Rumen Microbiome, Probiotics, and Fermentation Additives

Postbiotics from Saccharomyces cerevisiae fermentation stabilize microbiota in rumen liquid digesta during grain-based subacute ruminal acidosis (SARA) in lactating dairy cows

BACKGROUND

Subacute ruminal acidosis (SARA) is a common metabolic disorder of high yielding dairy cows, and it is associated with dysbiosis of the rumen and gut microbiome and host inflammation. This study evaluated the impact of two postbiotics from Saccharomyces cerevisiae fermentation products (SCFP) on rumen liquid associated microbiota of lactating dairy cows subjected to repeated grain-based SARA challenges. A total of 32 rumen cannulated cows were randomly assigned to 4 treatments from 4 weeks before until 12 weeks after parturition. Treatment groups included a Control diet or diets supplemented with postbiotics (SCFPa, 14 g/d Original XPC; SCFPb-1X, 19 g/d NutriTek; SCFPb-2X, 38 g/d NutriTek, Diamond V, Cedar Rapids, IA, USA). Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% DM of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. Total DNA from rumen liquid samples was subjected to V3-V4 16S rRNA gene amplicon sequencing. Characteristics of rumen microbiota were compared among treatments and SARA stages.

RESULTS

Both SARA challenges reduced the diversity and richness of rumen liquid microbiota, altered the overall composition (β-diversity), and its predicted functionality including carbohydrates and amino acids metabolic pathways. The SARA challenges also reduced the number of significant associations among different taxa, number of hub taxa and their composition in the microbial co-occurrence networks. Supplementation with SCFP postbiotics, in particular SCFPb-2X, enhanced the robustness of the rumen microbiota. The SCFP supplemented cows had less fluctuation in relative abundances of community members when exposed to SARA challenges. The SCFP supplementation promoted the populations of lactate utilizing and fibrolytic bacteria, including members of Ruminococcaceae and Lachnospiraceae, and also increased the numbers of hub taxa during non-SARA and SARA stages. Supplementation with SCFPb-2X prevented the fluctuations in the abundances of hub taxa that were positively correlated with the acetate concentration, and α- and β-diversity metrics in rumen liquid digesta.

CONCLUSIONS

Induction of SARA challenges reduced microbiota richness and diversity and caused fluctuations in major bacterial phyla in rumen liquid microbiota in lactating dairy cows. Supplementation of SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.

Postnatal Growth and Development of the Rumen: Integrating Physiological and Molecular Insights

The rumen plays an essential role in the physiology and production of agriculturally important ruminants such as cattle. Functions of the rumen include fermentation, absorption, metabolism, and protection. Cattle are, however, not born with a functional rumen, and the rumen undergoes considerable changes in size, histology, physiology, and transcriptome from birth to adulthood. In this review, we discuss these changes in detail, the factors that affect these changes, and the potential molecular and cellular mechanisms that mediate these changes. The introduction of solid feed to the rumen is essential for rumen growth and functional development in post-weaning calves. Increasing evidence suggests that solid feed stimulates rumen growth and functional development through butyric acid and other volatile fatty acids (VFAs) produced by microbial fermentation of feed in the rumen and that VFAs stimulate rumen growth and functional development through hormones such as insulin and insulin-like growth factor I (IGF-I) or through direct actions on energy production, chromatin modification, and gene expression. Given the role of the rumen in ruminant physiology and performance, it is important to further study the cellular, molecular, genomic, and epigenomic mechanisms that control rumen growth and development in postnatal ruminants. A better understanding of these mechanisms could lead to the development of novel strategies to enhance the growth and development of the rumen and thereby the productivity and health of cattle and other agriculturally important ruminants.

Yeast culture repairs rumen epithelial injury by regulating microbial communities and metabolites in sheep

