Changes in the Rumen Bacteriome Structure and Enzymatic Activities of Goats in Response to Dietary Supplementation with Schizochytrium spp

Evaluation of ruminal methane and ammonia formation and microbiota composition as affected by supplements based on mixtures of tannins and essential oils using Rusitec

BACKGROUND

Dietary supplements based on tannin extracts or essential oil compounds (EOC) have been repeatedly reported as a promising feeding strategy to reduce the environmental impact of ruminant husbandry. A previous batch culture screening of various supplements identified selected mixtures with an enhanced potential to mitigate ruminal methane and ammonia formation. Among these, Q-2 (named after quebracho extract and EOC blend 2, composed of carvacrol, thymol, and eugenol) and C-10 (chestnut extract and EOC blend 10, consisting of oregano and thyme essential oils and limonene) have been investigated in detail in the present study with the semi-continuous rumen simulation technique (Rusitec) in three independent runs. For this purpose, Q-2 and C-10, dosed according to the previous study, were compared with a non-supplemented diet (negative control, NC) and with one supplemented with the commercial EOC-based Agolin® Ruminant (positive control, PC).

RESULTS

From d 5 to 10 of fermentation incubation liquid was collected and analysed for pH, ammonia, protozoa count, and gas composition. Feed residues were collected for the determination of ruminal degradability. On d 10, samples of incubation liquid were also characterised for bacterial, archaeal and fungal communities by high-throughput sequencing of 16S rRNA and 26S ribosomal large subunit gene amplicons. Regardless of the duration of the fermentation period, Q-2 and C-10 were similarly efficient as PC in mitigating either ammonia (-37% by Q-2, -34% by PC) or methane formation (-12% by C-10, -12% by PC). The PC was also responsible for lower feed degradability and bacterial and fungal richness, whereas Q-2 and C-10 effects, particularly on microbiome diversities, were limited compared to NC.

CONCLUSIONS

All additives showed the potential to mitigate methane or ammonia formation, or both, in vitro over a period of 10 d. However, several differences occurred between PC and Q-2/C-10, indicating different mechanisms of action. The pronounced defaunation caused by PC and its suggested consequences apparently determined at least part of the mitigant effects. Although the depressive effect on NDF degradability caused by Q-2 and C-10 might partially explain their mitigation properties, their mechanisms of action remain mostly to be elucidated.

Microalgae as a Sustainable Source of Antioxidants in Animal Nutrition, Health and Livestock Development

Microalgae are a renewable and sustainable source of bioactive compounds, such as essential amino acids, polyunsaturated fatty acids, and antioxidant compounds, that have been documented to have beneficial effects on nutrition and health. Among these natural products, the demand for natural antioxidants, as an alternative to synthetic antioxidants, has increased. The antioxidant activity of microalgae significantly varies between species and depends on growth conditions. In the last decade, microalgae have been explored in livestock animals as feed additives with the aim of improving both animals' health and performance as well as product quality and the environmental impact of livestock. These findings are highly dependent on the composition of microalgae strain and their amount in the diet. The use of carbohydrate-active enzymes can increase nutrient bioavailability as a consequence of recalcitrant microalgae cell wall degradation, making it a promising strategy for monogastric nutrition for improving livestock productivity. The use of microalgae as an alternative to conventional feedstuffs is becoming increasingly important due to food-feed competition, land degradation, water deprivation, and climate change. However, the cost-effective production and use of microalgae is a major challenge in the near future, and their cultivation technology should be improved by reducing production costs, thus increasing profitability.

Special Issue “Rumen Microbial Communities”: Editorial

Ruminants represent a highly successful group of herbivores that have not only evolved to thrive across a wide range of habitats, but have also played a central role throughout human history [...]

