Characterization of Rumen Microbiota of Two Sheep Breeds Supplemented With Direct-Fed Lactic Acid Bacteria

Lycium barbarum (Wolfberry) Branches and Leaves Enhance the Growth Performance and Improve the Rumen Microbiota in Hu Sheep

The Lycium barbarum branches and leaves (LBL) are known to contain a range of active substances that have positive effects on animal immunity and antioxidation. This study aimed to examine how LBL impacts the growth and slaughter performance as well as rumen fermentation and microbiota in Hu sheep. A total of 50 male Hu sheep of indigenous origin, aged 3 months, were randomly divided into 5 groups of 10 sheep each. The groups were given different levels of LBL supplementation (0%, 3%, 6%, 9%, and 12%) to evaluate growth performance and nutrient apparent digestibility. Rumen fluid samples were collected for analysis of the fermentation parameters and rumen chyme was examined to study the rumen microbiota. The slaughter performance, meat quality, and organ index were evaluated at the conclusion of the experiment. The results showed that the final body weight and average daily gain of the LBL1 group were significantly higher than those of the CON group, LBL3 group, and LBL4 group (p < 0.05). The average dry matter intake of the LBL4 group was significantly lower than that of other experimental groups (p < 0.05). The apparent digestibility of CP in the LBL1 and LBL2 groups was higher than that in other experimental groups (p < 0.05). At the same time, the eye muscle area and grade-rule (GR) value of Hu sheep in the LBL1 group significantly increased and the quality of Hu sheep meat improved (p < 0.05). There was no significant difference in organ weight and organ index between the experimental groups (p > 0.05). The pH of the rumen fluid in the LBL1 group was significantly lower than that in the CON group (p < 0.05). There was no significant difference in the NH3-N content between the experimental groups (p > 0.05). The propionate and valerate in the rumen fluid of Hu sheep in the LBL2 group were significantly higher than those in other experimental groups (p < 0.05). In addition, this had no significant effect on the structure and abundance of the rumen microbiota (p > 0.05). LBL is a promising functional feed. Adding an appropriate amount of LBL to the diet can improve the feed efficiency, growth performance, and meat quality of Hu sheep but has no adverse effects on the rumen. In this experiment, the appropriate supplemental level of LBL in the diet was 3%.

Effects of Palm Oil Deodorizer Distillate on the Ruminal Environment of Sheep

This study aimed to assess the impact of palm oil deodorizer distillate (POD) on the ruminal environment, including (i) microbial community, (ii) ruminal degradability, and (iii) apparent digestibility in sheep. The data used were derived from twenty rumen-cannulated sheep fed five isoproteic and isofiber diets based on elephant grass (Pennisetum purpureum Schum. cv. Roxo) silage supplemented with 0, 25, 50, 75, or 100 g kg-1 POD on a dry matter (DM) basis. Rumen fluid samples were collected three hours after feeding directly from the ventral sac of the rumen via a cannula and then subjected to DNA extraction, which was subsequently used for 16S rDNA amplification, followed by sequencing and diversity analysis. In this study, the microbial diversity was dominated by Bacteroidetes and Firmicutes, followed by Euryarchaetoa, Actinobacteria, and Tenericutes, in the ruminal environment, and was slightly modified when supplemented with the POD up to 100 g/kg (10%), leading to only a slight decrease in the diversity index. The ruminal degradability, ruminal fermentation parameters, and apparent digestibility were slightly compromised by the inclusion of up to 25 g of POD per kg of DM, and larger inclusions interfered with the ruminal degradability of fibrous fractions and the apparent digestibility of dry matter. This lipid supplement showed good results for feeding sheep and is an inexpensive and abundant alternative in the regional market.