This study delves into the impact of yeast culture (YC) on rumen epithelial development, microbiota, and metabolome, with the aim of investigating YC's mechanism in regulating rumen fermentation. Thirty male lambs of Hu sheep with similar age and body weight were selected and randomly divided into three groups with 10 lambs in each group. Lambs were fed a total mixed ration [TMR; rough: concentrate (R:C) ratio ≈ 30:70] to meet their nutritional needs. The experiment adopted completely randomized design (CRD). The control group (CON) was fed the basal diet with high concentrate, to which 20 g/d of YC was added in the low dose YC group (LYC) and 40 g/d of YC in the high dose YC group (HYC). The pretrial period was 14 days, and the experimental trial period was 60 days. At the end of a 60-day trial, ruminal epithelial tissues were collected for histomorphological analysis, and rumen microorganisms were analyzed by 16S rDNA sequencing and rumen metabolites by untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics techniques. The results showed that YC improved rumen papilla development and increased rumen papilla length (p < 0.05), while decreased cuticle thickness (p < 0.05). The 16S rDNA sequencing results showed that YC reduced the relative abundance of Prevotella_1 (p < 0.05), while significantly increased the relative abundance of Ruminococcaceae_UCG-005, uncultured_bacterium_f_Lachnospiraceae, and Ruminococcus_1 genus (p < 0.05). Metabolomics analysis showed that YC changed the abundance of metabolites related to amino acid metabolism, lipid metabolism and vitamin metabolism pathways in the rumen. In summary, YC might maintain rumen health under high-concentrate diet conditions by changing rumen microbiota structure and fermentation patterns, thereby affecting rumen metabolic profiles and repairing rumen epithelial injury.

Microbiome-transcriptome analysis reveals that dietary supplementation with macleaya cordata extract alters multiple immune pathways with minimal impact on microbial structure

Background

As a potential antibiotic alternative, macleaya cordata extract (MCE) has anti-inflammatory, antioxidant, and antimicrobial properties. This study was conducted to assess the impact of MCE supplementation on the gut microbiota and its interplay with the host in young goats. Thirty female black goats with similar body weight (5.63 ± 0.30 kg) were selected and randomly allotted into one of three diets: a control diet (Control), a control diet with antibiotics (Antibiotics, 21 mg/kg/day vancomycin and 42 mg/kg/day neomycin), and a control diet with MCE (MCE, 3.75% w/w premix).

Results

Principal coordinate analysis of the microbial community showed that samples of Antibiotic clustered separately from both Control and MCE (p < 0.001). The random forest analysis revealed that, in comparison to the Control group, the impact of Antibiotics on the microbiota structure was more pronounced than that of MCE (number of featured microbiota, 13 in Antibiotics and >6 in MCE). In addition, the pathways of significant enrichment either from DEGs between Antibiotics and Control or from DEGs between MCE and Control were almost identical, including Th17 cell differentiation, butanoate metabolism, T-cell receptor signaling pathway, intestinal immune network for IgA production, antigen processing and presentation, and ABC transporters. Furthermore, an integrative analysis indicated that significant positive correlations (p < 0.05) were observed between HEPHL1 and the featured biomarkers Atopostipes, Syntrophococcus, Romboutsia, and Acinetobacter in the MCE group. Conversely, several significant negative correlations (p < 0.05) were identified between HEPHL1 and the featured biomarkers Clostridium_XlVa, Phascolarctobacterium, Desulfovibrio, Cloacibacillus, Barnesiella, Succinatimonas, Alistipes, Oscillibacter, Ruminococcus2, and Megasphaera in the Antibiotics group.

Conclusion

Collectively, the analysis of microbiome-transcriptome data revealed that dietary supplementation with MCE produced significant alterations in multiple immune pathways, while having minimal impact on the microbial structure.

Lactobacillus rhamnosus GG ATCC53103 and Lactobacillus plantarum JL01 improved nitrogen metabolism in weaned piglets by regulating the intestinal flora structure and portal vein metabolites

