quality of the purified DNA was superior with die ZR Fecal DNA kit. Significantly greater microbial diversity (P<0.05) was also noticed in cattle, goat and sheep rumen metagenomic DNA isolated using the ZR Fecal DNA kit. Further, the overall comparison between the methods, irrespective of the species, also revealed significantly (P< 0.001) greater microbial diversity coverage in the ZR Fecal DNA isolation kit than the RBBC method. In conclusion, the current study revealed that die ZR Fecal DNA Kit was comparatively better than the RBBC method for assessing microbial diversity in me rumen metagenomic samples of cattle, buffalo, goat and sheep.

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

BackgroundRumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.ResultsThe results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.ConclusionsCollectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

Manipulation of Rumen Fermentation and Microbial Diversity for Live-Weight Gains of Sheep as Influenced by Ginger Powder and Lime Peel

The study was conducted to determine the influence of ginger powder and lime peel on manipulation of rumen function for live-weight gains of sheep. Twenty four West African dwarf sheep of about 8 – 9 months old with average weight of 7.00 ± 0.95kg were randomly assigned to four treatment diets in a completely randomized design. The prepared diets contained; ED1 (0% ginger powder and 0% lime peel powder that served as control group), ED2 (0% ginger powder and 3% lime peel), ED3 (1.5% ginger powder and 1.5% lime peel) and ED4 (3% ginger powder and 0% lime peel). In all the diets examined, ED1 showed higher significant (p&lt;0.05) values in total fungi, Acetobact xylinum, Methanogens, total protozoa, Entodiniomorphs, Holotrichs, ammonia-nitrogen, total volatile fatty acids, acetate, butyrate and feed conversion ratio. However, total bacteria, Ruminococcus albus, Ruminococcus fibrisolvens, Bacillus spp, propionate, feed intake, nutrient digestibility, final and daily weight gains indicated significant (p&lt;0.05) higher values in diet ED3 than diets ED1, ED2 and ED4. Rumen pH was significantly (p&lt;0.05) higher in ED4 as compared with other diets. There was no significant (p&gt;0.05) difference in Fibrobacter succinogens, iso-butyrate, valerate, iso-valerate and initial weight among diets. It can be concluded that using 1.5% ginger powder and 1.5% lime peel in the diets enhanced rumen fermentation and ecology for growth performance of sheep.

Host and altitude factors affect rumen bacteria in cattle

There are many kinds of microorganisms in the gastrointestinal tract of mammals, some of which are closely related to the host. Rumen microorganisms are essential for normal physiological activities of their host by decomposing plant crude lignin and providing essential nutrients. The composition and diversity of this microbial population are influenced by the host, environment, and diet. Despite its importance, little is known about the effects of factors such as altitude variation on rumen microbial population abundance and diversity in different ruminants. Here, we described the changes in overall rumen bacteria in four groups of cattle, including the Zhongdian yellow cattle and Zhongdian yaks, grazing at high altitudes (3600m); the Jiangcheng yellow cattle and Jiangcheng buffalo were kept at an altitude of 1100m. We found that there was a significant difference in rumen bacterial abundance of the Zhongdian yellow cattle and Zhongdian yaks at high altitude and there was obvious homogeneity in rumen bacterial abundance and diversity in the Jiangcheng yellow cattle and Jiangcheng buffalo at low altitude. Therefore, our research concluded that under the same dietary environment, there were differences in the abundance and diversity of certain bacteria in the rumen of different breeds of cattle, indicating that host genetic factors and intestinal microorganisms related to altitudinal variation had a greater influence on rumen bacterial abundance in the cattle.

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.

Insights into Metatranscriptome, and CAZymes of Buffalo Rumen Supplemented with Blend of Essential Oils.

The aim of this study was to investigate the rumen microbial diversity and functionality in buffaloes fed with a blend of essential oils (BEO) using LSD switch over design. The BEO consisting of blend of Trachyspermum copticum (Ajwain) oil, Cymbopogon citratus (lemon grass) oil and Syzygium aromaticum (clove bud) oleoresin mixed in equal proportion, was fed at the rate of 0, 0.75 and 1.5ml/100kg of body weight in 0 (control), 0.75 and 1.5 groups, respectively. The metatranscriptomic libraries of the rumen microbiome were represented by 7 domains, 84 phyla, 64 archeal genera and 663 bacterial genera with Bacteroidetes and Firmicutes constituting 80% of phyla abundance irrespective of feeding regime. Methanogenic archaea was represented by 22 phyla with Methanobrevibacter as the major genus. BEO feeding reduced the abundance of Methanococcus and Thermoplasma (P < 0.05) at all levels. The results revealed that the feeding of BEO shifted the archeal and bacterial population at very low magnitude. The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.

