Metagenome of Mehsani buffalo rumen microbiota: an assessment of variation in feed-dependent phylogenetic and functional classification

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.

Rumen microbial diversity, enteric methane emission and nutrient utilization of crossbred Karan-Fries cattle (Bos taurus) and Murrah buffalo (Bubalus bubalis) consuming varied roughage concentrate ratio

Dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance. The goal of this study was to see how the roughage concentrate ratio 70:30 (Low concentrate; LC) vs 40:60 (High concentrate; HC) and the host species crossbred cattle vs buffalo affected rumen microbial diversity, enteric methane emissions and nutrient utilization. Dry matter intake (kg/d) and dry matter percent digestibility were considerably (p < 0.05) higher in the HC ration and buffalo compared to LC ration and crossbred cattle, respectively. Both dietary mix and host species had a substantial (p < 0.05) impact on intake of various nutrients, including organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Increased concentrate proportion in the ration improved nitrogen balance, resulting in increased average daily gain and considerably reduced methane (g/d) output (p < 0.05). Furthermore, 16S rRNA genes were sequenced using Oxford Nanopore Technology (ONT) and subsequently annotated using the Centrifuge workflow to uncover ruminal bacterial diversity. Firmicutes was considerably (p < 0.01) greater in the LC diet, whereas, Bacteroidetes was higher in the HC ration. Genus Prevotella dominated all rumen samples, and buffalo fed LC ration had significantly (p < 0.01) higher Oscillospira abundance. At the species level, simple sugar-utilizing bacteria such as Prevotella spp. and Selenomonas ruminantium predominated in the crossbred cattle, but fibrolytic bacteria such as Oscillospira guilliermondii were statistically (p < 0.01) more abundant in the buffalo. Overall, dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance, however, host species remained a major driving force to change ruminal community composition as compared to roughage concentrate ratio under similar environmental conditions.

Effects of starters with different NDF/starch ratio on rumen fermentation parameters and rumen microorganisms in lambs

Starch and NDF are the main components in the diets of ruminants worldwide and are the main energy source for rumen microorganisms and hosts. The purpose of this study was to investigate the effects of different NDF/starch ratios on rumen fermentation parameters, rumen development and rumen microbes in lambs and to predict the function of rumen microbes by metagenomic techniques. In this study, 30 lambs with birth weights of (3.0 ± 0.5) kg were selected. The lambs of Hu sheep were randomly divided into two groups, fed starter with an NDF/starch ratio of 0.5 (group A) or 1.0 (group C). Samples of the rumen tissue and contents were collected after slaughter. The results showed that the ADG and ADFI of group A were significantly higher than those of group C (P < 0.05), but there was no significant difference in the FCR (P > 0.05). Therefore, from the perspective of feed-related economic benefits, group C showed greater economic value; the A/P of group C was significantly lower than that of group A (0.05 < P < 0.1), and the TVFA showed no significant difference (P > 0.05); The lengths of the rumen papillae of group C was significantly higher than that of group A (0.05 < P < 0.1). There was no significant difference in the abundance of the top 10 species at the phylum level and genus level (P > 0.05). CAZymes gene enrichment was observed in the rumen microbial community of lambs in group C (P < 0.05). In conclusion, group C, fed with starter with a higher NDF/starch ratio, had a higher feeding value. This study provides comprehensive insights into the composition of NDF and starch in lamb starter.

Supplemental dietary Selenohomolanthionine affects growth and rumen bacterial population of Shaanbei white cashmere wether goats

