The microbiome of the digestive system of ruminants - a review

Beyond parasitism: Exploring the microbial profile of Haemonchus contortus and its predilection site (abomasum) in Kashmir Merino sheep

Gastrointestinal helminth infection, particularly by Haemonchus contortus, poses significant challenges to sheep farming worldwide. While anthelmintic drugs have been traditional control measures, the emergence of resistance calls for alternative strategies. Understanding the interaction between parasites, host, and their microbiome is crucial for management of helminth infection. This study intricately explores the interactions between microbial communities in Kashmir Merino sheep infected with H. contortus, to understand the complex interplay between host, parasite, and their microbiome. Sheep abomasal contents and H. contortus were collected from infected and control groups, processed for DNA extraction, and subjected to metagenomic sequencing of the 16 S rRNA gene. Downstream analysis unveils distinct microbial patterns, where Proteobacteria were dominant in H. contortus, while Bacteroidota and Firmicutes prevailed in the sheep abomasum. The revelation of unique genera and shifts in diversity indices underscored helminth-induced disruptions in the host. Beta diversity analysis further showed significant variations in bacterial profiles, providing insights into the intricate host, parasite, and microbiome dynamics. Additionally, this study elucidated the presence of pathogenic bacteria within H. contortus, accentuating their potential role in exacerbating sheep health issues. This finding underscores the complexity of the host-parasite-microbiome interaction showing helminth-induced microbiome alterations of the host.

Rodents consuming the same toxic diet harbor a unique functional core microbiome

Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.S. desert southwest from 20 populations (~ 150 individuals) with differential ingestion of creosote bush and analyzed three gut regions (foregut, cecum, hindgut) using16S sequencing and shotgun metagenomics. In each gut region sampled, we found a distinctive set of microbes in individuals feeding on creosote bush that were more abundant than other ASVs, enriched in creosote feeding woodrats, and occurred more frequently than would be predicted by chance. Creosote core members were from microbial families e.g., Eggerthellaceae, known to metabolize plant secondary compounds and three of the identified core KEGG orthologs (4-hydroxybenzoate decarboxylase, benzoyl-CoA reductase subunit B, and 2-pyrone-4, 6-dicarboxylate lactonase) coded for enzymes that play important roles in metabolism of plant secondary compounds. The results support the hypothesis that the ingestion of creosote bush sculpts the microbiome across all major gut regions to select for functional characteristics associated with the degradation of the PSCs in this unique diet.

The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis

Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.

Effects of Steviol Glycosides on Growth Performance, Ruminal Fermentation and Microbial Diversity of Hu Sheep

The experiment was conducted to investigate the potential effects of steviol glycosides on growth performance, rumen fermentation processes, and microbial diversity in Hu sheep. A single-factor design was used for the trial. Twenty healthy weaned Hu lambs, possessing comparable body weights averaging 18.31 ± 1.24 kg, were randomly allocated into two distinct groups: the control group (CON) and the experimental group (STE), with each comprising 10 lambs. The CON was fed the basal diet, and the STE was supplemented with 0.07% steviol glycosides based on the basal diet. During the experimental period, variations in body weight and feed intake were closely monitored and recorded. After feeding for 90 d, blood was collected to determine blood biochemical indices, and rumen fluid samples were gathered for an in-depth analysis of rumen fermentation parameters and microbial diversity. The outcomes revealed no statistically significant differences in growth performance or serum biochemical indices between the two groups (p > 0.05). Rumen pH in STE and CON was within the normal range. The rumen ammonia nitrogen (NH3-N) and acetic acid (AA) content of STE decreased significantly compared with CON (p < 0.05). No significant variations were observed in the levels of other volatile fatty acids (VFAs) between the two groups (p > 0.05). The rumen microbial OTUs count, as well as the Shannon, Simpson, Chao1, and Ace indices, were notably lower in the STE group compared to the CON group (p < 0.05). Additionally, at the phylum level, the relative abundance of Firmicutes, Bacteroidetes, and Proteobacteria collectively accounted for over 97% of the total phylum composition. In comparison to the CON group, the STE group exhibited an increase in the relative abundance of Proteobacteria (p < 0.05), accompanied by a significant reduction in the relative abundance of Patescibacteria and Desulfobacteria (p < 0.05). At the genus level, there was a notable increase in the relative abundance of Prevotella_7 and Succinivibrionaceae_UCG_001 in the STE group, whereas the relative abundance of Rikenellaceae_RC9_gut_group significantly decreased (p < 0.05). According to the correlation analysis between rumen microflora and VFAs, the relative abundance of Succinivibrionaceae_UCG_001 displayed a significant negative correlation with AA (p < 0.05), whereas Lactobacillus exhibited a notable positive correlation with isobutyric acid (IBA) (p < 0.05). In summary, steviol glycosides had no significant effect on the production performance and blood biochemical indexes of Hu sheep. Steviol glycosides can improve rumen fermentation parameters and rumen microflora structure of Hu sheep and have a certain effect on rumen microbial diversity and composition.

A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

Emerging microalgal feed additives for ruminant production and sustainability

The global demand for animal-derived foods has led to a substantial expansion in ruminant production, which has raised concerns regarding methane emissions. To address these challenges, microalgal species that are nutritionally-rich and contain bioactive compounds in their biomass have been explored as attractive feed additives for ruminant livestock production. In this review, we discuss the different microalgal species used for this purpose in recent studies, and review the effects of microalgal feed supplements on ruminant growth, performance, health, and product quality, as well as their potential contributions in reducing methane emissions. We also examine the potential complexities of adopting microalgae as feed additives in the ruminant industry.