Performance responses of lactating Rahmani ewes fed diet supplemented with Enterococcus faecium NRC-3 or Lactobacillus rhamnosus

Production of new types of probiotics for animal nutrition mainly depends on the appropriate bacterial strain and efficient substrate. Therefore, this study aimed to evaluate the impact of two probiotic strains containing 1.2 × 108 (CFU/g), produced on permeate media on performance responses of Rahmani ewes. Thirty early lactating ewes (about 2-3 years old and weighting on average 43.2 ± 0.3 kg) were randomly divided into three groups of 10 animals each using a completely randomized design. The 1st group was fed the basal diet (60% concentrate feed mixture (CFM) + 30% Egyptian clover + 10% bean straw). While the ewes in 2nd and 3rd groups were fed the basal diet + 2 g of Enterococcus faecium NRC-3(EF) and Lactobacillus rhamnosus (LR), respectively for 9 weeks. Ewes' diet supplementation with EF or LR increased (p < 0.05) dry matter, organic matter, crude protein, neutral detergent fiber, acid detergent fiber, and non-structural carbohydrates digestibility compared to ewes of the control group. Glucose, total protein, and albumin concentrations significantly increased in the blood of EF ewes than those of LR and control. Probiotics increased ewes' milk yield as well as milk protein, fat, and lactose yields, but no differences were observed between treatments when milk components were expressed as percentage. Milk fatty acids profile not changed due to EF or LR supplementation. Probiotics (E. faecium and L. rhamnosus) produced on cheese industry waste (permeate) have proven their ability to improve the productive performance of the lactating Rahmani ewes.

'Multi-omics' data integration: applications in probiotics studies

The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.

The gas production, ruminal fermentation parameters, and microbiota in response to Clostridium butyricum supplementation on in vitro varying with media pH levels

The aim of this study was to investigate the gas production (GP), dry matter disappearance (DMD), fermentation parameters, and rumen microbiota in response to Clostridium butyricum (CB) supplementation in batch culture using a high forage substrate. The doses of CB were supplemented at 0 (Control), 0.5 × 10⁶, 1 × 10⁶, and 2 × 10⁶  CFU/bottle, respectively, at either media pH 6.0 or pH 6.6. The 16S rRNA gene sequencing was used to detect the microbiota of fermentation culture in control and 1 × 10⁶  CFU/bottle after 24 h of incubation. The results showed that the GP (p < 0.001), DMD (p = 0.008), total volatile fatty acid (VFA) concentration (p < 0.001), acetate to propionate ratio (p < 0.001), and NH₃-N concentration (p < 0.001) were greater at media pH 6.6 than pH 6.0. Furthermore, the linearly increased DMD (pH 6.0, p = 0.002; pH 6.6, p < 0.001) and quadratically increased butyrate proportion (pH 6.0, p = 0.076; pH 6.6, p < 0.053) and NH₃-N concentration (pH 6.0, p = 0.003; pH 6.6, p = 0.014) were observed with increasing doses of CB. The Alpha diversity indexes of OTU number and Chao1 were higher (p = 0.045) at media pH 6.6 than pH 6.0, but they were not affected by CB supplementation. The PCoA analysis (unweighted uniFrac) demonstrated that the clustering of the bacterial microbiota of control and CB were distinctly separated from each other at media pH 6.0. At the phylum level, the abundance of Bacteroidota (p < 0.001) decreased, whereas that of Firmicutes (p = 0.026) increased when the media pH was elevated from 6.0 to 6.6. Supplementation of CB increased relative abundances of Rikenellaceae_RC9_gut_group (p = 0.002), Christensenellaceae_R-7_group (p < 0.001), and NK4A214_group (p = 0.002) at genus level. Interactions between media pH and CB addition were observed for bacteria at both phylum and genus levels. These results indicated that increasing the media pH level and CB supplementation increased in vitro rumen digestibility, and altered the ruminal fermentation pattern (by media pH) and microbiota.

Enteric Methane Emission, Rumen Fermentation and Microbial Profiles of Meat-Master Lambs Supplemented with Barley Fodder Sprouts

This study evaluated the effects of barley sprout on the ruminal fermentation characteristics, enteric methane emission and microbiome profiles of meat-master lambs. Twelve uncastrated lambs aged 3 months were used. They were randomly assigned to three dietary treatments: Eragrostis curvula hay as a control diet (T1), grass hay plus 25% barley sprouts (T2) and grass hay plus 50% barley sprouts (T3). Animals were fed the diet for 61 days, including 10 days of adaptation. Four animals per treatment were used to collect methane and rumen fluid. Methane emission was recorded for nine consecutive days, from day 52 to 60, using a hand-held laser detector. Rumen fluid was collected on day 61 using an esophageal stomach tube for volatile fatty acid and DNA sequencing. The sprout supplementation had significant (p < 0.05) effects on methane emission and ruminal fermentation. Significant effects on rumen fermentation were observed with regards to ammonia–nitrogen (NH3-N), acetic acid and a tendency (p < 0.0536) to increase propionic acid. Barley sprouts reduced methane gas emission, ammonia–nitrogen and the enhanced body weight of the animals. The bacteria Bacteroidota and Firmicutes were predominant among the identified phyla. In addition, there was a shift in the relative abundance of phylum among the treatments. The principal coordinate analysis showed a clear difference in microbiome among animals in T1 and those in T2 and T3. The sprout supplementation improves feed utilization efficiency by the animals. In conclusion, barley sprouts may be strategically used as a climate-smart feed resource for ruminants.