Selenium (Se) is an important trace element for all livestock growth. However, little is known about the dietary supplementation of Selenohomolanthionine (SeHLan) effect on growth and rumen microbiota of cashmere goats. In this study, thirty-two growing Shaanbei white cashmere wether goats with mean body weight (26.18 ± 2.71) kg were randomly assigned into 4 treatments, each with 8 replicates. The goats in 4 experimental groups were fed the basal diet (0.016 mg/kg Se) added with organic Se in the form of SeHLan, namely, control group (CG, added 0 mg/kg Se), low Se group (LSE, added 0.3 mg/kg Se), medium Se group (MSE, added 0.6 mg/kg Se), and high Se group (HSE, added 1.2 mg/kg Se). The feed experiment lasted for 70 days including 10-day adaptation, followed by 11 days digestibility trial including 7-day adaptation and 4-day collection period. On the last day of feeding experiment, rumen fluid was collected for microbial community analysis. The feed, orts, and fecal samples were collected for chemical analysis during digestibility trial. The results showed that average daily feed intake (ADFI) and the apparent digestibility of crude protein (CP) were both quadratic ally increased with increased SeHLan supply (P_quadratic < 0.05), while average daily gain (ADG) and feed conversion ratio (FCR) showed a linear response (P_linear < 0.05). The ADFI and ADG were all highest in the MSE group, which also had the lowest FCR (P < 0.05). Alpha diversity indices of the microbial community did not differ among four treatments. While principal coordinates analysis (PCoA) showed that rumen bacterial population differed among four groups. Taxonomic analysis revealed that Bacteroidetes, Firmicutes, and Euryarchaeota were the dominant phyla. The dominant families were Prevotellaceae, Selenomonadaceae, Methanobacteriaceae, and Bifidobacteriaceae. The significantly different rumen bacterial genera were found to be Methanobrevibacter, Quinella, Christensenellaceae_R-7_group, Veillonellaceae_UCG-001, and Succinivibrionaceae_UCG-002 (P < 0.05). In addition, Tax4fun analysis revealed that SeHLan supplemented groups enhanced the enrichment of genes related to energy metabolism, amino acid metabolism, carbohydrate metabolism, and enzymes. Twenty-eight pathways showed significant differences among four treatment groups (P < 0.05). In conclusion, dietary supplementation of medium SeHLan significantly affects rumen bacterial composition and ultimately promotes Shaanbei white cashmere wether goats nutrient digestibility and growth.

An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics

Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3−5 years old), E (6−8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.

In situ rumen degradation characteristics and bacterial colonization of whole cottonseed, cottonseed hull and cottonseed meal with different gossypol content

Regarding whole cottonseed (WCS), cottonseed meal (CSM), and cottonseed hull (CSH), in situ rumen incubation was applied to determine their nutrient and gossypol degradation characteristics and bacterial colonization profile in lactating Holstein cows. Nylon bags containing the cotton by-products were incubated for 0, 6, 12, 24, 36, 48 and 72 h in the rumen, respectively. The relationship between nutrient degradability and free gossypol (FG) content were examined, and the differences in the composition and inferred gene function of the colonized microbiota were studied. As a result, CSM presented highest effective degradability of dry matter, neutral detergent fibre and acid detergent fibre, but the highest effective degradability of crude protein was found in WCS. Free gossypol disappearance rate increased significantly in the first 6 h, and it reached approximately 94% at 72 h of incubation among all samples. The level of FG did not affect nutrient degradability of cotton by-products. Significant differences were noted in attached bacterial community structure among cotton by-products after 24 h rumen incubation. Among the most abundant taxa at genus level, a greater abundance of Cercis gigantea and Succiniclasticum was observed in WCS samples, whereas the CSH and CSM samples contained a greater proportion of Prevotella 1 and Rikenellaceae RC9 gut group. The redundancy analysis revealed that the level of neutral detergent fibre, ether extract, and FG in cotton by-products were significantly positive related with the composition of the attached bacteria. Collectively, our results revealed the dynamics of degradation characteristics, and the difference in the composition of bacterial colonization. These findings are of importance for the targeted improvement of cotton by-products nutrient use efficiency in ruminants and further understanding of the gossypol degradation mechanism in the rumen.