Acid-base properties of non-protein nitrogen affect nutrients intake, rumen fermentation and antioxidant capacity of fattening Hu sheep

This study conducted a comparison of the effects of non-protein nitrogen with different acid-base properties on feed intake, rumen fermentation, nutrient digestion and antioxidant capacity in fattening Hu sheep. Sixteen fattening male sheep (31.43 ± 2.41 kg) with permanent rumen cannulas were randomly assigned to two dietary treatments: 1% urea and 1.78% ammonium chloride (NH4Cl, AC). A 42 days experimental period was conducted, with 14 days for adaptation and 28 days for treatment. Daily feed intake was recorded and various samples including feed, feces, rumen fluid, and blood were collected at different time points during the final week. The results indicated that the urea group had significantly higher dry matter intake, average daily gain, and gain efficiency in comparison to the AC group (p < 0.01). There was no difference in rumen pH and concentration of ammonia nitrogen between different groups (p > 0.05), but the rumen pH of urea group was higher than that of the AC group at 1 and 3 h after feeding (p < 0.05). The urea group exhibited higher concentrations of total volatile fatty acids (VFA) and individual VFAs compared to the AC group at all-time points (p < 0.01). Compared to the urea group, the intake of all nutrients decreased in the AC group (p < 0.01), but the digestibility of dry matter and organic matter increased significantly (p < 0.01), and the digestibility of CP had an increasing trend (p = 0.06) in the AC group. Additionally, the urea group had lower levels of serum glucagon-like peptide-1, peptide YY, Cl, total protein and globulin than the AC group (p < 0.05). The overall levels of HCO3-, superoxide dismutase, glutathione peroxidase, catalase, albumin/globulin, blood urea nitrogen and total cholesterol in the urea group increased significantly compared to the AC group (p < 0.05). It was concluded that adding urea to the high-concentrate diet resulted in increased rumen pH and improved rumen fermentation and growth performance in fattening sheep compared to NH4Cl addition. Furthermore, urea addition improved sheep's antioxidant capacity and maintained their acid-base balance more effectively as compared to NH4Cl.

Impact of synbiotics on growth performance and gut health in Murrah buffalo calves

Synbiotics have been used as biotherapeutic supplements for prevention of new-born calf gastrointestinal disorders. Present study was conducted to evaluate the impact of fructo-oligosaccharide, mannan-oligosaccharide and inulin along with Lactobacillus plantarum CRD-7 and Lactobacillus acidophilus NCDC15 on the nutrient digestibility, growth performance and faecal microbial population of pre-ruminant buffalo calves. Twenty-four Murrah calves (5 days old) were randomly assigned to four groups of six calves in each using randomized block design. Calves in Group I (control) received only a basic diet of milk, calf starter and berseem with no additives. Calves in Group II (SYN1) were fed 6 g fructo-oligosaccharide (FOS) + Lactobacillus plantarum CRD-7 (100 ml). Calves in Group III (SYN2) were fed 9 g inulin + L. plantarum CRD-7 (50 ml), while calves in Group IV (SYN3) received 4 g MOS + L. acidophilus NCDC15 (200 ml) as fermented milk having 108 CFU/ml/calf/day in addition to the basal diet. The results revealed that digestibility of dry matter, crude protein, ether extract and average daily gain were all higher (P < 0.05) in SYN1 as compared to control group. The antioxidant enzyme activity, humoral and cell mediated immunity performed well in SYN1, SYN2 and SYN3 as compared to control. Diarrhoea and faecal scouring were lower (P < 0.05) in all supplemented groups than control. Faecal Lactobacilli and Bifidobacterium counts were also higher in SYN1 group followed by SYN2 and SYN3. Faecal ammonia, lactate, pH, and volatile fatty acids level were increased in SYN1 supplemented groups. The synbiotic combination of 6 g FOS + L. plantarum CRD-7 had better response on digestibility, average daily gain, antioxidant enzymes, immune response, faecal microbiota and metabolites and also reduce the faecal score and diarrhoea incidence. Therefore, supplementation of 6 g FOS + L. plantarum CRD-7 can be advised for general use in order to promote long-term animal production.

Parasitism-Induced Changes in Microbial Eukaryotes of Peruvian Alpaca Gastrointestinal Tract

Alpacas, important genetic resources in the Andean region of Peru, are vulnerable to diarrhea caused by pathogenic parasites such as Eimeria lamae and Giardia sp., which can be fatal, especially in neonates, due to their physiological immaturity and limited adaptability. The study investigated the diversity and abundance of intestinal fungi and protists in alpacas infected with Eimeria lamae and Giardia sp. compared to healthy alpacas. A total of 19 alpacas, aged between one and two months, were included. They were divided into two groups, one with pathological conditions (nine) and the other healthy (ten). Parasitological analyses for the detection of parasites and subsequent molecular analysis were performed on the collected fecal samples. The results revealed a greater diversity and abundance of protists in infected alpacas in comparison with healthy alpacas, while the fungal composition did not show significant changes. Therefore, parasitic infections affect the protist component of the alpaca gut microbiota. Also, it was observed that Blastocystis was identified in all healthy alpacas, serving as a possible marker of the health of the intestinal microbiota; in addition, Prussia and Pichia are beneficial fungi that help control diseases. This groundbreaking study in neonatal alpacas is the first to explore potential changes in the intestinal microbiota during an infectious state, underscoring the importance of further research to comprehend its effects on alpaca health and immune responses.

Host and microbiome jointly contribute to environmental adaptation

Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm lines, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.