Effects of Dietary Energy Levels on Rumen Fermentation, Microbial Diversity, and Feed Efficiency of Yaks (Bos grunniens)

The microbial community of the yak (Bos grunniens) rumen plays an important role in surviving the harsh Tibetan environment where seasonal dynamic changes in pasture cause nutrient supply imbalances, resulting in weight loss in yaks during the cold season. A better understanding of rumen microbiota under different feeding regimes is critical for exploiting the microbiota to enhance feed efficiency and growth performance. This study explored the impact of different dietary energy levels on feed efficiency, rumen fermentation, bacterial community, and abundance of volatile fatty acid (VFA) transporter transcripts in the rumen epithelium of yaks. Fifteen healthy castrated male yaks were divided into three groups and fed with low (YL), medium (YM), and high energy (YH) levels diet having different NEg of 5.5, 6.2, and 6.9 MJ/kg, respectively. The increase in feed efficiency was recorded with an increase in dietary energy levels. The increase in dietary energy levels decreased the pH and increased the concentrations of acetate, propionate, butyrate, and valerate in yak rumens. The increase in the mRNA abundance of VFA transporter genes (MCT1, DRA, PAT1, and AE2) in the rumen epithelium of yaks was recorded as dietary energy level increased. High relative abundances of Firmicutes and Bacteroidetes were recorded with the increase in dietary energy levels. Significant population shifts at the genus level were recorded among the three treatments. This study provides new insights into the dietary energy-derived variations in rumen microbial community.

Dietary lysophospholipids supplementation inhibited the activity of lipolytic bacteria in forage with high oil diet: an in vitro study.

ObjectiveThe objective of this study was to evaluate the effects of lysophospholipids (LPL) supplementation on rumen fermentation, degradability, and microbial diversity in forage with high oil diet in an in vitro system.MethodsFour experimental treatments were used: i) annual ryegrass (CON), ii) 93% annual ryegrass +7% corn oil on a dry matter (DM) basis (OiL), iii) OiL with a low level (0.08% of dietary DM) of LPL (LLPL), and iv) OiL with a high level (0.16% of dietary DM) of LPL (HLPL). An in vitro fermentation experiment was performed using strained rumen fluid for 48 h incubations. In vitro DM degradability (IVDMD), in vitro neutral detergent fiber degradability, pH, ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and microbial diversity were estimated.ResultsThere was no significant change in IVDMD, pH, NH3-N, and total VFA production among treatments. The LPL supplementation significantly increased the proportion of butyrate and valerate (Linear effect [Lin], p = 0.004 and <0.001, respectively). The LPL supplementation tended to increase the total bacteria in a linear manner (p = 0.089). There were significant decreases in the relative proportions of cellulolytic (Fibrobacter succinogenes and Ruminococcus albus) and lipolytic (Anaerovibrio lipolytica and Butyrivibrio proteoclasticus) bacteria with increasing levels of LPL supplementation (Lin, p = 0.028, 0.006, 0.003, and 0.003, respectively).ConclusionThe LPL supplementation had antimicrobial effects on several cellulolytic and lipolytic bacteria, with no significant difference in nutrient degradability (DM and neutral detergent fiber) and general bacterial counts, suggesting that LPL supplementation might increase the enzymatic activity of rumen bacteria. Therefore, LPL supplementation may be more effective as an antimicrobial agent rather than as an emulsifier in the rumen.

Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau.