Analysis of bacterial community in rumen fluid of cattle supplemented with different protein and energy sources

Context Source and composition of feed influence rumen microbial community, which determines efficiency of feed digestion and thus productivity in ruminants. Therefore, changes in the structure, function and diversity of the rumen microbial populations in response to changes in diet provide an understanding in the rumen fermentation process. Aims The present study, consisting of two experiments, was conducted to determine the effects of supplementing different protein and energy sources on the rumen bacterial community in cattle. Methods The dietary treatments of the first experiment, which evaluated the effect of protein sources, were as follows: (i) Hymenachne acutigluma grass, rice straw and rice bran (1.5 kg/head.day; C1), (ii) C1 plus 120 g urea/head.day (C1 + U), (iii) C1 plus 720 g soybean/head.day (C1 + SM), and (iv) C1 plus 720 g of blood and feather meal (in 1:1 ratio)/head.day (C1 + BFM). The treatments in the second experiment were (i) Hymenachne acutigluma grass, rice straw and concentrate (1.5 kg/head.day; C2), (ii) C2 plus 250 g fish oil/head.day (C2 + FO) and (iii) C2 + 250 g soybean oil/head.day (C2 + SO). At the end of the 90-day feeding trial, rumen fluids were extracted for microbial DNA isolation to identify the microbe species by the polymerase chain reaction–denaturing gradient gel electrophoresis method and sequencing of the 16S rRNA region. Key results The sequences of some DNA bands were closely related to the bacteria strains of the Prevotella, Cytophaga, Capnocytophaga, Cyanobacterium, Catonella, Faecalibacterium, Lachnospiraceae, Ruminococcaceae, Propionivibrio, Galbibacter, Moorellaglycerin, Escherichia coli and Klebsiella alba groups, with similarity levels ranging from 73% to 96%. In addition, the Prevotella species was found in both the protein and the energy supplement trials, and irrespective of diet supplements, the Firmicutes and Bacteroidetes were the prominent groups in the rumen. Conclusions Firmicutes and Bacteroidetes are the two dominant groups of rumen microflora, and Bacteroidia and Clostridia classes together with the Prevotella genus are predominant in the rumen irrespective of protein and energy sources. Implications Our findings provided evidence on the effect of diet on the interaction of rumen microbial community and have important implications in establishing optimal diets for cattle.

Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

Vaccination against the brown stomach worm, Teladorsagia circumcincta, followed by parasite challenge, induces inconsistent modifications in gut microbiota composition of lambs

Background

Growing evidence points towards a role of gastrointestinal (GI) helminth parasites of ruminants in modifying the composition of the host gut flora, with likely repercussions on the pathophysiology of worm infection and disease, and on animal growth and productivity. However, a thorough understanding of the mechanisms governing helminth-microbiota interactions and of their impact on host health and welfare relies on reproducibility and replicability of findings. To this aim, in this study, we analysed quantitative and qualitative fluctuations in the faecal microbiota composition of lambs vaccinated against, and experimentally infected with, the parasitic GI nematode Teladorsagia circumcincta over the course of two separate trials performed over two consecutive years.

Methods

Two trials were conducted under similar experimental conditions in 2017 and 2018, respectively. In each trial, lambs were randomly assigned to one of the following experimental groups: (i) vaccinated/infected, (ii) unvaccinated/infected and (iii) unvaccinated/uninfected. Faecal samples collected from individual animals were subjected to DNA extraction followed by high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and bioinformatics and biostatistical analyses of sequence data.

Results

Substantial differences in the populations of bacteria affected by immunisation against and infection by T. circumcincta were detected when comparing data from the two trials. Nevertheless, the abundance of Prevotella spp. was significantly linked to helminth infection in both trials.

Conclusions

Despite the largely conflicting findings between the two trials, our data revealed that selected gut microbial populations are consistently affected by T. circumcincta infection and/or vaccination. Nevertheless, our study calls for caution when interpreting data generated from in vivo helminth-microbiome interaction studies that may be influenced by several intrinsic and extrinsic host-, parasite- and environment-related factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04688-4.

Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro

Aims

This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities.

Methods and Results

Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others.

Conclusions

When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio.