Effects of melatonin on rumen microorganisms and methane production in dairy cow: results from in vitro and in vivo studies

BACKGROUND

Methane (CH4) is a major greenhouse gas, and ruminants are one of the sources of CH4 which is produced by the rumen microbiota. Modification of the rumen microbiota compositions will impact the CH4 production. In this study, the effects of melatonin on methane production in cows were investigated both in the in vitro and in vivo studies.

RESULTS

Melatonin treatment significantly reduced methane production in both studies. The cows treated with melatonin reduced methane emission from their respiration by approximately 50%. The potential mechanisms are multiple. First, melatonin lowers the volatile fatty acids (VFAs) production in rumen and reduces the raw material for CH4 synthesis. Second, melatonin not only reduces the abundance of Methanobacterium which are responsible for generating methane but also inhibits the populations of protozoa to break the symbiotic relationship between Methanobacterium and protozoa in rumen to further lowers the CH4 production. The reduced VFA production is not associated with food intake, and it seems also not to jeopardize the nutritional status of the cows. This was reflected by the increased milk lipid and protein contents in melatonin treated compared to the control cows. It is likely that the energy used to synthesize methane is saved to compensate the reduced VFA production.

CONCLUSION

This study enlightens the potential mechanisms by which melatonin reduces rumen methane production in dairy cows. Considering the greenhouse effects of methane on global warming, these findings provide valuable information using different approaches to achieve low carbon dairy farming to reduce the methane emission. Video Abstract.

Selected bacteria in sheep stool depending on breed and physiology state

One of the important factors influencing the microbial community of ruminants, besides environment or diet, are breed and physiology. Therefore, the purpose of this study was to assess these changes in the levels of basic microbial phyla and families. For this study, qPCR analysis was performed to determine the level of bacteria (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria clusters and Clostridiaceae, Lactobacillaceae families) in the feces of ewes of three native Polish sheep breeds (Polish Lowland Sheep (PON), Świniarka Sheep (SW), and synthetic line BCP) at different physiological periods (conception, early pregnancy, lambing, end of lactation). The animals were kept in the same environment and were at the same age (2-years). The results showed a significant effect of both breed (p = 0.038) and physiological period (p < 0.05, p < 0.01) on the levels of bacteria analyzed. The breed showed differences across physiological periods. The influence of the race factor was noted primarily between the BCP synthetic line and the other two breeds (differences in terms of all analyzed clusters and families except Actinobacteria phyla). In the case of SW and PON, however, the observed differences were only at the level of Proteobacteria cluster and Clostridiaceae family. On the other hand, the early pregnant and lambing periods were the most microbiologically diverse in terms of the analyzed clusters and families of bacteria.

Isoacids supplementation improves growth performance and feed fiber digestibility associated with ruminal bacterial community in yaks

Introduction

This study was conducted to assess the effect of mixed isoacid (MI) supplementation on fermentation characteristics, nutrient apparent digestibility, growth performance, and rumen bacterial community in yaks.

Methods

A 72-h in vitro fermentation experiment was performed on an ANKOM RF gas production system. MI was added to five treatments at doses of 0, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% on the dry matter (DM) basis of substrates using a total of 26 bottles (4 bottles per treatment and 2 bottles as the blank). Cumulative gas production was measured at 4, 8, 16, 24, 36, 48, and 72 h. Fermentation characteristics including pH, the concentration of volatile fatty acids (VFAs), ammonia nitrogen (NH₃-N), microbial proteins (MCP), and the disappearance rate of dry matter (DMD), neutral detergent fiber (NDFD), and acid detergent fiber (ADFD) were measured after a 72-h in vitro fermentation to determine an optimal MI dose. Fourteen Maiwa male yaks (180-220 kg, 3-4 years old of age) were randomly assigned to the control group (without MI, n = 7) and the supplemented MI group (n = 7, supplemented with 0.3% MI on DM basis) for the 85-d animal experiment. Growth performance, nutrient apparent digestibility, rumen fermentation parameters, and rumen bacterial diversity were measured.

Results

Supplementation with 0.3% MI achieved the greatest propionate and butyrate content, NDFD and ADFD compared with other groups (P < 0.05). Therefore, 0.3% was used for the animal experiment. Supplementation with 0.3% MI significantly increased the apparent digestibility of NDF and ADF (P < 0.05), and the average daily weight gain of yaks (P < 0.05) without affecting the ruminal concentration of NH₃-N, MCP, and VFAs. 0.3% MI induced rumen bacteria to form significantly different communities when compared to the control group (P < 0.05). g__norank_f__Bacteroidales_BS11_gut_group, g__norank_f__Muribaculaceae, g__Veillonellaceae_UCG-001, g__Ruminococcus_gauvreauii_group, g__norank_f__norank_o__RF39 and g__Flexilinea were identified as the biomarker taxa in responding to supplementation with 0.3% MI. Meanwhile, the abundance of g__Flexilinea and g__norank_f__norank_o__RF39 were significantly positively correlated with the NDF digestibility (P < 0.05).

Conclusion

In conclusion, supplementation with 0.3% MI improved the in vitro rumen fermentation characteristics, feed fiber digestibility, and growth performance in yaks, which was associated with changes of the abundance of g__Flexilinea and g__norank_f__norank_o__RF39.