Impact of Probiotics on Dairy Production Efficiency

There has been growing interest on probiotics to enhance weight gain and disease resistance in young calves and to improve the milk yield in lactating animals by reducing the negative energy balance during the peak lactation period. While it has been well established that probiotics modulate the microbial community composition in the gastrointestinal tract, and a probiotic-mediated homeostasis in the rumen could improve feed conversation competence, volatile fatty acid production and nitrogen flow that enhances the milk composition as well as milk production, detailed changes on the molecular and metabolic level prompted by probiotic feed additives are still not understood. Moreover, as living biotherapeutic agents, probiotics have the potential to directly change the gene expression profile of animals by activating the signalling cascade in the host cells. Various direct and indirect components of probiotic approaches to improve the productivity of dairy animals are discussed in this review.

Formulation of Chemically Defined Media and Growth Evaluation of Ligilactobacillus salivarius ZJ614 and Limosilactobacillus reuteri ZJ625

Lactic acid bacteria are increasingly becoming important dietary supplements due to their health benefits when consumed in adequate quantity. The increasing attention on these important microbes has necessitated an in-depth understanding of their physiological processes, such as nutritional requirements and growth patterns, to better harness their probiotic potentials. This study was carried out to determine the nutritional requirements for the growth of L. salivarius ZJ614 and L. reuteri ZJ625 from a chemically defined medium and evaluate growth kinetics by fitting different sigmoidal growth models. The complete CDM contains 49 nutritional ingredients such as glucose, Tween 80^®, mineral salts, buffers, amino acids, vitamins, and nucleotides at defined concentrations. In addition, the minimal nutritional requirements of the isolates were determined in a series of single-omission experiments (SOEs) to compose the MDM. Growth curve data were generated by culturing in an automated 96-well micro-plate reader at 37°C for 36 h, and photometric readings (optical density: OD₆₀₀) were taken. The data were summarized in tables and charts using Microsoft Excel, while growth evaluation was carried out using open-source software (Curveball) on Python. The results revealed that omission of the amino acids, vitamins, and nucleotides groups resulted in 2.0, 20.17, and 60.24% (for L. salivarius ZJ614) and 0.95, 42.7, and 70.5% (for L. reuteri ZJ625) relative growths, respectively. Elimination of the individual CDM components also indicates varying levels of growth by the strains. The growth curve data revealed LogisticLag2 and Baranyi–Roberts models as the best fits for L. reuteri ZJ625 and L. salivarius ZJ614, respectively. All the strains showed appreciable growth on the CDM and MDM as observed in de Man–Rogosa–Sharpe (MRS) broth. We also described the growth kinetics of L. reuteri ZJ625 and L. salivarius ZJ614 in the CDM, and the best models revealed the estimated growth parameters.

Biological Functions of Exopolysaccharides from Lactic Acid Bacteria and Their Potential Benefits for Humans and Farmed Animals

Lactic acid bacteria (LAB) synthesize exopolysaccharides (EPS), which are structurally diverse biopolymers with a broad range of technological properties and bioactivities. There is scientific evidence that these polymers have health-promoting properties. Most commercialized probiotic microorganisms for consumption by humans and farmed animals are LAB and some of them are EPS-producers indicating that some of their beneficial properties could be due to these polymers. Probiotic LAB are currently used to improve human health and for the prevention and treatment of specific pathologic conditions. They are also used in food-producing animal husbandry, mainly due to their abilities to promote growth and inhibit pathogens via different mechanisms, among which the production of EPS could be involved. Thus, the aim of this review is to discuss the current knowledge of the characteristics, usage and biological role of EPS from LAB, as well as their postbiotic action in humans and animals, and to predict the future contribution that they could have on the diet of food animals to improve productivity, animal health status and impact on public health.