At present, most studies have shown that probiotics have a positive regulatory effect on the nutritional metabolism of the body, but the mechanism is still unclear. Here, 48 piglets were divided into four groups. The control group was not fed probiotics, the Lac group was fed L. Rhamnosus GG ATCC53103, the Rha group was fed L. Plantarum JL01, and the mix group was fed two types of probiotics. Nitrogen metabolism and mRNA levels of mTOR and S6K in skeletal muscle were observed in each group. Then, metagenome and non-targeted metabonomics were used to observe the changes of intestinal microorganisms and plasma metabolites in portal channels after probiotics feeding. Finally, we combined the results of omics analysis to reveal the mechanism of probiotics on nitrogen metabolism in weaned piglets. The results showed that L. Rhmnosus GG ATCC53103 and L. Plantarum JL01 increased nitrogen apparent digestibility, nitrogen deposition rate, and nitrogen utilization rate of weaned piglets (P < 0.05); the relative expression of mTOR and SK6 mRNA in skeletal muscle increased significantly (P < 0.05). When L. rhamnosus GG ATCC53103 and L. plantarum JL01 were combined, we found that Clostridium and Prevotella significantly increased in the jejunum (P < 0.05). The relative abundance of Lactobacillus, Ruminococcus, Streptococcus, and Prevotella in the ileum increased significantly (P < 0.05). Compared with the control group, L-Tryptophan, 3-Phosphonyloxypyruvate, cis-Aconitate, and Carbamoyl phosphate were significantly increased in the mixed group portal vein. The result of the combinatorial analysis showed that the significantly increased microorganisms could encode the enzyme genes for the synthesis of L-Tryptophan, 3-Phosphonooxypyruvate, cis-Aconitate, and Carbamoyl phosphate. In summary, our results demonstrated that L. Rhamnosus GG ATCC53103 and L. Plantarum JL01 could stimulate the expression of skeletal muscle protein synthesis genes of weaned piglets by modulating the structure of the gut microbiota and its metabolites, thereby improving nitrogen metabolism in weaned piglets.

Candida tropicalis as a novel dietary additive to reduce methane emissions and nitrogen excretion in sheep

The goal of this study was to investigate Candida tropicalis as a kind of environmentally friendly dietary additive to manipulate ruminal fermentation patterns, reduce methane emissions and nitrogen excretion, and to screen the appropriate dose for sheep. Twenty-four Dorper × thin-tailed Han crossbred ewes (51.12 kg ± 2.23 kg BW) were selected and randomly divided into four groups which were fed Candida tropicalis at dose of 0 (control), 4 × 10⁸ (low dose), 4 × 10⁹ (medium dose), and 4 × 10¹⁰ (high dose) colony-forming units (CFU)/d per head, respectively. The experiment lasted 33 days with 21 days for adaptation and 12 days for nutrient digestibility trial and respiratory gases sampling. The results showed that nutrients intake was not affected by Candida tropicalis supplementation (P > 0.05), whereas apparent digestibility of nutrients significantly increased compared with the control group (P < 0.05). Nitrogen and energy utilization increased with Candida tropicalis supplementation (P < 0.05). Compared with the ewes of the control group, rumen fluid pH and NH₃-N concentration were not affected (P > 0.05), whereas total volatile fatty acid concentration and molar proportion of propionate were greater (P < 0.05), and molar proportion of acetate and the ratio of acetate to propionate were less (P < 0.05) when the ewes were fed Candida tropicalis. Daily total CH₄ production (L/d) and CH₄ emissions yield (L/d of CH₄ per kg of dry matter intake, metabolic weight, or digestibility dry matter intake) were decreased at the low dose group (P < 0.05). The abundance of total bacteria, methanogen, and protozoa in rumen fluid was significantly higher at medium dose and high dose of Candida tropicalis supplementation (P < 0.05) compared with low dose and the control group. In summary, Candida tropicalis supplementation has a potential to reduce CH₄ emissions and nitrogen excretion, and the optimal dose should be 4 × 10⁸ CFU/d per head.

Evaluation of a Colombian oregano oil (Lippia origanoides Kunth) and a novel yeast product from Pichia guilliermondii, alone or in combination, on rumen fermentation, methanogenesis and the microbiome in the rumen simulation technique

In this study, Lippia origanoides Kunth, native to the Alto Patía region in Southwest Colombia, and Pichia guilliermondii LV196, an inactivated yeast from the germplasm bank of Agrosavia (Colombian Agricultural Research Corporation), alone or combined, were tested for their long-term effect on rumen fermentation and methanogenesis whilst also characterising their effect on bacterial and methanogen communities. Whereas essential oils act through selective inhibition of microbial groups, yeasts are thought to work through the selective stimulation of key microbes in the rumen. We hypothesized that yeast supplementation could modulate the antimicrobial effect of a high thymol-containing oregano oil, allowing a more efficient feed utilization whilst decreasing methane production. When added to a rumen simulating fermentor (RUSITEC), L. origanoides Kunth at 132 µL/d had a detrimental effect on rumen fermentation which was accompanied by a reduction in the relative abundance of protozoa and fungi and a profound impact on the bacterial and archaeal communities. P. guilliermondii LV196 at 0.5 g/L, however, had no effect on fermentation parameters or nutrient utilization, and neither changes in microbial abundances or in the structure of bacterial and archaeal communities were observed. P. guilliermondii LV196 did not stimulate microbial numbers nor activity and, consequently we could not test whether it could have counterbalanced the antimicrobial effect of the essential oil. Future studies need to both investigate lower levels of essential oil addition, but also to re-examine the effects of P. guillermondii in the rumen and/or to replace it with other yeast of known biological activity when combined with oils extracted from L. origanoides Kunth.