The Effect of Probiotic Supplementation on the Gut-Brain Axis in Psychiatric Patients

The pathophysiology of several psychiatric diseases may entail disturbances in the hypothalamic-pituitary-adrenal (HPA) axis and metabolic pathways. Variations in how these effects present themselves may be connected to individual variances in clinical symptoms and treatment responses, such as the observation that a significant fraction of participants do not respond to current antipsychotic drugs. A bidirectional signaling pathway between the central nervous system and the gastrointestinal tract is known as the microbiota-gut-brain axis. The large and small intestines contain more than 100 trillion microbial cells, contributing to the intestinal ecosystem's incredible complexity. Interactions between the microbiota and intestinal epithelium can alter brain physiology and affect mood and behavior. There has recently been a focus on how these relationships impact mental health. According to evidence, intestinal microbiota may play a role in neurological and mental illnesses. Intestinal metabolites of microbial origin, such as short-chain fatty acids, tryptophan metabolites, and bacterial components that might stimulate the host's immune system, are mentioned in this review. We aim to shed some on the growing role of gut microbiota in inducing/manipulating several psychiatric disorders, which may pave the way for novel microbiota-based therapies.

The inhibition of high ammonia to in vitro rumen fermentation is pH dependent

Ammonia is an important rumen internal environment indicator. In livestock production, feeding a large amount of non-protein nitrogen to ruminants will create high ammonia stress to the animals, which increases the risk of ammonia toxicity. However, the effects of ammonia toxicity on rumen microbiota and fermentation are still unknown. In this study, an in vitro rumen fermentation technique was used to investigate the effects of different concentrations of ammonia on rumen microbiota and fermentation. To achieve the four final total ammonia nitrogen (TAN) concentrations of 0, 8, 32, and 128 mmol/L, ammonium chloride (NH4Cl) was added at 0, 42.8, 171.2, and 686.8 mg/100 mL, and urea was added at 0, 24, 96, and 384 mg/100 mL. Urea hydrolysis increased, while NH4Cl dissociation slightly reduced the pH. At similar concentrations of TAN, the increased pH of the rumen culture by urea addition resulted in a much higher free ammonia nitrogen (FAN) concentration compared to NH4Cl addition. Pearson correlation analysis revealed a strong negative correlation between FAN and microbial populations (total bacteria, protozoa, fungi, and methanogens) and in vitro rumen fermentation profiles (gas production, dry matter digestibility, total volatile fatty acid, acetate, propionate, etc.), and a much weaker correlation between TAN and the above indicators. Additionally, bacterial community structure changed differently in response to TAN concentrations. High TAN increased Gram-positive Firmicutes and Actinobacteria but reduced Gram-negative Fibrobacteres and Spirochaetes. The current study demonstrated that the inhibition of in vitro rumen fermentation by high ammonia was pH-dependent and was associated with variations of rumen microbial populations and communities.

The Colonization of Rumen Microbiota and Intervention in Pre-Weaned Ruminants

In pre-weaned ruminants, the microbiota colonizes rapidly in the rumen after birth and constantly interacts with the host to sustain health and metabolism. The developing microbial community is more malleable, so its manipulation may improve ruminant health and productivity as well as may have long-term effects on ruminants. Hence, understanding the process of rumen microbiota establishment is helpful for nutritional interventions of rumen microbiota in pre-weaned ruminants. This paper reviews the latest advances in the colonization of rumen microbiota while providing insights into the most suitable time for manipulating rumen microbial colonization in early life. In addition, different factors that affect rumen microbiota establishment during the pre-weaned ruminants are discussed in the current manuscript. The purpose of this review is to aid in the development of guidelines for manipulating rumen microbiota to improve animal productivity and health.

Transcriptome-Based Evaluation of Optimal Reference Genes for Quantitative Real-Time PCR in Yak Stomach throughout the Growth Cycle

Efficient nutritional assimilation and energy metabolism in the stomachs of yaks contribute to their adaption to harsh environments. Accurate gene expression profile analysis will help further reveal the molecular mechanism of nutrient and energy metabolism in the yak stomach. RT-qPCR is regarded as an accurate and dependable method for analyzing gene expression. The selection of reference genes is essential to obtain meaningful RT-qPCR results, especially in longitudinal gene expression studies of tissues and organs. Our objective was to select and validate optimal reference genes from across the transcriptome as internal controls for longitudinal gene expression studies in the yak stomach. In this study, 15 candidate reference genes (CRGs) were determined according to transcriptome sequencing (RNA-seq) results and the previous literature. The expression levels of these 15 CRGs were quantified using RT-qPCR in the yak stomach, including the rumen, reticulum, omasum and abomasum at five stages: 0 days, 20 days, 60 days, 15 months and three years old (adult). Subsequently, the expression stabilities of these 15 CRGs were evaluated via four algorithms: geNorm, NormFinder, BestKeeper and the comparative C_T method. Furthermore, RefFinder was employed to obtain a comprehensive ranking of the stability of CRGs. The analysis results indicate that RPS15, MRPL39 and RPS23 are the most stable genes in the yak stomach throughout the growth cycle. In addition, to verify the reliability of the selected CRGs, the relative expression levels of HMGCS2 were quantified via RT-qPCR using the three most stable or the three least stable CRGs. Overall, we recommend combining RPS15, MRPL39 and RPS23 as reference genes for the normalization of RT-qPCR data in the yak stomach throughout the growth cycle.