The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle

Simple SummaryAnti-stress is an emergent research point to current cattle industry. Land transport stress, a negative off-site fattening mode, causing a serious problems to beef cattle production, such as nutrition-metabolism, hormone secretion levels, and immune competence are imbalanced. In this paper we compared among Simmental Crossbred Cattle (SC), Native Yellow Cattle (NY), and Cattle Yak (CY) about ruminal microbe diversity and immune functions before and after transportation. The results showing that transport stress leads to increase secretion of hormone, both pro-inflammatory cytokines and rumen lipopolysaccharide. Meanwhile, the ruminal microbiota OTUs, Chao1, and Shannon were also changed, and Prevotella1 in NY group was higher than other groups before transport; after transport Firmicutes and Lactobacillus were increased than other groups in CY. The rumen microbiota also related with serum cytokine. Under transport stress, rumen microbiota affect the secretion of hormone levels and immune functions and breed factors affect the performance of stress resistance.The intensity and specialization of beef cattle production make off-site fattening, and introduce new breeds need transportation to achieve the goals. The present study was aimed to investigate effects of land transport stress on hormones levels, microbial fermentation, microbial composition, immunity and correlation among them among Simmental Crossbred Cattle (SC), Native Yellow Cattle (NY), and Cattle Yak (CY). High-throughput sequencing was used to investigate the rumen microbial diversity. After transport stress cortisol (COR), adrenocorticotropic hormone (ACTH) and pro-inflammatory cytokines IL-6, TNF-α, and IL-1β were increased (p < 0.05) in all groups. Rumen lipopolysaccharide (LPS) was increased (p < 0.05) in SC and CY groups. Total volatile fatty acids were increased (p < 0.05) in all groups. The ruminal microbiota about OTUs, Chao1, and Shannon in SC and CY groups were higher than before transport. Prevotella1 in NY group was higher (p < 0.05) than other groups before transport; after transport Firmicutes and Lactobacillus were increased (p < 0.05) than other groups in CY. Lactobacillus was positively correlated with IL-6 and IL-4. Under transport stress, cattle may suffer from inflammatory response through modulating HPA axis and microbiota metabolite affects the secretion of hormone levels and immune function and breeds factor affect the performance of stress resistance.

Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach

Black Bengal goats possess a rich source of rumen microbiota that helps them to adapt for the better utilization of plant biomaterial into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiota. Therefore the study was designed in order to explore the taxonomic profile of rumen microbial communities and potential biomass degradation enzymes present in the rumen of back Bengal goat using Illumina Nextseq-500 platform. A total of 83.18 million high-quality reads were generated and bioinformatics analysis was performed using various tools and subsequently, the predicted ORFs along with the rRNA containing contigs were then uploaded to MG-RAST to analyze taxonomic and functional profiling. The results highlighted that Bacteriodetes (41.38–59.74%) were the most abundant phyla followed by Firmicutes (30.59–39.96%), Proteobacteria (5.07–7.61%), Euryarcheaota (0.71–7.41%), Actinobacteria (2.05–2.75%). Genes that encode glycoside hydrolases (GHs) had the highest number of CAZymes, and accounted for (39.73–37.88%) of all CAZymes in goat rumen. The GT families were the second-most abundant in CAZymes (23.73–23.11%) and followed by Carbohydrate Binding module Domain (17.65–15.61%), Carbohydrate Esterase (12.90–11.95%). This study indicated that goat rumen had complex functional microorganisms produce numerous CAZymes, and that can be further effectively utilised for applied ruminant research and industry based applications.

Long-Term Encapsulated Nitrate Supplementation Modulates Rumen Microbial Diversity and Rumen Fermentation to Reduce Methane Emission in Grazing Steers.

This study investigated the long-term effects (13 months) of encapsulated nitrate supplementation (ENS) on enteric methane emissions, rumen fermentation parameters, ruminal bacteria, and diversity of archaea in grazing beef cattle. We used a total of thirty-two Nellore steers (initial BW of 197 ± 15.3 kg), 12 of which were fitted with rumen cannulas. For 13 months, the animals were maintained in 12 paddocks and fed a concentrate of ground corn, soybean meals, mineral supplements, and urea (URS) or encapsulated nitrate (EN) containing 70 g of EN/100 kg of BW (corresponding to 47 g NO3-/100 kg BW). Encapsulated nitrate supplementation resulted in similar forage, supplement and total DMI values as URS (P > 0.05), but ENS tended to increase (+48 g/d; P = 0.055) average daily weight gain. Daily reductions in methane emissions (-9.54 g or 18.5%) were observed with ENS when expressed as g of CH4/kg of forage dry matter intake (fDMI) (P = 0.037). Lower concentrations of NH3-N and a higher ruminal pH were observed in ENS groups 6 h after supplementation (P < 0.05). Total VFA rumen concentration 6 h (P = 0.009) and 12 h after supplementation with EN resulted in lower acetate concentrations in the rumen (P = 0.041). Steers supplemented with EN had a greater ruminal abundance of Bacteroides, Barnesiella, Lactobacillus, Selenomonas, Veillonella, Succinimonas, Succinivibrio, and Duganella sp. (P < 0.05), but a lower abundance of Methanobrevibacter sp. (P = 0.007). Strong negative correlations were found between daily methane emissions and Proteobacteria, Erysipelotrichaceae, Prevotellaceae, and Roseburia, Kandleria, Selenomonas, Veillonella, and Succinivibrio sp. (P < 0.05) in the rumen of ENS steers. Encapsulated nitrate is a feed additive that persistently affects enteric methane emission in grazing steers, thereby decreasing Methanobrevibacter abundance in the rumen. In addition, ENS can promote fumarate-reducer and lactate-producer bacteria, thereby reducing acetate production during rumen fermentation.