Microbiome-Metabolome Responses in Ruminal Content and Feces of Lactating Dairy Cows With N-Carbamylglutamate Supplementation Under Heat Stress

The objective of the present study was to investigate the effects of N-carbamylglutamate (NCG) supplementation on metabolic profile and microbiota in ruminal content and feces of lactating dairy cows under heat stress (HS). Forty-eight lactating Holstein cows (154 ± 13.6 days in milk) were assigned randomly to four treatments (n = 12), to receive 0, 15, 20, or 25 g/day of commercial NCG (proportion: 97.7%) for the period of 60 days. The recorded ambient temperature–humidity index (THI) suggested that the cows were exposed to HS for almost the entire experimental period (average THI: 80.6). Samples of ruminal content and feces were collected at the end of the trial (day 60) to determine the biological effects of NCG supplementation on metabolome and microbiota using mass spectrometry-based metabolomics and 16S rRNA gene sequencing techniques, respectively. Results showed that NCG supplementation enhanced the levels of ruminal microbial protein, total volatile fatty acids (VFAs), and the molar proportion of propionate in the rumen, but lowered the ruminal pH, ammonia nitrogen (NH3-N), and the ratio of acetate to propionate. NCG at doses of 20 and 25 g/day reduced the community richness and diversity of ruminal microbiota with the decrease of Shannon and Simpson diversity. Compositions of ruminal and fecal microbiotas were altered by NCG, and the PICRUSt results revealed that metabolic pathways of the bacteria, such as amino acid metabolism, energy metabolism, and pyruvate metabolism, were enriched in NCG groups. Distinct changes in the metabolomic profile of ruminal fluid were observed between the control and NCG groups. Changes of 26 metabolites mainly involved in arginine metabolism, glutamate metabolism, and nitrogen metabolism were observed associated with NCG supplementation. These results provided new insights into the effects of NCG on metabolomic profile and microbiota in ruminal content and feces, and the optimal dose of NCG supplemented to dairy cows was 20 g/hd/day, which contributed to understanding the effects of NCG on HS in lactating dairy cows.

Screening of Candidate Bioactive Secondary Plant Metabolite Ion-Features from Moringa oleifera Accessions Associated with High and Low Enteric Methane Inhibition from Ruminants

This study evaluated the relationship of secondary bioactive plant metabolite ion-features (MIFs) of Moringa oleifera accessions with antimethanogenesis to identify potential MIFs that were responsible for high and low methane inhibition from ruminants. Plant extracts from 12 Moringa accessions were evaluated at a 50 mg/kg DM feed for gas production and methane inhibition. Subsequently, the accessions were classified into low and high enteric methane inhibition groups. Four of twelve accessions (two the lowest and two the highest methane inhibitors), were used to characterize them in terms of MIFs. A total of 24 samples (12 from lower and 12 from higher methane inhibitors) were selected according to their methane inhibition potential, which ranged from 18% to 29%. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and untargeted metabolomics with univariate and multivariate statistical analysis with MetaboAnalyst were used in the study. Although 86 MIFs showed (p < 0.05) variation between higher and lower methane inhibition groups and lay within the detection ranges of the UPLC-MS column, only 14 were significant with the volcano plot. However, Bonferroni correction reduced the candidate MIFs to 10, and their R2-value with methane production ranged from 0.39 to 0.64. Eventually, MIFs 4.44_609.1462 and MIF 4.53_433.1112 were identified as bioactive MIFs associated with higher methane inhibition, whereas MIF 9.06_443.2317 and 15.00_487.2319 were associated with lower methane inhibition with no significant effect on in vitro organic matter digestibility of the feed. These MIFs could be used by plant breeders as potential markers to develop new M. oleifera varieties with high methane inhibition characteristics. However, further investigation on identifying the name, structure, and detailed biological activities of these bioactive metabolites needs to be carried out for future standardization, commercialization, and application as dietary methane mitigation additives.

