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.

Dietary supplementation of Aloe vera extract modulates rumen microbes and improves the functional food value of milk by altering phenolic content, antioxidant capacity, and fatty acid profile in lactating goats.

Twenty-four cross-breed (Alpine × Beetal) lactating goats (average body weight: 37.5 ± 2.7 kg and milk yield: 1.78 ± 0.31 kg/day) were chosen for the ninety days duration of the experiment and divided into three groups following a completely randomized design. Group I acted as control (T0) and received only a basal diet as per requirement, whereas group II (T1) and group III (T2) received basal diet added with Aloe vera extract at 2% and 4% of dry matter intake (DMI), respectively. Total phenolic compounds (TPC) and milk antioxidant status were higher (p < 0.05) in T1 and T2 than T0. Relative abundance of methanogen, protozoa, Butyrivibrio proteoclasticus, and Ruminococcus flavefaciens in the rumen were lower, while Butyrivibrio fibrisolvens population was higher (p < 0.05) in T2 and T1 compared to T0. Saturated fatty acids levels in milk were lower, whereas different polyunsaturated fatty acids levels were higher (p < 0.05) in T1 and T2 than T0. Nutritional indices of milk increased in both supplemented groups. Overall, it may be concluded that dietary supplementation of Aloe vera extract at 2% and 4% of DMI may enhance the functional characteristics of milk by boosting TPC and antioxidant status, as well as the FA profile and nutritional quality indices of milk fat.

Supplementation of Aloe vera extract in lactating goats' diet: effects on rumen fermentation efficiency, nutrient utilization, lactation performance, and antioxidant status.

The present work was conducted to investigate the effects of supplementing Aloe vera extract on rumen fermentation efficiency, nutrient utilization, lactation performance, and antioxidant status of goats. Twenty-four crossbreed lactating goats (Alpine × Beetal) were divided into three experimental groups (AV0, AV2, and AV4). AV0 had no supplementation, groups AV2 and AV4 received ready to feed aqueous extract of Aloe vera at 20 and 40 g/kg dry matter intake, respectively, along with basal diet and experiment lasted for 100 days. Average DMI did not vary (P > 0.05) among treatment groups; however, the metabolic bodyweight of AV4 was significantly lower (P < 0.05) than the AV0 and AV2 groups (AV0 = AV2 > AV4). Intake and digestibility of DM, OM, CP, NDF, ADF, and EE were unaffected (P > 0.05) by Aloe vera supplementation. The milk production, yield of milk fat, protein, lactose, and solid not fat (SNF) of goats in the AV4 group were significantly higher (P < 0.05) than other groups (AV4 > AV2 = AV0). The activity of superoxide dismutase and catalase enzymes and levels of plasma ferric reducing total antioxidant power were high (P < 0.01) in the Aloe vera supplemented group (AV4 = AV2 > AV0). There was no significant difference (P = 0.979) in the pH, acetic acid (P = 0.449), and butyric acid (P = 0.864) concentration of the rumen liquor among the treatment groups. The propionic acid concentration was similar between AV2 and AV4 and significantly higher (P = 0.024) than the AV0 group (AV4 = AV2 > AV0). Moreover, C2:C3 values were significantly lower (P = 0.037) in the AV4 group compared to the control (AV0). Thus, Aloe vera supplementation enhanced milk yield, propionic acid production, and antioxidant status without affecting nutrient utilization; however, results were better in the AV4 group. The inclusion of Aloe vera at 40 g/kg of DMI would improve the rumen fermentation efficiency, lactation performance, and overall health status of the dairy goats.