Significance and Impact of the Study

The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.

Increasing the Sustainability of Maize Grain Production by Using Arbuscular Mycorrhizal Fungi Does Not Affect the Rumen of Dairy Cattle (Bos taurus) and Buffalo (Bubalus bubalis)

New approaches are needed to improve the sustainability of feed production and utilization by ruminants. Promising approaches include increased use of buffaloes for more sustainable milk production, and arbuscular mycorrhizal fungi (AMF) to reduce crop production input needs. However, studies assessing the effect of crops grown in the presence of AMF on rumen microbial utilization are limited. Based on current knowledge, we hypothesized that maize grain grown on AMF-inoculated soil affected ruminal fermentation and microbiota, and that this effect differed between buffalo and cattle. A dietary cross-over study (four weeks per diet) was conducted using rumen-cannulated cattle (n = 5) and buffalo (n = 6) to assess the effect of maize grain (3.9% (w/v) of diet) grown on soil with or without AMF (15 kg/ha) on ruminal fermentation and microbiota. Production of maize on AMF-treated soil did not affect any of the assessed ruminal fermentation parameters, microbial concentrations, or prokaryotic community composition (using prokaryotic 16S rRNA gene sequence analysis). In contrast, host type had numerous effects. Protozoal counts, lactate, total VFA and isobutyrate, were significantly higher in buffaloes compared to cattle. Conversely, butyrate was significantly lower in buffaloes than in cattle. Host type explained 9.3% of the total variation in prokaryotic community composition, and relative abundance of nine amplicon sequence variants significantly differed between host types. These findings indicate that AMF treatment of maize crops has no detrimental impact on the value of the resulting maize grains as a ruminant feed, and provides additional insight into rumen-based differences between cattle and buffalo.

MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.

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.

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants

Over the years, rumen fluid transplantation (RT) has been successfully applied to treat acute rumen acidosis in ruminants, but how it functions in the ruminal microbial homeostasis and host function remains largely unknown. Here, we investigated the dynamic changes of rumen fermentation and bacterial communities following RT and its beneficial effects on rumen epithelial morphology and function in a sheep model of rumen acidosis. The results showed that RT resulted in dynamic changes in rumen fermentation and increased the concentrations of total volatile fatty acid, acetate, propionate, and butyrate, but it decreased the levels of lactate and LPS in the rumen. Illumina MiSeq Sequencing data showed that RT facilitated rapid rebuilt of ruminal bacterial homeostasis (8 d in control vs. 2 d in RT) from a markedly dysbiotic acidosis state to a healthy level (similar with those of donors). At the genus level, RT increased the relative abundance of unclassified Bacteroidales, unclassified Prevotellaceae, unclassified Ruminococcaceae, and Acetitomaculum. Additionally, RT also accelerated recovery of the predicted metagenomic function of ruminal bacteria. Rumen papillae morphology results showed that RT alleviated the damage of rumen epithelia induced by acute rumen acidosis and increased the length of rumen papillae. Furthermore, real-time PCR results showed that RT modulated mRNA expression of genes related to cytokines and tight junctions in the rumen epithelia. In summary, these results reveal that RT accelerates recovery of rumen fermentation and bacterial homeostasis and modulates rumen epithelial morphology and function for sheep suffering from rumen acidosis.-Liu, J., Li, H., Zhu, W., Mao, S. Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants.

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.

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.

Age-Related Response of Rumen Microbiota to Mineral Salt and Effects of Their Interactions on Enteric Methane Emissions in Cattle