Association between host genetics of sheep and the rumen microbial composition

A synergy between the rumen microbiota and the host genetics has created a symbiotic relationship, beneficial to the host's health. In this study, the association between the host genetics and rumen microbiome of Damara and Meatmaster sheep was investigated. The composition of rumen microbiota was estimated through the analysis of the V3-V4 region of the 16S rRNA gene, while the sheep blood DNA was genotyped with Illumina OvineSNP50 BeadChip and the genome-wide association (GWA) was analyzed. Sixty significant SNPs dispersed in 21 regions across the Ovis aries genome were found to be associated with the relative abundance of seven genera: Acinetobacter, Bacillus, Clostridium, Flavobacterium, Prevotella, Pseudomonas, and Streptobacillus. A total of eighty-four candidate genes were identified, and their functional annotations were mainly associated with immunity responses and function, metabolism, and signal transduction. Our results propose that those candidate genes identified in the study may be modulating the composition of rumen microbiota and further indicating the significance of comprehending the interactions between the host and rumen microbiota to gain better insight into the health of sheep.

Effects of Management, Dietary Intake, and Genotype on Rumen Morphology, Fermentation, and Microbiota, and on Meat Quality in Yaks and Cattle

Traditionally, yaks graze only natural grassland, even in harsh winters. Meat from grazing yaks is considered very healthy; however, feedlot fattening, which includes concentrate, has been introduced. We questioned whether this change in management and diet would have an impact on the rumen and meat quality of yaks. This study examined the morphology, fermentation, and microbiota of the rumen and the quality of meat of three groups of bovines: (1) grazing yaks (GYs, 4-year olds), without dietary supplements; (2) yaks (FYs, 2.5-year olds) feedlot-fattened for 5 months after grazing natural pasture; and (3) feedlot-fattened cattle (FC, Simmental, 2-year olds). This design allowed us to determine the role of diet (with and without concentrate) and genotype (yaks vs. cattle) on variables measured. Ruminal papillae surface area was greater in the FYs than in the GYs (P = 0.02), and ruminal microbial diversity was greater but richness was lesser in the GYs than in the FC and FYs. Concentrations of ruminal volatile fatty acids were greater in the yaks than in the cattle. In addition, both yak groups had higher protein and lower fat contents in meat than the FC. Meat of GY had a lower n6:n3 ratio than FY and FC, and was the only group with a ratio below r, which is recommended for healthy food. Essential amino acids (EAA), as a proportion of total AA and of non-essential AA of yak meat, met WHO criteria for healthy food; whereas FC did not.

The Impact of Host Genotype, Intestinal Sites and Probiotics Supplementation on the Gut Microbiota Composition and Diversity in Sheep

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Effects of Lactobacillus rhamnosus and Enterococcus faecalis Supplementation as Direct-Fed Microbials on Rumen Microbiota of Boer and Speckled Goat Breeds

The effects on rumen microbial communities of direct-fed probiotics, Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination as feed supplements to both the Boer and Speckled goats were studied using the Illumina Miseq platform targeting the V3-V4 region of the 16S rRNA microbial genes from sampled rumen fluid. Thirty-six goats of both the Boer and Speckled were divided into five experimental groups: (T1) = diet + Lactobacillus rhamnosus; (T2) = diet + Enterococcus faecalis; (T3) = diet + Lactobacillus rhamnosus + Enterococcus faecalis; (T4, positive control) = diet + antibiotic and (T5, negative control) = diet without antibiotics and without probiotics. Our results revealed that Bacteroidetes, Firmicutes, TM7, Proteobacteria, and Euryarchaeota dominate the bacterial communities. In our observations, Lactobacillus rhamnosus and Enterococcus faecalis supplements reduced the archaeal population of Methanomassiliicocca in the T1, T2 and T3 groups, and caused an increase in the T4 group. Chlamydiae were present only in the T5 group, suggesting that probiotic and antibiotic inhibit the growth of pathogens in the rumen. We inferred, based on our results, that Lactobacillus rhamnosus and Enterococcus faecalis favour the survival of beneficial microbial communities in the goats’ rumen. This may lead to an overall improved feed efficacy and growth rate.