Characterization and Comparison of the Rumen Luminal and Epithelial Microbiome Profiles Using Metagenomic Sequencing Technique

Bacterial dysbiosis as a result of nutritional, bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health of cattle. The purpose of this project was to characterize the commensal microbiota present in two locations of the rumen concomitantly in vivo with the animals undergoing habitual husbandry, as it was hypothesized that there are major differences in the commensal microbiota present in the two locations of the adult bovine major forestomach. A surgically fitted rumen cannula was used to allow ruminal lumen contents and mucosal biopsies to be collected from six crossbred yearling steers. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was randomly sampled three times over a 3 week period. 16S rRNA sequencing was performed to provide a detailed descriptive analysis from phylum to genus taxonomic level. Significant differences were observed between luminal and epimural bacterial populations in the bovine rumen. As expected, a core microbiome composed by Firmicutes and Bacteroidetes represented over 90% of the microbiome, however, further analysis showed distinct diversity and distribution of the microbiome between the two locations. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty and the contribution of this study to the literature is the use of live cattle which allowed real-time sample collections and analysis of the rumen microbiome providing an understanding of what is normal in the live animal.

O efeito de probióticos fúngicos adicionados a uma dieta rica em grãos no trato gastrointestinal de ovinos

Resumo Objetivou-se avaliar as características microbiológicas e físico-químicas do fluido ruminal e histológicas do trato gástrico intestinal (TGI) de ovinos sob dieta de alto grão com probiótico fungos Aspergillus terreus e/ou Rhizomucor spp. Analisou-se quatro probióticos (sem inóculos, com Rhizomucor spp., com Aspergillus terreus e com mistura dos dois fungos) e dois processamentos de milho (moído/inteiro), em fatorial 4x2 em em Delineamento Inteiramente Casualizados (DIC). Borregos Santa Inês/Dorper foram alojados em oito baias com cinco borregos em cada, durante 75 dias. Coletou-se fluido ruminal para o estudo do perfil microbiológico do rúmen, da característica macroscópica, da concentração de nitrogênio amoniacal e da atividade microbiológica, além dos fragmentos do TGI para análises histológicas. Pelas análises dos fluidos, os animais apresentaram baixo índice de acidose. O odor aromático e a cor castanho-enegrecido predominaram, o que caracteriza ambiente com pH neutro. As amostras do fluido apresentaram alta atividade microbiana. O pH ruminal diferenciou-se (P<0,05) quanto ao tipo de processamento, sendo maior para milho grão moído (MGM). Não houve diferença para nenhuma das comunidades microbiológicas analisadas (P>0,05) (bactérias Lac+ e Lac-, fungos, leveduras e protozoários). Seis gêneros de fungos anaeróbicos facultativos foram identificados num total de 15 observações. O Cladosporium spp. foi o gênero mais prevalente (46,66%), seguido do Aspergillus spp. (26,66%). A largura da base das papilas ruminais apresentou interação significativa, sendo maior para MGM (P<0,05) com Rhizomucor e o controle (P<0,05). O fluido ruminal de ovinos sob dieta de alto concentrado de grão com adição dos fungos Aspergillus terreus e Rhizomucor spp. não tiveram afetadas as características microbiológicas e físico-químicas.

The effect of fungal probiotics added to a high-grain diet on the gastrointestinal tract of sheep

Abstract This study aimed to evaluate the microbiological and physicochemical characteristics of the ruminal fluid and histological characteristics of the gastrointestinal tract (GIT) of sheep on a high-grain diet containing the probiotic fungi Aspergillus terreus and Rhizomucor spp. The study included four treatment groups (without probiotic, with Rhizomucor spp., with Aspergillus terreus, and with a mixture of both fungi), and two types of corn (ground/whole), in a Completely Randomized Design (CRD) arranged in 4 x 2 factorial design. Santa Inês x Dorper lambs were housed in eight pens with five lambs each for 75 days. Rumen fluid was collected to study the rumen microbiological profile, macroscopic characteristics, ammonia nitrogen concentration, and microbiological activity. In addition, GIT samples were taken for histological analysis. Fluid analyses showed that the animals presented a low acidosis index. The samples presented a predominantly aromatic odor and blackish-brown color, indicating a neutral pH and high microbial activity. The rumen pH differed (P < 0.05) according to the level of processed corn consumed, being higher for ground grain corn (GGC). There was no difference for any of the microbiological communities analyzed (P > 0.05) (Lac+ and Lac- bacteria, fungi, yeasts, and protozoa). Six genera of facultative anaerobic fungi were identified in 15 observations. Cladosporium spp. was the most prevalent genus (46.66%), followed by Aspergillus spp. (26,66%). The width of the base of rumen papillae showed significant correlation being greater for GCG (P < 0.05) with Rhizomucor and for the control (P < 0.05). The rumen fluid of sheep on a high-grain diet with added Aspergillus terreus and Rhizomucor spp. showed no microbiological and physicochemical changes.