Mineral salt bricks are often used in cow raising as compensation for mineral losses to improve milk yield, growth, and metabolic activity. Generally, effects of minerals are partially thought to result from improvement of microbial metabolism, but their influence on the rumen microbiota has rarely been documented to date. In this study, we investigated the response of microbiota to mineral salt in heifer and adult cows and evaluated ruminal fermentation and enteric methane emissions of cows fed mineral salts. Twelve lactating Holstein cows and twelve heifers fed a total mixed ration (TMR) diet were randomly allocated into two groups, respectively: a treatment group comprising half of the adults and heifers that were fed mineral salt and a control group containing the other half fed a diet with no mineral salt supplement. Enteric methane emissions were reduced by 9.6% (P < 0.05) in adults ingesting a mineral salt diet, while concentrations of ruminal ammonia, butyrate, and propionate were increased to a significant extent (P < 0.05). Enteric methane emissions were also reduced in heifers ingesting a mineral salt diet, but not to a significant extent (P > 0.05). Moreover, the concentrations of ammonia and volatile fatty acids (VFAs) were not significantly altered in heifers (P > 0.05). Based on these results, we performed high-throughput sequencing to explore the bacterial and archaeal communities of the rumen samples. Succiniclasticum and Prevotella, two propionate-producing bacteria, were predominant in samples of both adults and heifers. At the phylotype level, mineral salt intake led to a significant shift from Succiniclasticum to Prevotella and Prevotellaceae populations in adults. In contrast, reduced abundance of Succiniclasticum and Prevotella phylotypes was observed, with no marked shift in propionate-producing bacteria in heifers. Methanogenic archaea were not significantly abundant between groups, either in adult cows or heifers. The shift of Succiniclasticum to Prevotella and Prevotellaceae in adults suggests a response of microbiota to mineral salt that contributes to higher propionate production, which competes for hydrogen utilized by methanogens. Our data collectively indicate that a mineral salt diet can alter interactions of bacterial taxa that result in enteric methane reduction, and this effect is also influenced in an age-dependent manner.

Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis)

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.

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.

Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants

Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis)

BACKGROUND

The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach.

RESULTS

Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples.

CONCLUSIONS

Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.

Deep insights into carbohydrate metabolism in the rumen of Mehsani buffalo at different diet treatments

Ruminants are known to harbour a vast and diverse microbial community that functions in utilizing the fibrous and starchy feedstuffs. The microbial fermentation of fibrous and starchy feed is carried out by different groups of microbiota, which function in synergistic mechanism. The exploration of the shift in carbohydrate utilizing microbial community with the change in diet will reveal the efficient role of that group of microbial community in particular carbohydrate utilization. The present study explains the shifts in microbial enzymes for carbohydrate utilization with the change in the feed proportions and its correlation with the microbial community abundance at that particular treatment. The sequencing data of the present study is submitted to NCBI SRA with experiment accession IDs (ERX162128, ERX162129, ERX162130, ERX162131, ERX162139, ERX162134, ERX162140, ERX162141, ERX197218, ERX197219, ERX197220, ERX197221, ERX162158, ERX162159, ERX162160, ERX162161, ERX162176, ERX162164, ERX162165, ERX162166, ERX162167, ERX162168, ERX162169, ERX162177).

Functional Characterization Reveals Novel Putative Coding Sequences in Prevotella ruminicola Genome Extracted from Rumen Metagenomic Studies

AIM

To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome.

METHOD

Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis.

RESULTS

Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference.

CONCLUSION

The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements.

Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy

Gastric cancer (GC) is among the most common malignancy in the world with poor prognosis and limited treatment options. It has been established that gastric carcinogenesis is caused by a complex interaction between host and environmental factors. Copy number variation (CNV) refers to a form of genomic structural variation that results in abnormal gene copy numbers, including gene amplification, gain, loss and deletion. DNA CNV is an important influential factor for the expression of both protein-coding and non-coding genes, affecting the activity of various signaling pathways. CNV arises as a result of preferential selection that favors cancer development, and thus, targeting the amplified 'driver genes' in GC may provide novel opportunities for personalized therapy. The detection of CNVs in chromosomal or mitochondrial DNA from tissue or blood samples may assist the diagnosis, prognosis and targeted therapy of GC. In this review, we discuss the recent CNV discoveries that shed light on the molecular pathogenesis of GC, with a specific emphasis on CNVs that display diagnostic, prognostic or therapeutic significances in GC.