Effects of the supplementation of plant-based formulations on microbial fermentation and predicted metabolic function in vitro

This study aimed at testing the effects of three different formulations of feed supplements based on three different combinations of plant derived alkaloids, prebiotics, tannins, vitamins and minerals on rumen fermentation and the microbiome in vitro. A Rusitec experiment was conducted in 2 identical runs using a complete randomized design with 3 replicates per treatment resulting in total of 6 treatment combinations (n = 6). Each run lasted 12 d with sampling occurring in the last 5 d. Diets were a standard dairy ration (60:40; concentrate:forage) supplemented with one of 3 different plant-based combinations (PI, PII, and PIII) at a level of 100 mg/l and a non-supplemented control (basal diet, control). Microbial DNA samples were taken on the last day of each run and the 16S rRNA target gene sequenced using Illumina MiSeq technology. The supplementations had no effect on the pH, methane and carbon dioxide production. However, both total SCFA (P = 0.08) and molar concentrations of acetate (P = 0.06) tended to be increased in the treatment groups in comparison to control, with PII having the highest overall values (102.7 mmol/L and 43.3 mmol/L, respectively). Alpha diversity indices Shannon, Simpson and Chao1 showed no effect of supplementations or combinations. The addition of PII increased the relative abundance of Bacteroidetes compared to all other treatments (P = 0.05). Supplementation with plant-based combinations reduced the relative abundance of Pyramidobacter from the family Dethiosulfovibrionaceae in comparison with the control diet (P = 0.05). Evaluation of predicted gene function through PICRUSt analysis showed variation in predicted cellular function and metabolism between bacterial communities supplemented with plant-based combinations compared to the control diet. This shows that the addition of plant-based combinations can have the potential to modulate the metabolic function of rumen microbes, and likely the production of small-sized rumen metabolites, without disrupting the rumen microbial community structure and diversity.

Assessment of rumen microbial diversity of buffalo raised under typical feeding condition using Illumina Sequencing technique

There are many factors determining the diversity of rumen microbial, such as feed and breed of animal. The purpose of this study was to assess the diversity of rumen bacterial of buffalo raised under typical feeding condition using Illumina sequencing method. Three adult buffalo were fed on a combination of elephant grass and rice straw for four weeks before taking the rumen fluid samples. In addition, each animal was also given feed supplement at 0.5% of body weight (dry matter base). The samples were analyzed for rumen fermentation pattern, including rumen pH, rumen NH3, and rumen VFA. The samples were also analyzed for rumen microbial diversity using Illumina sequencing technique. The results of the study indicated that the rumen condition of the animal was optimum, indicated by the values of rumen pH (6.8), rumen NH3 (155 mg/L), and rumen VFA (159.3 mmol/L) fell within the acceptable range. Based on the SILVA taxonomic database, two dominant phyla were identified, i.e. Bacteroidetes and Firmicutes. At the genera level, the most dominant group was Prevotella, followed by Christencenellaceae R-7 group, Rikenellaceae RC9 gut group, Ruminococcaceae NK4A214 group. In conclusion, the optimum rumen condition of the animal might contribute to the diversity of rumen bacterial of the buffalo, which was assessed by the Illumina sequencing technique. The study also revealed some number of unidentified rumen microbial of buffalo that need further attention.

Metadata Analysis Approaches for Understanding and Improving the Functional Involvement of Rumen Microbial Consortium in Digestion and Metabolism of Plant Biomass.