Effect of Spirulina Dietary Supplementation in Modifying the Rumen Microbiota of Ewes

Supplementing ruminant diets with microalgae, may prove an effective nutritional strategy to manipulate rumen microbiota. Forty-eight ewes were divided into four homogenous groups (n = 12) according to their fat-corrected milk yield (6%), body weight, age, and days in milk, and were fed individually with concentrate, alfalfa hay, and wheat straw. The concentrate of the control group (CON) had no Spirulina supplementation, while in the treated groups 5 (SP5), 10 (SP10), and 15 g (SP15) of Spirulina were supplemented as an additive in the concentrate. An initial screening using metagenomic next-generation sequencing technology was followed by RT-qPCR analysis for the targeting of specific microbes, which unveiled the main alterations of the rumen microbiota under the Spirulina supplementation levels. The relative abundance of Eubacterium ruminantium and Fibrobacter succinogenes in rumen fluid, as well as Ruminococcus albus in rumen solid fraction, were significantly increased in the SP15 group. Furthermore, the relative abundance of Prevotella brevis was significantly increased in the rumen fluid of the SP5 and SP10 groups. In contrast, the relative abundance of Ruminobacter amylophilus was significantly decreased in the rumen fluid of the SP10 compared to the CON group, while in the solid fraction it was significantly decreased in the SP groups. Moreover, the relative abundance of Selenomonas ruminantium was significantly decreased in the SP5 and SP15 groups, while the relative abundance of Streptococcus bovis was significantly decreased in the SP groups. Consequently, supplementing 15 g Spirulina/ewe/day increased the relative abundance of key cellulolytic species in the rumen, while amylolytic species were reduced only in the solid fraction.

Meta-analysis of flavonoids use into beef and dairy cattle diet: Performance, antioxidant status, ruminal fermentation, meat quality, and milk composition

The objective of this study was to evaluate the effects of dietary supplementation with flavonoids (FLAs) on animal performance, diet digestibility, antioxidant status in blood serum, rumen parameters, meat quality, and milk composition in beef and dairy cattle through a meta-analysis. Thirty-six peer-reviewed publications were included in the data set. The weighted mean differences (WMD) between the FLAs treatments and the control treatment were used to assess the effect size. Dietary supplementation with FLAs decreased feed conversion ratio (WMD = -0.340 kg/kg; p = 0.050) and increased (p < 0.05) dry matter intake (WMD = 0.191 kg/d), dry matter digestibility (WMD = 15.283 g/kg of DM), and daily weight gain (WMD = 0.061 kg/d). In blood serum, FLAs supplementation decreased the serum concentration of malondialdehyde (WMD = -0.779 nmol/mL; p < 0.001) and increased (p < 0.01) the serum concentration of superoxide dismutase (WMD = 8.516 U/mL), glutathione peroxidase (WMD = 12.400 U/mL) and total antioxidant capacity (WMD = 0.771 U/mL). A higher ruminal propionate concentration (WMD = 0.926 mol/100 mol; p = 008) was observed in response to FLAs supplementation. In meat, the dietary inclusion of FLAs decreased (p < 0.05) shear force (WMD = -1.018 kgf/cm²), malondialdehyde content (WMD = -0.080 mg/kg of meat), and yellowness (WMD = -0.460). Supplementation with FLAs decreased milk somatic cell count (WMD = -0.251 × 103 cells/mL; p < 0.001) and increased (p < 0.01) milk production (WMD = 1.348 kg/d), milk protein content (WMD = 0.080/100 g) and milk fat content (WMD = 0.142/100 g). In conclusion, dietary supplementation with FLAs improves animal performance and nutrient digestibility in cattle. In addition, FLAs improve the antioxidant status in blood serum and the quality of meat and milk.

The gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Essential Oils as a Dietary Additive for Small Ruminants: A Meta-Analysis on Performance, Rumen Parameters, Serum Metabolites, and Product Quality