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet

BACKGROUND

Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal tract (GIT) microbiota to digest plant feed. However, the region-specific taxonomic composition and function of the GIT microbiome in dairy cattle and the mechanistic basis for the diet-induced effects remain to be elucidated.  RESULTS: We collected 120 digesta samples from 10 GIT regions of 12 Holstein cows fed forage- and grain-based diets and characterized their GIT microbiome via functional shotgun metagenomics and the resolution of metagenome-assembled genomes. Our results demonstrated that the GIT microbiome was mainly partitioned into three distinct clusters, four-chambered stomach, small intestine, and large intestine. Moreover, we found that the four-chambered stomach microbiome with the highest diversity had a strong ability to degrade recalcitrant polysaccharide substrates, underpinned by the prevalence of potential cellulosome--producing and plant-derived polysaccharide utilization loci-encoding consortia. In contrast, the post-gastric intestinal microbiome orchestrated alternative fermentation pathways to adapt to nutrient availability and energy acquisition. Diet shifts selectively modified the metabolic cascades of the microbiome in specific GIT regions, evidenced by the loss of fiber-degrading taxa and increased hydrogen sinks in propionate after grain introduction.

CONCLUSIONS

Our findings provide new insights into GIT microbial organization and function in dairy cattle by GIT regions and diet regimes, which offers clues for improving animal production and health in the future. Video Abstract.

A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota

Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Polyphenols for Livestock Feed: Sustainable Perspectives for Animal Husbandry?

There is growing interest in specialized metabolites for fortification strategies in feed and/or as an antioxidant, anti-inflammatory and antimicrobial alternative for the containment of disorders/pathologies that can also badly impact human nutrition. In this context, the improvement of the diet of ruminant species with polyphenols and the influence of these compounds on animal performance, biohydrogenation processes, methanogenesis, and quality and quantity of milk have been extensively investigated through in vitro and in vivo studies. Often conflicting results emerge from a review of the literature of recent years. However, the data suggest pursuing a deepening of the role of phenols and polyphenols in ruminant feeding, paying greater attention to the chemistry of the single compound or to that of the mixture of compounds more commonly used for investigative purposes.

Ruminal background of predisposed milk urea (MU) concentration in Holsteins

Efforts to reduce nitrogen (N) emissions are currently based on the optimization of dietary- N supply at average herd N requirements. The implementation of the considerable individual differences and predispositions in N- use efficiency and N- excretion in breeding programs is hampered by the difficulty of data collection. Cow individual milk urea (MU) concentration has been proposed as an easy-to-measure surrogate trait, but recent studies questioned its predictive power. Therefore, a deeper understanding of the biological mechanisms underlying predisposed higher (HMUg) or lower (LMUg) MU concentration in dairy cows is needed. Considering the complex N- metabolism in ruminants, the distinction between HMUg and LMUg could be based on differences in (i) the rumen microbial community, (ii) the host-specific transcription processes in the rumen villi, and (iii) the host-microbe interaction in the rumen. Therefore, rumen fluid and rumen epithelial samples from 10 HMUg and 10 LMUg cows were analyzed by 16S sequencing and HiSeq sequencing. In addition, the effect of dietary-N reduction on ruminal shifts was investigated in a second step. In total, 10 differentially abundant genera (DAG) were identified between HMUg and LMUg cows, elucidating greater abundances of ureolytic Succinivibrionaceae_UCG-002 and Ruminococcaceae_unclassified in LMUg animals and enhanced occurrences of Butyvibrio in HMUg cows. Differential expression analysis revealed genes of the bovine Major Histocompatibility Complex (BOLA genes) as well as MX1, ISG15, and PRSS2 displaying candidates of MU predisposition that further attributed to enhanced immune system activities in LMUg cows. A number of significant correlations between microbial genera and host transcript abundances were uncovered, including strikingly positive correlations of BOLA-DRA transcripts with Roseburia and Lachnospiraceae family abundances that might constitute particularly prominent microbial-host interplays of MU predisposition. The reduction of feed-N was followed by 18 DAG in HMUg and 19 DAG in LMUg, depicting pronounced interest on Shuttleworthia, which displayed controversial adaption in HMUg and LMUg cows. Lowering feed-N further elicited massive downregulation of immune response and energy metabolism pathways in LMUg. Considering breeding selection strategies, this study attributed information content to MU about predisposed ruminal N-utilization in Holstein-Friesians.

Identification, Superantigen Toxin Gene Profile and Antimicrobial Resistance of Staphylococci Isolated from Polish Primitive Sheep Breeds

The study aimed to analyze staphylococcal microbiota of the nasal cavity of the primitive sheep breeds Polish Świniarka and Wrzosówka kept on the same ecological farm. The research included the identification of staphylococcal species, evaluation of the prevalence of genes encoding enterotoxins, staphylococcal enterotoxin-like proteins, exfoliative toxins, toxic shock syndrome toxin 1, and detection of antimicrobial resistance. From 61 swab samples gathered from Świniarka (33) and Wrzosówka (28) healthy sheep, 127 coagulase-negative staphylococci (CoNS) were isolated. Based on PCR-RFLP analysis of the gap gene using AluI and HpyCH4V enzymes, the isolates were identified as: Staphylococcus xylosus (33.9%), S. equorum (29.1%), S. arlettae (15%), S. warneri (9.4%), S. lentus (7.9%), S. succinus (3.9%) and S. sciuri (0.8%). Three of these species, S. lentus, S. succinus, and S. sciuri, were detected only from the Świniarka breed. It was found that 77.2% of isolates harbored from 1 to 7 out of 21 analyzed genes for superantigenic toxins. The greatest diversity of toxin genes was recorded for S. equorum (16 different genes). The most prevalent gene was ser (40.2%). The incidence and number of resistances to antimicrobials were found to be bacterial species but not sheep breed dependent. The highest percentage of resistance was found for S. sciuri. The most frequent resistance was observed to clindamycin (45.7%). The findings of this study prove that toxigenic and antimicrobial resistant CoNS can colonize the nasal cavity of healthy sheep.