Rumen is one of the most complex gastro-intestinal system in ruminating animals. With bountiful of microorganisms supporting in breakdown and consumption of minerals and nutrients from the complex plant biomass. It is predicted that a table spoon of ruminal fluid can reside up to 150 billion microorganisms including various species of bacteria, fungi and protozoa. Several studies in the past have extensively explained about the structural and functional physiology of the rumen. Studies based on rumen and its microbiota has increased significantly in the last decade to understand and reveal applications of the rumen microbiota in food processing, pharmaceutical, biofuel and biorefining industries. Recent high-throughput meta-genomic and proteomic studies have revealed humongous information on rumen microbial diversity. In this study, we have extensively reviewed and reported present-day's progress in understanding the rumen microbial diversity. As of today, NCBI resides about 821,870 records based on rumen with approximately 889 genome sequencing studies. We have retrieved all the rumen-based records from NCBI and extensively catalogued the rumen microbial diversity and the corresponding genomic and proteomic studies respectively. Also, we have provided a brief inventory of metadata analysis software packages and reviewed the metadata analysis approaches for understanding the functional involvement of these microorganisms. Knowing and understanding the present progress on rumen microbiota and performing metadata analysis studies will significantly benefit the researchers in identifying the molecular mechanisms involved in plant biomass degradation. These studies are also necessary for developing highly efficient microorganisms and enzyme mixtures for enhancing the benefits of cattle-feedstock and biofuel industries.

Effect of Graded Levels of Bromoethanesulfonic Acid Supplementation on Methane Production, Rumen Microbial Diversity and Fermentation Characteristics

Bromoethanesulfonic acid (BES) was examined as a methane inhibitor and its impact on rumen microbial populations in male cattle calves. Ten crossbred cattle calves (average body weight, 132±2 kg) were divided into two groups of five each and were fed on a diet containing 19.9% CP and 72.6% TDN. In the experimental group, BES was fed at the rate of 5 mg for first 10 days, 10 mg for next 10 days (11–20th day) and 15 mg/kg BW for another 10 days (21 to 30th days) of the experiment. Rumen liquor was collected by stomach tube from calves after feeding of each level of BES and was used for studying the microbial profile by real time PCR and as an inoculum for in vitro gas production test. The in vitro methane production (ml/g DDM) was reduced (P<0.05) by 35, 8.1 and 15 per cent on feeding BES at the levels of 5, 10 and 15 mg/kg BW (P<0.001, P=0.007 and P=0.009, respectively). The in vitro true digestibility of feed was not affected at lower levels but was significantly improved at 15 mg BES level (P=0.026). The population of protozoa, was significantly reduced at 5 mg BES (P=0.014) level but at 10 mg level, fungi and methanogens were reduced significantly (P=0.031, P=0.034) and at 15 mg BES level only fungal population was reduced (P=0.029). The results indicated that BES can reduce rumen methanogenesis but cannot eliminate methanogens completely from the rumen.

Impact of dehydration on retention of bioactive profile and biological activities of different grape (Vitis vinifera L.) pomace varieties

The effects of drying method [sun (7 days), oven (72 h at 60 °C) and freeze (∼72 h)] and grape (Vitis vinifera L. cv. Pinotage, Shiraz and Sauvignon Blanc) variety on pomace fatty acid composition, polyphenolic content and antioxidant capacity were evaluated. Furthermore, the influence of sun-dried pomaces on rumen microbial diversity was assessed in vitro. Freeze-dried Shiraz had the highest proportions of 18:1n-9, 18:2n-6, total monounsaturated fatty acid (MUFA), polyunsaturated fatty acids (PUFA) and content of polyphenolics compared to other drying × variety interactions (P ≤ 0.05). Freeze-dried Sauvignon Blanc had the highest proanthocyanidin content and antioxidant activity for both 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) relative to other drying × variety interactions (P ≤ 0.05). Regardless of variety and inclusion level, grape pomace variety reduced bacterial species abundance, but improved species diversity, evenness and richness compared to the control (P ≤ 0.05). Overall, freeze-dried Shiraz had the best fatty acid profile and highest polyphenolic content, while freeze-dried Sauvignon Blanc had the highest proanthocyanidin content and antioxidant activity.

An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation.

Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.

Comparative Study of SSCP Pattern of V3 and V4-V5 Region of 16S rRNA of Metagenomic DNA for the Identification Rumen Microbial Diversity

Comparative Study of SSCP Pattern of V3 and V4-V5 Region of 16S rRNA of Metagenomic DNA for the Identification Rumen Microbial Diversity