Adaptively evolved human oral actinomyces-sourced defensins show therapeutic potential

The development of eukaryote‐derived antimicrobial peptides as systemically administered drugs has proven a challenging task. Here, we report the first human oral actinomyces‐sourced defensin—actinomycesin—that shows promise for systemic therapy. Actinomycesin and its homologs are only present in actinobacteria and myxobacteria, and share similarity with a group of ancient invertebrate‐type defensins reported in fungi and invertebrates. Signatures of natural selection were detected in defensins from the actinomyces colonized in human oral cavity and ruminant rumen and dental plaque, highlighting their role in adaptation to complex multispecies bacterial communities. Consistently, actinomycesin exhibited potent antibacterial activity against oral bacteria and clinical isolates of Staphylococcus and synergized with two classes of human salivary antibacterial factors. Actinomycesin specifically inhibited bacterial peptidoglycan synthesis and displayed weak immunomodulatory activity and low toxicity on human and mammalian cells and ion channels in the heart and central nervous system. Actinomycesin was highly efficient in mice infected with Streptococcus pneumoniae and mice with MRSA‐induced experimental peritoneal infection. This work identifies human oral bacteria as a new source of systemic anti‐infective drugs.

Comparative Analysis of the Microbiota Between Rumen and Duodenum of Twin Lambs Based on Diets of Ceratoides or Alfalfa

In our previous study, diet directly impacted the microbiota of the rumen in twin lambs. The duodenum is the first part of the small intestine, so we seek to determine whether there is a difference in the digesta between the two feed groups HFLP (high fiber, low protein) and LFHP (low fiber, high protein), and its impact on the biodiversity and metabolism of the duodenum. Results showed that the number of Operational Taxonomic Units (OTUs) in the duodenum (2,373 OTUs) was more than those in the rumen (1,230 OTUs), and 143 OTUs were significantly different in the duodenum between the two groups. The two most predominant phyla were Bacteriodetes and Firmicutes, but this ratio was reversed between the rumen and duodenum of lambs fed different feedstuffs. The difference in the digesta that greatly changed the biodiversity of the rumen and duodenum could affect the microbial community in the gastrointestinal tract (GIT). Sixteen metabolites were significantly different in the duodenum between the two groups based on the metabolome analysis. The relationships were built between the microbiome and the metabolome based on the correlation analysis. Some metabolites have a potential role in influencing meat quality, which indicated that the diet could affect the microbiota community and finally change meat quality. This study could explain how the diet affects the rumen and duodenum’s microbiota, lay a theoretical basis for controlling feed intake, and determine the relationship between the duodenum’s microbiota and metabolism.

Probiotic effect of Bacillus subtilis B-2998D, B-3057D, and Bacillus licheniformis B-2999D complex on sheep and lambs

Objectives:

Probiotics are well documented for their health benefits by developing a balanced intestinal microbiota and boosting immunity. The present study was conducted to determine the effects of a probiotic preparation Enzimsporin^TM (consisting of spore-forming bacteria Bacillus subtilis B-2998D, B-3057D, and Bacillus licheniformis B-2999D) on the biochemical, hematological, immunological parameters, intestinal microbiota, and growth dynamics of sheep and lambs.

Materials and Methods:

Enzimsporin was fed to lambs and sheep at different doses to determine the bacteria’s probiotic effects. Sheep were divided into three groups (six each), which received 0, 1, and 3 gm of Enzimsporin/per head/day, respectively, and two groups of lambs (10 each), who received 0 gm and 1 gm of Enzimsporin/per head/day for 30 days in addition to their regular ration. On day 30, blood samples were collected, followed by the determination of biochemical, hematological, and natural resistance indicators. Fecal samples were examined to determine the intestinal microflora, and animals were weighed daily to determine their growth dynamics.