In Vitro Fermentation of Browsable Native Shrubs in New Zealand

Information on the nutritive value and in vitro fermentation characteristics of native shrubs in New Zealand is scant. This is despite their potential as alternatives to exotic trees and shrubs for supplementary fodder, and their mitigation of greenhouse gases and soil erosion on hill-country sheep and beef farms. The objectives of this study were to measure the in vitro fermentation gas production, predict the parameters of the in vitro fermentation kinetics, and estimate the in vitro fermentation of volatile fatty acids (VFA), microbial biomass (MBM), and greenhouse gases of four native shrubs (Coprosma robusta, Griselinia littoralis, Hoheria populnea, and Pittosporum crassifolium) and an exotic fodder tree species, Salix schwerinii. The total in vitro gas production was higher (p < 0.05) for the natives than for the S. schwerinii. A prediction using the single-pool model resulted in biologically incorrect negative in vitro total gas production from the immediately soluble fraction of the native shrubs. However, the dual pool model better predicted the in vitro total gas production and was in alignment with the measured in vitro fermentation end products. The in vitro VFA and greenhouse gas production from the fermentation of leaf and stem material was higher (p < 0.05), and the MBM lower (p < 0.05), for the native shrubs compared to the S. schwerinii. The lower in vitro total gas production, VFA, and greenhouse gases production and higher MBM of the S. schwerinii may be explained by the presence of condensed tannins (CT), although this was not measured and requires further study. In conclusion, the results from this study suggest that when consumed by ruminant livestock, browsable native shrubs can provide adequate energy and microbial protein, and that greenhouse-gas production from these species is within the ranges reported for typical New Zealand pastures.

The Occurrence of Microplastics and the Formation of Biofilms by Pathogenic and Opportunistic Bacteria as Threats in Aquaculture

Aquaculture is the most rapidly growing branch of animal production. The efficiency and quality of the produced food depends on sustainable management, water quality, feed prices and the incidence of diseases. Micro- (MP < 5 mm) and nanoplastic (NP < 1000 nm) particles are among the current factors causing serious water pollution. This substance comes solely from products manufactured by humans. MP particles migrate from the terrestrial to the aquatic environment and adversely affect, especially, the health of animals and humans by being a favorable habitat and vector for microbial pathogens and opportunists. More than 30 taxa of pathogens of humans, aquacutural animals and plants, along with opportunistic bacteria, have been detected in plastic-covering biofilm to date. The mobility and durability of the substance, combined with the relatively closed conditions in aquacultural habitats and pathogens’ affinity to the material, make plastic particles a microbiological medium threatening the industry of aquaculture. For this reason, in addition to the fact of plastic accumulation in living organisms, urgent measures should be taken to reduce its influx into the environment. The phenomenon and its implications are related to the concept of one health, wherein the environment, animals and humans affect each other’s fitness.

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing

The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François’ langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François’ langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.

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.

Glutathione S-transferase (GST) and cortisol levels vs. microbiology of the digestive system of sheep during lambing

Background

During parturition, animals exhibit variation in hormone levels, homeostasis disturbance and dysfunction of the immune system as a result of stress. Glutathione S-transferase (GST) is responsible for the occurrence of oxidative stress in the cells. Cortisol is known as the stress hormone, but it is also involved in the metabolism of proteins, carbohydrates and metabolism processes led by adipose tissue. The aim of the this study was to determine how the levels of GST and cortisol change depending on the parity. Additionally, the influence of lambing on the microbiological composition of the digestive system and placenta in Olkuska sheep was investigated.

Methods

Eighteen ewes were selected for the experiment - primiparas (n = 9) and multiparas (n = 9), they were kept in the same environmental conditions, had the same diet and did not show any disease symptoms. Fecal samples were collected individually from each ewe (n = 18) and then bacterial DNA isolation was made, then qPCR analysis for Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria phyla and Lactobacillaceae family bacteria levels was performed. These samples were also used to analyze cortisol levels by ELISA test. In addition, placenta fragments were collected during delivery, and then the GST level from the tissue was tested.

Results

The analysis of the results showed a higher level of cortisol in primiparous sheep than in multiparous ones, as in the case of glutathione transferase. There were differences between both studied groups in the microbiological composition of the digestive system. In primiparous sheep, the levels of the tested microorganisms were significantly lower than in multiparous ones. A similar relationship occurred in the study of the placental microbiome.

Conclusion

The results show that sheep microbiome, cortisol and GST levels are different in primiparas and multiparas. The study conducted may constitute an introduction to further analyzes that would help positively affect the welfare and homeostasis of the female organism.

Hemicellulolytic bacteria in the anterior intestine of the earthworm Eisenia fetida (Sav.)