There is an increasing pressure to identify natural feed additives that improve the productivity and health of livestock, without affecting the quality of derived products. The objective of this study was to evaluate the effects of dietary supplementation with essential oils (EOs) on productive performance, rumen parameters, serum metabolites, and quality of products (meat and milk) derived from small ruminants by means of a meta-analysis. Seventy-four peer-reviewed publications were included in the data set. Weighted mean differences (WMD) between the EOs treatments and the control treatment were used to assess the magnitude of effect. Dietary inclusion of EOs increased (p < 0.05) dry matter intake (WMD = 0.021 kg/d), dry matter digestibility (WMD = 14.11 g/kg of DM), daily weight gain (WMD = 0.008 kg/d), and feed conversion ratio (WMD = −0.111). The inclusion of EOs in small ruminants’ diets decreased (p < 0.05) ruminal ammonia nitrogen concentration (WMD = −0.310 mg/dL), total protozoa (WMD = −1.426 × 105/mL), methanogens (WMD = −0.60 × 107/mL), and enteric methane emissions (WMD = −3.93 L/d) and increased ruminal propionate concentration (WMD = 0.726 mol/100 mol, p < 0.001). The serum urea concentration was lower (WMD = −0.688 mg/dL; p = 0.009), but serum catalase (WMD = 0.204 ng/mL), superoxide dismutase (WMD = 0.037 ng/mL), and total antioxidant capacity (WMD = 0.749 U/mL) were higher (p < 0.05) in response to EOs supplementation. In meat, EOs supplementation decreased (p < 0.05) the cooking loss (WMD = −0.617 g/100 g), malondialdehyde content (WMD = −0.029 mg/kg of meat), yellowness (WMD = −0.316), and total viable bacterial count (WMD = −0.780 CFU/g of meat). There was higher (p < 0.05) milk production (WMD = 0.113 kg/d), feed efficiency (WMD = 0.039 kg/kg), protein (WMD = 0.059 g/100 g), and lactose content in the milk (WMD = 0.100 g/100 g), as well as lower somatic cell counts in milk (WMD = −0.910 × 103 cells/mL) in response to EOs supplementation. In conclusion, dietary supplementation with EOs improves productive performance as well as meat and milk quality of small ruminants. In addition, EOs improve antioxidant status in blood serum and rumen fermentation and decrease environmental impact.

Biodegradation and hydrolysis of rice straw with corn steep liquor and urea-alkali pretreatment

The current study evaluated the corn steep liquor (CSL) and urea-alkali pretreatment effect to enhance biodegradation and hydrolysis of rice straw (RS) by ruminal microbiome. The first used RS (1) without (Con) or with additives of (2) 4% CaO (Ca), (3) 2.5% urea plus 4% CaO (UCa) and (4) 9% corn steep liquor + 2.5% urea + 4% CaO (CUCa), and then the efficacy of CSL plus urea-alkali pretreatment was evaluated both in vitro and in vivo. The Scanning electron microscopy, X-ray diffraction analysis, cellulose degree of polymerization and Fourier-transform infrared spectroscopy, respectively, results showed that Ca, UCa, and CUCa pretreatment altered the physical and chemical structure of RS. CSL plus Urea-alkali pretreated enhanced microbial colonization by improving the enzymolysis efficiency of RS, and specially induced adhesion of Carnobacterium and Staphylococcus. The CUCa pretreatment could be developed to improve RS nutritional value as forage for ruminants, or as feedstock for biofuel production.

Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province

BACKGROUND

The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai-Tibet Plateau (QTP).

RESULTS

Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak.

CONCLUSIONS

In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.

Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research

Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.

Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats' Rumen by Metagenomic Deep Sequencing

Simple Summary

Prevotella is an abundant genus which plays an important role for lignocellulose digestion in goat rumen and is significant to the yield and quality of milk and meat in cows. In a previous study, we sequenced bacterial metagenome from Vietnamese native goat rumen to get 8.4 GB clean data and found very diverse genes related to lignocellulose degradation. However, due to the limitation in the metagenomic size, low amount of complete lignocellulase genes, and high bacterial diversity, further analysis was restricted. In this study, metagenomic deep sequencing was used to obtain 48.66 GB of reliable data, thus some lignocellulolytic enzymes were first seen and a picture of bacterial enzymes involved in lignocellulose digestion in the goat rumen was drawn. The loci for galactan-, xylan-, and arabinan-processing in Prevotella were observed for the first time. We confirm that Prevotella plays pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin conversion in the goat rumen. A gene coding endoxylanase was expressed in E. coli. The recombinant enzyme was tolerant with some salts, detergents, and had high activity, thus is a good candidate for lignocellulose processing and as an animal feed food additive to effectively improve xylooligosaccharide production.

Abstract

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.