Results:

Supplementation of probiotics (Enzimsporin^TM) improved the lambs’ body weight gain by 18.8%. Analysis of the clinical parameters showed improvements in the levels of total protein, globulins, and urea by 5.3%, 10.8%, and 6.2%, respectively, in the blood of probiotic-supplemented lambs. Similarly, an increment in the total protein, albumins, and globulins was observed in the sheep with Enzimsporin^TM supplementation. The decrease in bilirubin and cholesterol levels in the blood and increased bactericidal and phagocytic index in the sheep and lambs with probiotic supplementation indicated a positive influence of Enzimsporin^TM on the liver function and natural resistance. Furthermore, an increase in Lactobacillus and Bifidobacterium and a decrease in the Escherichia coli, Enterococcus, and Yeast in the fecal contents of experimental sheep and lambs indicated the potentiality of Enzimsporin^TM on maintaining good gut health.

Conclusion:

Spore-forming bacteria B. subtilis B-2998D, B-3057D, and B. licheniformis B-2999D can be used in feeding sheep and lambs of 2 months of age to increase body weight gain, improve intestinal microbiota, strengthen the immune system, and maintain normal metabolic processes.

Probiotic microorganisms and herbs in ruminant nutrition as natural modulators of health and production efficiency – a review

Probiotics, prebiotics, synbiotics, direct-fed microbials, and herbs may improve the production efficiency in ruminants. The beneficial effect of selected specific microbes on animal health is reflected in protection against pathogens, stimulation of immunological response, increased production capacity, and mitigation of stress effects. Phytobiotic plants used in the nutrition of ruminant animals increase feed palatability. This in turn has a positive effect on feed intake and, consequently, increases production performance. Pectins, terpenes, phenols, saponins, and antibioticlike substances contained in phytobiotics prevent irritation, diarrhea, and increase the activity of digestive enzymes. Thanks to the abundance of biologically active substances such as flavonoids, glycosides, coumarins, carotenoids, polyphenols, etc., phytobiotics exhibit immunostimulatory and antioxidant properties as well. Given such a wide range of effects on health status and production parameters in animals, an attempt was made in this review to compile the current knowledge on the possible application of these natural growth stimulants in ruminant nutrition and to demonstrate their potential benefits and/or risks for breeding these animals.

Ruminal microbiota-host interaction and its effect on nutrient metabolism

Rumen microbiota has a close and intensive interaction with the ruminants. Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host, making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk. Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism. Recently, the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers. This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.

Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing

Background and Aim

Due to the incomplete development of the immune system in immature piglets, the respiratory tract is susceptible to invasion by numerous pathogens that cause a range of potential respiratory diseases. However, few studies have reported the changes in pig lung microorganisms during respiratory infection. Therefore, we aimed to explore the differences in lung environmental microorganisms between healthy piglets and piglets with respiratory diseases.

Materials and Methods

Histopathological changes in lung sections were observed in both diseased and healthy pigs. Changes in the composition and abundance of microbiomes in alveolar lavage fluid from eleven 4-week-old Chinese Kele piglets (three clinically healthy and eight diseased) were studied by IonS5™ XL sequencing of the bacterial16S rRNA genes.

Results

Histopathological sections showed that diseased pigs displayed more lung lesions than healthy pigs. Diseased piglets harbored lower bacterial operational taxonomic units, α-diversity, and bacterial community complexity in comparison to healthy piglets. Taxonomic composition analysis showed that in the diseased piglets, the majority of flora was composed of Ureaplasma, Mycoplasma, and Actinobacillus; while Actinobacillus, Sphingomonas, and Stenotrophomonas were dominant in the control group. The abundance of Ureaplasma was significantly higher in ill piglets (p<0.05), and the phylogenetic tree indicated that Ureaplasma was clustered in Ureaplasma diversum, a conditional pathogen that has the potential to affect the swine respiratory system.

Conclusion

The results of this study show that the microbial species and structure of piglets' lungs were changed during respiratory tract infection. The finding of Ureaplasma suggested that besides known pathogens such as Mycoplasma and Actinobacillus, unknown pathogens can exist in the respiratory system of diseased pigs and provide a potential basis for clinical treatment.

Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle

BACKGROUND

Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear.

RESULTS

In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs' rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs.

CONCLUSION

Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.

Influence of dietary supplementation with Bacillus licheniformis and Saccharomyces cerevisiae as alternatives to monensin on growth performance, antioxidant, immunity, ruminal fermentation and microbial diversity of fattening lambs

Alternatives to antibiotics for improving productivity and maintaining the health of livestock health are urgently needed. The scope of this research was conducted to investigate the effects of two alternatives (Bacillus licheniformis and Saccharomyces cerevisiae) to monensin on growth performance, antioxidant capacity, immunity, ruminal fermentation and microbial diversity of fattening lambs. One hundred and sixty Dorper × Thin-tailed Han sheep (32 ± 3.45 kg BW) were randomly assigned into 5 treatments of n = 32 lambs/group. Lambs in the control group were fed a basal diet (NC) while the other four treatments were fed basal diets supplemented with monensin (PC), Bacillus licheniformis (BL), Saccharomyces cerevisiae (SC), and the combination of Bacillus licheniformis and Saccharomyces cerevisiae with protease (BS), respectively. The experiment lasted for 66 d. Feed intake was recorded every 2 d and lambs were weighed every 20 d. Ten lambs from each group were slaughtered at the end of the trial, and samples of serum and rumen fluid were collected. The results indicated that the dietary regimen did not affect the dry matter intake (DMI). The average daily gain (ADG) of BS treatment was significantly higher than NC group (P < 0.05). Compared with the NC treatment, the other four supplementation treatments increased the concentration of growth hormone (GH), insulin-like growth factor I (IGF-I) and insulin (INS) (P < 0.05). The malondialdehyde (MDA) and total antioxidant capacity (TAOC) showed no significant difference among the 5 treatments while the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) of BS group was significantly increased (P < 0.05). The supplementation regimen decreased the concentration of ammonia Nitrogen (NH3-N) and increased the content of microbial crude proteins (MCP) (P < 0.05). The supplementation of antibiotics and probiotics reduced the concentrations of acetate and increased the concentrations of propionate (P < 0.05). The supplementation treatments increased the relative abundance of Lentisphaerae, Fibrobacteres and Tenericutes at the phylum level, whereas at the genus level, they increased the relative abundance of Fibrobacter (P < 0.05). Overall, this study confirmed the facilitating effect of B. licheniformis, S. cerevisiae and their compounds on growth performance, improve the antioxidant capacity and immune function, and beneficially manipulate ruminal fermentation and microbial diversity of fatting lambs.

Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur

The advent of next generation sequencing and bioinformatics tools have greatly advanced our knowledge about the phylogenetic diversity and ecological role of microbes inhabiting the mammalian gut. However, there is a lack of information on the evaluation of these computational tools in the context of the rumen microbiome as these programs have mostly been benchmarked on real or simulated datasets generated from human studies. In this study, we compared the outcomes of two methods, Kraken (mRNA based) and a pipeline developed in-house based on Mothur (16S rRNA based), to assess the taxonomic profiles (bacteria and archaea) of rumen microbial communities using total RNA sequencing of rumen fluid collected from 12 cattle with differing feed conversion ratios (FCR). Both approaches revealed a similar phyla distribution of the most abundant taxa, with Bacteroidetes, Firmicutes, and Proteobacteria accounting for approximately 80% of total bacterial abundance. For bacterial taxa, although 69 genera were commonly detected by both methods, an additional 159 genera were exclusively identified by Kraken. Kraken detected 423 species, while Mothur was not able to assign bacterial sequences to the species level. For archaea, both methods generated similar results only for the abundance of Methanomassiliicoccaceae (previously referred as RCC), which comprised more than 65% of the total archaeal families. Taxon R4-41B was exclusively identified by Mothur in the rumen of feed efficient bulls, whereas Kraken uniquely identified Methanococcaceae in inefficient bulls. Although Kraken enhanced the microbial classification at the species level, identification of bacteria or archaea in the rumen is limited due to a lack of reference genomes for the rumen microbiome. The findings from this study suggest that the development of the combined pipelines using Mothur and Kraken is needed for a more inclusive and representative classification of microbiomes.