Tropical agriculture produces large amounts of lignocellulosic residues that can potentially be used as a natural source of value-added products. The complexity of lignocellulose makes industrial-scale processing difficult. New processing techniques must be developed to improve the yield and avoid this valuable resource going to waste. Hemicelluloses comprise a variety of polysaccharides with different backbone compositions and decorations (such as methylations and acetylations), and form part of an intricate framework that confers structural stability to the plant cell wall. Organisms that are able to degrade these biopolymers include earthworms (Eisenia fetida), which can rapidly decompose a wide variety of lignocellulosic substrates. This ability probably derives from enzymes and symbiotic microorganisms in the earthworm gut. In this work, two substrates with similar C/N ratios but different hemicellulose content were selected. Palm fibre and coffee husk have relatively high (28%) and low (5%) hemicellulose contents, respectively. A vermicomposting mixture was prepared for the earthworms to feed on by mixing a hemicellulose substrate with organic market waste. Xylanase activity was determined in earthworm gut and used as a selection criterion for the isolation of hemicellulose-degrading bacteria. Xylanase activity was similar for both substrates, even though their physicochemical properties principally pH and electrical conductivity, as shown by the MANOVA analysis) were different for the total duration of the experiment (120 days). Xylanolytic strains isolated from earthworm gut were identified by sequence analysis of the 16S rRNA gene. Our results indicate that the four Actinobacteria, two Proteobacteria, and one Firmicutes isolated are active participants of the xylanolytic degradation by microbiota in the intestine of E. fetida. Most bacteria were more active at pH 7 and 28 °C, and those with higher activities are reported as being facultatively anaerobic, coinciding with the microenvironment reported for the earthworm gut. Each strain had a different degradative capacity.

Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep

In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.

The Recent Trend in the Use of Multistrain Probiotics in Livestock Production: An Overview

It has been established that introducing feed additives to livestock, either nutritional or non-nutritional, is beneficial in manipulating the microbial ecosystem to maintain a balance in the gut microbes and thereby improving nutrient utilization, productivity, and health status of animals. Probiotic use has gained popularity in the livestock industry, especially since antimicrobial growth promoter's use has been restricted due to the challenge of antibiotic resistance in both animals and consumers of animal products. Their usage has been linked to intestinal microbial balance and improved performance in administered animals. Even though monostrain probiotics could be beneficial, multistrain probiotics containing two or more species or strains have gained considerable attention. Combining different strains has presumably achieved several health benefits over single strains due to individual isolates' addition and positive synergistic adhesion effects on animal health and performance. However, there has been inconsistency in the effects of the probiotic complexes in literature. This review discusses multistrain probiotics, summarizes selected literature on their effects on ruminants, poultry, and swine productivity and the various modes by which they function.

Levels of Main Bacterial Phyla in the Gastrointestinal Tract of Sheep Depending on Parity and Age

Simple Summary

The ruminant microbiome is considered a specific ecosystem found within the gastrointestinal tract. A balanced intestinal microbiota is important not only for maintaining gut homeostasis, but also for regulating immune function and has a direct impact on the gut–brain axis. Factors, such as pregnancy, age, or genetics, can influence the microbial composition of the digestive system. The results of the study suggest that the parity, as well as the age of the animals, may affect the level of microorganisms in the digestive system.

Abstract

During pregnancy and parturition, the homeostasis of the body is disturbed, and the immune system is undermined, which is associated with hormonal changes within the body. Recently, it has also been suggested that physiological and hormonal changes associated with pregnancy may affect the composition of the gastrointestinal microbiome. Therefore, the aim of this study was to determine the composition of the microbiome in the third month of pregnancy in sheep in their first and second parity. Eighteen females in total were selected for the experiment, and they were divided into two groups: primiparous (aged 1 year) and multiparous ones (aged 2 years). The animals were fed the same fodder, and did not show any disease symptoms. Fecal samples were collected individually from each female (n = 20), and then bacterial DNA isolation and real-time PCR were performed for the main bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) and families (Lactobacillaceae and Clostridia). The obtained results showed the differentiation in the microbiome between the primiparous and multiparous ewes with respect to the following groups: Bacteroidetes, Proteobacteria, and Actinobacteria—the level was higher in the case of the primiparas. These results suggest that the parity and age of the females may affect the gastrointestinal microbiome, but further studies are recommended.

Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

Background

The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability.

Results

The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups.

Conclusion

The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

Selected Alternative Feed Additives Used to Manipulate the Rumen Microbiome

Simple Summary

The continuous intensification of ruminant production drives towards the expansion of feed components and additives that are utilizes for the coverage of animal’s demand for nutrients. Additionally, in recent years, studies are focused on the investigation of how feed additives affect the microbiome of the digestive system in order to obtain improved performance and/or reduce methane emissions by ruminants. The use of additives such as algae, probiotics, fermented feed or essential oils can serve as an alternative to antibiotics or other synthetic compounds that may pose a danger to the environment.

Abstract

In recent years, a boost in the ruminant population has been observed, and consequently, an increase in the animals’ demand for nutrients and methane emissions. Methane emission is generated during the microbial fermentation of feed in the rumen, and a percentage even up to 12% of the energy obtained by this process can be wasted. In addition, the use of antibiotics in animal husbandry is being increasingly restricted. restricted. As a result, there is a continuous search for innovative feed additives that can serve as alternatives to antibiotics, and will also be safe for both people and the environment. In the present review article, additives were selected on basis that, according to studies conducted so far, may positively affect the microbiome of the digestive system by improving indicators and/or reducing methane production. Among them, probiotics, prebiotics or their combination—synbiotics are at the forefront of research. However, additives in the form of algae or plant origin are also gaining ground in popularity, such as essential oils, fermented wheat straw or Gelidium amansii, due to their general recognition as safe (GRAS) for both humans and environment.

Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?

The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.

Influence of industry standard feeding frequencies on behavioral patterns and rumen and fecal bacterial communities in Holstein and Jersey cows

This study aimed to evaluate the effects of feeding frequency on behavioral patterns and on diurnal fermentation and bacteriome profiles of the rumen and feces in Holstein and Jersey cows. Ten Holstein and 10 Jersey cows were offered a TMR (53:47 forage-to-concentrate ratio dry matter basis) for ad libitum consumption and were randomly allocated within breed to one of the following feeding frequencies: (1) TMR delivered 1×/d (at 0600 h) or (2) TMR delivered 2×/d (at 0600 and 1800 h). The experiment lasted for 28 d with the first 14 d for cow adaptation to the Calan gates and the next 14 d for data collection. On d 23 and 24, an observer manually recorded the time budget (time spent lying, eating, drinking, standing, and milking), rumination activity, and number of visits to the feeding gate from each animal. On d 28, 5 concomitant collections of rumen and fecal samples were performed at intervals of 6 h via esophageal tubing and fecal grab, respectively. The bacteriome composition from these samples was determined through sequencing of the V4 region of the 16S rRNA gene. Feeding frequency did not affect behavioral patterns; however, Holstein cows spend more time lying (15.4 vs. 13.5 ± 0.8 h) and ruminating (401 vs. 331 ± 17.5 min) than Jersey cows. Fermentation profiles were similar by feeding frequency in both breeds. While no major diurnal fluctuations were observed in the fecal bacterial community from both breeds, diurnal fluctuations were identified in the rumen bacterial community from Holstein cows which appeared to follow pH responses. Overall, the bacterial community composition was not differentiated by industry standard feeding frequencies but was differentiated by breed and sample type.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation

Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate-glutamate and arginine-proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.

Effect of Intense Exercise on the Level of Bacteroidetes and Firmicutes Phyla in the Digestive System of Thoroughbred Racehorses

Exercise significantly affects the body of both animals and humans, including the composition of the digestive microbiome. This study aimed to determine the changes in the composition of the most numerous bacterial phyla (Firmicutes and Bacteroidetes, as well as the level of the Lactobacillaceae family) in the digestive system of horses under the influence of physical effort. The study included a group of 17 Thoroughbred racehorses at the age of 3 years, fed the same forage, from whom feces samples were collected individually before and 48 h after physical effort. The obtained samples were subjected to DNA isolation and RT-PCR analysis. The results showed a significant increase in the level of both phyla after exercise compared to the state before physical effort; there were no such differences in the level of facultative aerobes, i.e., the Lactobacillaceae family (although a decreasing tendency was found after exercise). In addition, the analysis of the level of the studied phyla indicates individual differences in horses' response to the effort.

Impact of selected environmental factors on microbiome of the digestive tract of ruminants

Ruminants are an important part of world animal production. The main factors affecting their production rates are age, diet, physiological condition and welfare. Disorders related to low level of welfare can significantly affect the microbiological composition of the digestive system, which is essential to maintain high production rates. The microbiology of the ruminant gastrointestinal tract may be significantly affected by inappropriate keeping system (especially in juveniles), psychological stress (e.g. transport), or heat stress. This results in an increased risk of metabolic diseases, reduced fertility and systemic diseases. Therefore, the paper focuses on selected disorders i.e., aforementioned inappropriate maintenance system, psychological stress, heat stress and their effects on the microbiome of the digestive system.

Evaluation of Changes in the Levels of Firmicutes and Bacteroidetes Phyla of Sheep Feces Depending on the Breed

Simple Summary

The microbiome plays an important role in the digestive system of ruminants. It affects the health status of animals and their development and production rates. However, its composition may be influenced by factors such as diet, age, gender, and health condition. The study was conducted on three breeds of sheep that were kept in one environment and fed with the same feed. The microbiological analysis showed that the animal microbiome is also influenced by breed.

Abstract

Studies carried out so far have indicated the effect of the microbiome on the composition of ruminant products. Recent studies have shown that not only diet, but also genetic factors can affect the microbiological composition of the digestive system. The aim of the study was to determine the differences in the levels of selected bacterial phyla in terms of breed differences. Three sheep breeds, i.e., Olkuska, Romanov, and old-type Polish Merino, differing in their use (meat–wool, meat, prolificacy) and country of breed origin were included in the study. Sheep at the same age and of the same sex were kept for a period of 3 months in the same environmental conditions and fed the same feed in the same proportions. The study included real-time PCR (polymerase chain reaction) analysis of feces collected before the slaughter and measurements of body weight and chilled carcasses. The obtained results showed significant differences between the breeds in the levels of bacterial populations tested. There were also differences in body weight between the breeds during the first weight measurements, however, the final results did not show any differences—after three months of maintenance all of them reached similar body weights, despite differences in fecal microbiological composition. The study suggests that in addition to diet and environmental conditions, the microbiology can also be influenced by breed.

Development of Swine's Digestive Tract Microbiota and Its Relation to Production Indices-A Review

Simple Summary

Proper cooperation between digestive system microbiota and the host is an important issue in maintaining proper health condition, and—in the case of farm animals—production indices. In the case of pigs, microbiota significantly affect production parameters such as meat quality, growth rate or improvement of immune response to infections. Understanding of pig digestive system microbiota and factors affecting this is an important issue. This may enable improvement of animal performance and stabilization of microbiota during their growth, reducing the risk of metabolic or systemic diseases.

Abstract

The development of research methods and tools related to microbiome investigation, as well as widened knowledge and awareness concerning the significance of microorganisms inhabiting mammalian organisms, has led to an increasing popularity of studies in this field. This review paper presents some issues related to the swine microbiome, its development starting from an early age of life and its status in adult animals, as well as factors affecting the microbiome in pigs. Attention is paid to the role of probiotics and prebiotics as alternatives to antibiotics in the context of post-weaning diarrhea treatment, and to the role of microorganisms inhabiting the digestive tract of pigs in performance indices formation. In veterinary and pork production practice, understanding of the swine microbiome and its relationships with the host organism may be useful in the prevention of some diseases and also in improvement of performance results of animals.